def exercise_ls_cycles(self):
xs = self.xray_structure.deep_copy_scatterers()
xs.shake_adp() # it must happen before the reparamtrisation is constructed
# because the ADP values are read then and only then.
connectivity_table = smtbx.utils.connectivity_table(xs)
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=connectivity_table)
ls = least_squares.crystallographic_ls(
self.fo_sq.as_xray_observations(), reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=oop.null())
cycles = normal_eqns_solving.naive_iterations(
ls,
n_max_iterations=10,
track_all=True)
assert approx_equal(ls.scale_factor(), 1, eps=1e-4)
assert approx_equal(ls.objective(), 0)
# skip next-to-last one to allow for no progress and rounding error
n = len(cycles.objective_history)
assert cycles.objective_history[0] > cycles.objective_history[n-1],\
cycles.objective_history
assert approx_equal(cycles.gradient_norm_history[-1], 0, eps=1e-6)
for sc0, sc1 in zip(self.xray_structure.scatterers(), xs.scatterers()):
assert approx_equal(sc0.u_star, sc1.u_star)
def exercise_null():
n = oop.null("a", 1, [])
assert not n
assert isinstance(n.f, oop.null)
assert isinstance(n.g(1, b=2), oop.null)
h = n.h = 2
assert h == 2
assert isinstance(n.h, oop.null)
assert isinstance(n[23085], oop.null)
x = n[234] = 2
assert x == 2
assert isinstance(n[234], oop.null)
def exercise_ls_cycles(self):
xs = self.xray_structure.deep_copy_scatterers()
xs.shake_adp(
) # it must happen before the reparamtrisation is constructed
# because the ADP values are read then and only then.
connectivity_table = smtbx.utils.connectivity_table(xs)
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=connectivity_table)
ls = least_squares.crystallographic_ls(
self.fo_sq.as_xray_observations(),
reparametrisation,
weighting_scheme=least_squares.mainstream_shelx_weighting(a=0),
origin_fixing_restraints_type=oop.null())
try:
cycles = normal_eqns_solving.naive_iterations(
ls, gradient_threshold=1e-12, track_all=True)
assert approx_equal(ls.scale_factor(), 1, eps=1e-4)
assert approx_equal(ls.objective(), 0)
assert cycles.gradient_norm_history[-1] < cycles.gradient_threshold
for sc0, sc1 in zip(self.xray_structure.scatterers(),
xs.scatterers()):
assert approx_equal(sc0.u_star, sc1.u_star)
except RuntimeError, err:
import re
m = re.search(
r'^cctbx::adptbx::debye_waller_factor_exp: \s* arg_limit \s+ exceeded'
'.* arg \s* = \s* ([\d.eE+-]+)', str(err), re.X)
assert m is not None, eval
print "Warning: refinement of ADP's diverged"
print ' argument to debye_waller_factor_exp reached %s' % m.group(
1)
print 'Here is the failing structure'
xs.show_summary()
xs.show_scatterers()
raise self.refinement_diverged()
def exercise_ls_cycles(self):
xs = self.xray_structure.deep_copy_scatterers()
xs.shake_adp() # it must happen before the reparamtrisation is constructed
# because the ADP values are read then and only then.
connectivity_table = smtbx.utils.connectivity_table(xs)
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=connectivity_table)
ls = least_squares.crystallographic_ls(
self.fo_sq.as_xray_observations(), reparametrisation,
weighting_scheme=least_squares.mainstream_shelx_weighting(a=0),
origin_fixing_restraints_type=oop.null())
try:
cycles = normal_eqns_solving.naive_iterations(
ls,
gradient_threshold=1e-12,
track_all=True)
assert approx_equal(ls.scale_factor(), 1, eps=1e-4)
assert approx_equal(ls.objective(), 0)
assert cycles.gradient_norm_history[-1] < cycles.gradient_threshold
for sc0, sc1 in zip(self.xray_structure.scatterers(), xs.scatterers()):
assert approx_equal(sc0.u_star, sc1.u_star)
except RuntimeError, err:
import re
m = re.search(
r'^cctbx::adptbx::debye_waller_factor_exp: \s* arg_limit \s+ exceeded'
'.* arg \s* = \s* ([\d.eE+-]+)', str(err), re.X)
assert m is not None, eval
print "Warning: refinement of ADP's diverged"
print ' argument to debye_waller_factor_exp reached %s' % m.group(1)
print 'Here is the failing structure'
xs.show_summary()
xs.show_scatterers()
raise self.refinement_diverged()
def __init__(self, command_stream, builder=None):
from libtbx import object_oriented_patterns as oop
if builder is None: builder = oop.null()
parser.__init__(self, command_stream, builder)
self.instructions = {}
def get_control (self, name) : return self._controls.get(name, oop.null())
def process_input_array(self, arr):
#array = self.miller_array.deep_copy()
array = arr.deep_copy()
multiplicities = None
if self.merge_equivalents:
if self.settings.show_anomalous_pairs:
merge = array.merge_equivalents()
multiplicities = merge.redundancies()
asu, matches = multiplicities.match_bijvoet_mates()
mult_plus, mult_minus = multiplicities.hemispheres_acentrics()
anom_mult = flex.int(
min(p, m)
for (p, m) in zip(mult_plus.data(), mult_minus.data()))
#flex.min_max_mean_double(anom_mult.as_double()).show()
anomalous_multiplicities = miller.array(
miller.set(asu.crystal_symmetry(),
mult_plus.indices(),
anomalous_flag=False), anom_mult)
anomalous_multiplicities = anomalous_multiplicities.select(
anomalous_multiplicities.data() > 0)
array = anomalous_multiplicities
multiplicities = anomalous_multiplicities
else:
merge = array.merge_equivalents()
array = merge.array()
multiplicities = merge.redundancies()
settings = self.settings
data = array.data()
self.missing_set = oop.null()
#if (array.is_xray_intensity_array()):
# data.set_selected(data < 0, flex.double(data.size(), 0.))
if (array.is_unique_set_under_symmetry()) and (settings.map_to_asu):
array = array.map_to_asu()
if (multiplicities is not None):
multiplicities = multiplicities.map_to_asu()
if (settings.d_min is not None):
array = array.resolution_filter(d_min=settings.d_min)
if (multiplicities is not None):
multiplicities = multiplicities.resolution_filter(
d_min=settings.d_min)
self.filtered_array = array.deep_copy()
if (settings.expand_anomalous):
array = array.generate_bijvoet_mates()
original_symmetry = array.crystal_symmetry()
if (multiplicities is not None):
multiplicities = multiplicities.generate_bijvoet_mates()
if (self.settings.show_missing):
self.missing_set = array.complete_set().lone_set(array)
if self.settings.show_anomalous_pairs:
self.missing_set = self.missing_set.select(
self.missing_set.centric_flags().data(), negate=True)
if (settings.expand_to_p1):
original_symmetry = array.crystal_symmetry()
array = array.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
#array = array.niggli_cell().expand_to_p1()
#self.missing_set = self.missing_set.niggli_cell().expand_to_p1()
self.missing_set = self.missing_set.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
if (multiplicities is not None):
multiplicities = multiplicities.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
data = array.data()
self.r_free_mode = False
self.phases = flex.double(data.size(), float('nan'))
self.radians = flex.double(data.size(), float('nan'))
self.ampl = flex.double(data.size(), float('nan'))
#if not self.foms:
# self.foms = flex.double(data.size(), float('nan'))
self.sigmas = None
#self.sigmas = flex.double(data.size(), float('nan'))
if isinstance(data, flex.bool):
self.r_free_mode = True
data_as_float = flex.double(data.size(), 0.0)
data_as_float.set_selected(data == True,
flex.double(data.size(), 1.0))
data = data_as_float
self.data = data.deep_copy()
else:
if isinstance(data, flex.double):
self.data = data.deep_copy()
elif isinstance(data, flex.complex_double):
self.data = data.deep_copy()
self.ampl = flex.abs(data)
self.phases = flex.arg(data) * 180.0 / math.pi
# purge nan values from array to avoid crash in fmod_positive()
b = flex.bool([bool(math.isnan(e)) for e in self.phases])
# replace the nan values with an arbitrary float value
self.phases = self.phases.set_selected(b, 42.4242)
# indicate the coresponding phase/radian is completely undetermnined
#self.foms = self.foms.set_selected(b, 0.0)
# Now cast negative degrees to equivalent positive degrees
self.phases = flex.fmod_positive(self.phases, 360.0)
self.radians = flex.arg(data)
# replace the nan values with an arbitrary float value
self.radians = self.radians.set_selected(b, 0.424242)
elif hasattr(array.data(), "as_double"):
self.data = array.data().as_double()
else:
raise RuntimeError("Unexpected data type: %r" % data)
if (settings.show_data_over_sigma):
if (array.sigmas() is None):
raise Sorry("sigmas not defined.")
sigmas = array.sigmas()
non_zero_sel = sigmas != 0
array = array.select(non_zero_sel)
array = array.customized_copy(data=array.data() /
array.sigmas())
self.data = array.data()
if (multiplicities is not None):
multiplicities = multiplicities.select(non_zero_sel)
if array.sigmas() is not None:
self.sigmas = array.sigmas()
else:
self.sigmas = None
work_array = array
work_array.set_info(arr.info())
multiplicities = multiplicities
return work_array, multiplicities
self._caller_wait.put(None)
else:
result = self._callback(*args, **kwds)
if (result == False):
return False
last_iteration = self._queue.get()
if (last_iteration):
return False
return result
def resume(self, last_iteration=False):
if (self.isAlive()):
self._queue.put(last_iteration)
return self
null_callback = oop.null()
class queue_monitor_thread (threading.Thread) :
def __init__ (self, q, callback, sleep_interval=1.0) :
self.q = q
self.cb = callback
self._exit = False
self._sleep_interval = sleep_interval
threading.Thread.__init__(self)
def run (self) :
t = self._sleep_interval
while not self._exit :
if (self.q.qsize() > 0) :
result = self.q.get(timeout=1)
self.cb(result)
def exercise_floating_origin_restraints(self):
n = self.n_independent_params
eps_zero_rhs = 1e-6
connectivity_table = smtbx.utils.connectivity_table(self.xray_structure)
reparametrisation = constraints.reparametrisation(
structure=self.xray_structure,
constraints=[],
connectivity_table=connectivity_table)
obs = self.fo_sq.as_xray_observations()
ls = least_squares.crystallographic_ls(
obs, reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=oop.null())
ls.build_up()
unrestrained_normal_matrix = ls.normal_matrix_packed_u()
assert len(unrestrained_normal_matrix) == n*(n+1)//2
ev = eigensystem.real_symmetric(
unrestrained_normal_matrix.matrix_packed_u_as_symmetric())
unrestrained_eigenval = ev.values()
unrestrained_eigenvec = ev.vectors()
ls = least_squares.crystallographic_ls(
obs,
reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=
origin_fixing_restraints.homogeneous_weighting)
ls.build_up()
# Let's check that the computed singular directions span the same
# space as the expected ones
singular_test = flex.double()
jac = ls.reparametrisation.jacobian_transpose_matching_grad_fc()
m = 0
for s in ls.origin_fixing_restraint.singular_directions:
assert s.norm() != 0
singular_test.extend(jac*s)
m += 1
for s in self.continuous_origin_shift_basis:
singular_test.extend(flex.double(s))
m += 1
singular_test.reshape(flex.grid(m, n))
assert self.rank(singular_test) == len(self.continuous_origin_shift_basis)
assert ls.opposite_of_gradient()\
.all_approx_equal(0, eps_zero_rhs),\
list(ls.gradient())
restrained_normal_matrix = ls.normal_matrix_packed_u()
assert len(restrained_normal_matrix) == n*(n+1)//2
ev = eigensystem.real_symmetric(
restrained_normal_matrix.matrix_packed_u_as_symmetric())
restrained_eigenval = ev.values()
restrained_eigenvec = ev.vectors()
# The eigendecomposition of the normal matrix
# for the unrestrained problem is:
# A = sum_{0 <= i < n-p-1} lambda_i v_i^T v_i
# where the eigenvalues lambda_i are sorted in decreasing order
# and p is the dimension of the continous origin shift space.
# In particular A v_i = 0, n-p <= i < n.
# In the restrained case, it becomes:
# A' = A + sum_{n-p <= i < n} mu v_i^T v_i
p = len(self.continuous_origin_shift_basis)
assert approx_equal(restrained_eigenval[p:], unrestrained_eigenval[:-p],
eps=1e-12)
assert unrestrained_eigenval[-p]/unrestrained_eigenval[-p-1] < 1e-12
if p > 1:
# eigenvectors are stored by rows
unrestrained_null_space = unrestrained_eigenvec.matrix_copy_block(
i_row=n-p, i_column=0,
n_rows=p, n_columns=n)
assert self.rank(unrestrained_null_space) == p
restrained_space = restrained_eigenvec.matrix_copy_block(
i_row=0, i_column=0,
n_rows=p, n_columns=n)
assert self.rank(restrained_space) == p
singular = flex.double(
self.continuous_origin_shift_basis)
assert self.rank(singular) == p
rank_finder = flex.double(n*3*p)
rank_finder.resize(flex.grid(3*p, n))
rank_finder.matrix_paste_block_in_place(unrestrained_null_space,
i_row=0, i_column=0)
rank_finder.matrix_paste_block_in_place(restrained_space,
i_row=p, i_column=0)
rank_finder.matrix_paste_block_in_place(singular,
i_row=2*p, i_column=0)
assert self.rank(rank_finder) == p
else:
# this branch handles the case p=1
# it's necessary to work around a bug in the svd module
# ( nx1 matrices crashes the code )
assert approx_equal(
restrained_eigenvec[0:n].angle(
unrestrained_eigenvec[-n:]) % math.pi, 0)
assert approx_equal(
unrestrained_eigenvec[-n:].angle(
flex.double(self.continuous_origin_shift_basis[0])) % math.pi, 0)
# Do the floating origin restraints prevent the structure from floating?
xs = self.xray_structure.deep_copy_scatterers()
ls = least_squares.crystallographic_ls(
obs,
reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=
origin_fixing_restraints.atomic_number_weighting
)
barycentre_0 = xs.sites_frac().mean()
while True:
xs.shake_sites_in_place(rms_difference=0.15)
xs.apply_symmetry_sites()
barycentre_1 = xs.sites_frac().mean()
delta = matrix.col(barycentre_1) - matrix.col(barycentre_0)
moved_far_enough = 0
for singular in self.continuous_origin_shift_basis:
e = matrix.col(singular[:3])
if not approx_equal(delta.dot(e), 0, eps=0.01, out=None):
moved_far_enough += 1
if moved_far_enough: break
# one refinement cycle
ls.build_up()
ls.solve()
shifts = ls.step()
# That's what floating origin restraints are for!
# Note that in the presence of special position, that's different
# from the barycentre not moving along the continuous shift directions.
# TODO: typeset notes about that subtlety.
for singular in self.continuous_origin_shift_basis:
assert approx_equal(shifts.dot(flex.double(singular)), 0, eps=1e-12)
def add_controls(self):
'''
All the buttoms on the lef hand panel is defined here
'''
self._index_span = None
self._last_sg_sel = None
# # d_min control
self.d_min_ctrl = floatspin.FloatSpin(parent=self,
increment=0.05,
digits=2)
self.d_min_ctrl.Bind(wx.EVT_SET_FOCUS, lambda evt: None)
if (wx.VERSION >= (2, 9)): # XXX FloatSpin bug in 2.9.2/wxOSX_Cocoa
self.d_min_ctrl.SetBackgroundColour(self.GetBackgroundColour())
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
label = wx.StaticText(self, -1, "High resolution:")
box.Add(label, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
box.Add(self.d_min_ctrl, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.Bind(floatspin.EVT_FLOATSPIN, self.OnChangeResolution,
self.d_min_ctrl)
##Kau added start
self.column_ctrl = oop.null()
self.column_ctrl = wx.Choice(
self.panel,
-1,
# choices=["jinga","manga","linga","some lable", "ranga"],
choices=[],
size=(160, -1))
# self.Bind(wx.EVT_CHOICE, self.OnChangeSpaceGroup, self.array_ctrl)
self.Bind(wx.EVT_CHOICE, self.OnChangeColumn, self.column_ctrl)
# example_file=os.path.join("combine_4zg3.mtz")
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
box.Add(wx.StaticText(self.panel, -1, "labels :"), 0, wx.ALL, 5)
box.Add(self.column_ctrl, 0, wx.ALL, 5)
##This is to include I/SigI column details
self.IoverSigI_ctrl = floatspin.FloatSpin(parent=self,
increment=0.25,
digits=2)
self.IoverSigI_ctrl.Bind(wx.EVT_SET_FOCUS, lambda evt: None)
if (wx.VERSION >= (2, 9)): # XXX FloatSpin bug in 2.9.2/wxOSX_Cocoa
self.IoverSigI_ctrl.SetBackgroundColour(self.GetBackgroundColour())
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
label = wx.StaticText(self, -1, "I/SigI:")
box.Add(label, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
box.Add(self.IoverSigI_ctrl, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.Bind(floatspin.EVT_FLOATSPIN, self.OnChangeIoverSigI,
self.IoverSigI_ctrl)
##Kau added ends
# # scale control
# box = wx.BoxSizer(wx.HORIZONTAL)
# self.panel_sizer.Add(box)
# label = wx.StaticText(self, -1, "Scale:")
# box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
# self.scale_ctrl = wx.Slider(self, size=(120,-1), style=wx.SL_AUTOTICKS)
# self.scale_ctrl.SetMin(0)
# self.scale_ctrl.SetMax(16)
# self.scale_ctrl.SetTickFreq(4, 1)
# self.Bind(wx.EVT_SLIDER, self.OnSetScale, self.scale_ctrl)
# for x in [0, 4, 8, 12, 16] :
# self.scale_ctrl.SetTick(x)
# self.scale_ctrl.SetValue((self.settings.scale * 4) - 4)
# box.Add(self.scale_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
# #
###Kau added starts here
# # information control
# box = wx.BoxSizer(wx.HORIZONTAL)
# self.panel_sizer.Add(box)
# label = wx.StaticText(self, -1, "Information content:")
# box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
# self.scale_ctrl = wx.Slider(self, size=(120,-1), style=wx.SL_AUTOTICKS)
# self.scale_ctrl.SetMin(0)
# self.scale_ctrl.SetMax(16)
# self.scale_ctrl.SetTickFreq(4, 1)
# self.Bind(wx.EVT_SLIDER, self.OnSetScale, self.scale_ctrl)
# for x in [0, 4, 8, 12, 16] :
# self.scale_ctrl.SetTick(x)
# self.scale_ctrl.SetValue((self.settings.scale * 4) - 4)
# box.Add(self.scale_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
# #
###Kau added ends here
ctrls = self.create_controls(setting="black_background",
label="Black background")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
ctrls = self.create_controls(setting="show_axes",
label="Show h,k,l axes")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
# ctrls = self.create_controls(
# setting="show_data_over_sigma",
# label="Use I or F over sigma")
# self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
if (not self.is_3d_view):
# ctrls = self.create_controls(
# setting="uniform_size",
# label="Use same radius for all points")
# self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
# ctrls = self.create_controls(
# setting="sqrt_scale_radii",
# label="Scale radii to sqrt(value)")
# self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
# ctrls = self.create_controls(
# setting="sqrt_scale_colors",
# label="Scale colors to sqrt(value)")
# self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
self.sg_ctrl = oop.null()
if (self.is_3d_view):
self.sg_ctrl = wx.Choice(self.panel,
-1,
choices=[],
size=(160, -1))
self.Bind(wx.EVT_CHOICE, self.OnChangeSpaceGroup, self.sg_ctrl)
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
box.Add(wx.StaticText(self.panel, -1, "Space group:"), 0, wx.ALL,
5)
box.Add(self.sg_ctrl, 0, wx.ALL, 5)
ctrls = self.create_controls(setting="expand_to_p1",
label="Expand data to P1")
ctrls2 = self.create_controls(setting="expand_anomalous",
label="show Friedel pairs")
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
box.Add(ctrls[0], 0, wx.ALL, 5)
box.Add(ctrls2[0], 0, wx.ALL, 5)
ctrls = self.create_controls(
setting="spheres", label="Display reflections as spheres")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
self.spheres_ctrl = ctrls[0]
else:
self.spheres_ctrl = oop.null()
###Kau added start
# d_min control
# self.d_min_ctrl = floatspin.FloatSpin(parent=self, increment=0.05, digits=2)
# self.d_min_ctrl.Bind(wx.EVT_SET_FOCUS, lambda evt: None)
# if (wx.VERSION >= (2,9)) : # XXX FloatSpin bug in 2.9.2/wxOSX_Cocoa
# self.d_min_ctrl.SetBackgroundColour(self.GetBackgroundColour())
# box = wx.BoxSizer(wx.HORIZONTAL)
# self.panel_sizer.Add(box)
# label = wx.StaticText(self,-1,"High resolution:")
# box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
# box.Add(self.d_min_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
# self.Bind(floatspin.EVT_FLOATSPIN, self.OnChangeResolution, self.d_min_ctrl)
##kau added end
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
txt = wx.StaticText(self.panel, -1, "Color scheme:")
box.Add(txt, 0,
wx.TOP | wx.BOTTOM | wx.LEFT | wx.ALIGN_CENTER_VERTICAL, 5)
self.color_ctrl = wx.Choice(self.panel,
-1,
choices=[
"rainbow", "heatmap", "redblue",
"grayscale", "monochrome"
])
self.color_ctrl.SetStringSelection(self.settings.color_scheme)
box.Add(self.color_ctrl, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.Bind(wx.EVT_CHOICE, self.OnChangeColor, self.color_ctrl)
ctrls = self.create_controls(setting="show_missing",
label="Show missing reflections")
ctrls2 = self.create_controls(setting="show_only_missing",
label="only")
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
box.Add(ctrls[0], 0, wx.ALL, 5)
box.Add(ctrls2[0], 0, wx.ALL, 5)
ctrls = self.create_controls(setting="show_systematic_absences",
label="Show systematic absences")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
if (self.is_3d_view):
ctrls = self.create_controls(setting="sphere_detail",
label="Sphere detail level",
min=4,
max=20)
box = wx.BoxSizer(wx.HORIZONTAL)
box.Add(ctrls[0], 0,
wx.TOP | wx.BOTTOM | wx.LEFT | wx.ALIGN_CENTER_VERTICAL, 5)
box.Add(ctrls[1], 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.panel_sizer.Add(box)
ctrls = self.create_controls(
setting="slice_mode",
label="Show only a slice through reciprocal space")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
self.slice_ctrl = ctrls[0]
ctrls = self.create_controls(
setting="keep_constant_scale",
label="Keep scale constant across all slices")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
box2 = wx.BoxSizer(wx.HORIZONTAL)
box2.Add(wx.StaticText(self.panel, -1, "View slice:"), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
ctrls = self.create_controls
self.hkl_choice = wx.Choice(self.panel, -1, choices=["h", "k", "l"])
self.hkl_choice.SetStringSelection(self.settings.slice_axis)
box2.Add(self.hkl_choice, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
box2.Add(wx.StaticText(self.panel, -1, "="), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.slice_index = wx.SpinCtrl(self.panel, -1)
self.slice_index.SetValue(self.settings.slice_index)
box2.Add(self.slice_index, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.panel_sizer.Add(box2)
self.Bind(wx.EVT_CHOICE, self.OnSetSlice, self.hkl_choice)
self.Bind(wx.EVT_SPINCTRL, self.OnSetSlice, self.slice_index)
# reflection info box
box = wx.StaticBox(self.panel, -1, "Reflection info")
box_szr = wx.StaticBoxSizer(box, wx.VERTICAL)
self.panel_sizer.Add((1, 10))
self.panel_sizer.Add(box_szr, 0, wx.EXPAND | wx.ALL)
grid_szr = wx.FlexGridSizer(rows=3, cols=2)
box_szr.Add(grid_szr, 0, wx.EXPAND | wx.ALL)
grid_szr.Add(wx.StaticText(self.panel, -1, "Clicked:"), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.hkl_info = wx.TextCtrl(self.panel,
-1,
size=(80, -1),
style=wx.TE_READONLY)
grid_szr.Add(self.hkl_info, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
grid_szr.Add(wx.StaticText(self.panel, -1, "Resolution:"), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.d_min_info = wx.TextCtrl(self.panel,
-1,
size=(80, -1),
style=wx.TE_READONLY)
grid_szr.Add(self.d_min_info, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.add_value_widgets(grid_szr)
def add_controls (self) :
self._index_span = None
self._last_sg_sel = None
# d_min control
self.d_min_ctrl = floatspin.FloatSpin(parent=self, increment=0.05, digits=2)
self.d_min_ctrl.Bind(wx.EVT_SET_FOCUS, lambda evt: None)
if (wx.VERSION >= (2,9)) : # XXX FloatSpin bug in 2.9.2/wxOSX_Cocoa
self.d_min_ctrl.SetBackgroundColour(self.GetBackgroundColour())
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
label = wx.StaticText(self,-1,"High resolution:")
box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
box.Add(self.d_min_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.Bind(floatspin.EVT_FLOATSPIN, self.OnChangeResolution, self.d_min_ctrl)
# scale control
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
label = wx.StaticText(self, -1, "Scale:")
box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.scale_ctrl = wx.Slider(self, size=(120,-1), style=wx.SL_AUTOTICKS)
self.scale_ctrl.SetMin(0)
self.scale_ctrl.SetMax(16)
self.scale_ctrl.SetTickFreq(4, 1)
self.Bind(wx.EVT_SLIDER, self.OnSetScale, self.scale_ctrl)
for x in [0, 4, 8, 12, 16] :
self.scale_ctrl.SetTick(x)
self.scale_ctrl.SetValue((self.settings.scale * 4) - 4)
box.Add(self.scale_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
ctrls = self.create_controls(
setting="black_background",
label="Black background")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
ctrls = self.create_controls(
setting="show_axes",
label="Show h,k,l axes")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
ctrls = self.create_controls(
setting="show_data_over_sigma",
label="Use I or F over sigma")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
if (not self.is_3d_view) :
ctrls = self.create_controls(
setting="uniform_size",
label="Use same radius for all points")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
ctrls = self.create_controls(
setting="sqrt_scale_radii",
label="Scale radii to sqrt(value)")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
ctrls = self.create_controls(
setting="sqrt_scale_colors",
label="Scale colors to sqrt(value)")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
self.sg_ctrl = oop.null()
if (self.is_3d_view) :
self.sg_ctrl = wx.Choice(self.panel, -1,
choices=[],
size=(160,-1))
self.Bind(wx.EVT_CHOICE, self.OnChangeSpaceGroup, self.sg_ctrl)
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
box.Add(wx.StaticText(self.panel, -1, "Space group:"), 0, wx.ALL, 5)
box.Add(self.sg_ctrl, 0, wx.ALL, 5)
ctrls = self.create_controls(
setting="expand_to_p1",
label="Expand data to P1")
ctrls2 = self.create_controls(
setting="expand_anomalous",
label="show Friedel pairs")
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
box.Add(ctrls[0], 0, wx.ALL, 5)
box.Add(ctrls2[0], 0, wx.ALL, 5)
ctrls = self.create_controls(
setting="spheres",
label="Display reflections as spheres")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
self.spheres_ctrl = ctrls[0]
else :
self.spheres_ctrl = oop.null()
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
txt = wx.StaticText(self.panel, -1, "Color scheme:")
box.Add(txt, 0, wx.TOP|wx.BOTTOM|wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 5)
self.color_ctrl = wx.Choice(self.panel, -1,
choices=["rainbow","heatmap","redblue","grayscale","monochrome"])
self.color_ctrl.SetStringSelection(self.settings.color_scheme)
box.Add(self.color_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.Bind(wx.EVT_CHOICE, self.OnChangeColor, self.color_ctrl)
ctrls = self.create_controls(
setting="show_missing",
label="Show missing reflections")
ctrls2 = self.create_controls(
setting="show_only_missing",
label="only")
box = wx.BoxSizer(wx.HORIZONTAL)
self.panel_sizer.Add(box)
box.Add(ctrls[0], 0, wx.ALL, 5)
box.Add(ctrls2[0], 0, wx.ALL, 5)
ctrls = self.create_controls(
setting="show_systematic_absences",
label="Show systematic absences")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
if (self.is_3d_view) :
ctrls = self.create_controls(
setting="sphere_detail",
label="Sphere detail level",
min=4,
max=20)
box = wx.BoxSizer(wx.HORIZONTAL)
box.Add(ctrls[0], 0, wx.TOP|wx.BOTTOM|wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 5)
box.Add(ctrls[1], 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.panel_sizer.Add(box)
ctrls = self.create_controls(
setting="slice_mode",
label="Show only a slice through reciprocal space")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
self.slice_ctrl = ctrls[0]
ctrls = self.create_controls(
setting="keep_constant_scale",
label="Keep scale constant across all slices")
self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5)
box2 = wx.BoxSizer(wx.HORIZONTAL)
box2.Add(wx.StaticText(self.panel, -1, "View slice:"), 0,
wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
ctrls = self.create_controls
self.hkl_choice = wx.Choice(self.panel, -1, choices=["h","k","l"])
self.hkl_choice.SetStringSelection(self.settings.slice_axis)
box2.Add(self.hkl_choice, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
box2.Add(wx.StaticText(self.panel, -1, "="), 0,
wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.slice_index = wx.SpinCtrl(self.panel, -1)
self.slice_index.SetValue(self.settings.slice_index)
box2.Add(self.slice_index, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.panel_sizer.Add(box2)
self.Bind(wx.EVT_CHOICE, self.OnSetSlice, self.hkl_choice)
self.Bind(wx.EVT_SPINCTRL, self.OnSetSlice, self.slice_index)
# reflection info box
box = wx.StaticBox(self.panel, -1, "Reflection info")
box_szr = wx.StaticBoxSizer(box, wx.VERTICAL)
self.panel_sizer.Add((1,10))
self.panel_sizer.Add(box_szr, 0, wx.EXPAND|wx.ALL)
grid_szr = wx.FlexGridSizer(rows=3, cols=2)
box_szr.Add(grid_szr, 0, wx.EXPAND|wx.ALL)
grid_szr.Add(wx.StaticText(self.panel, -1, "Clicked:"), 0,
wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.hkl_info = wx.TextCtrl(self.panel, -1, size=(80,-1),
style=wx.TE_READONLY)
grid_szr.Add(self.hkl_info, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
grid_szr.Add(wx.StaticText(self.panel, -1, "Resolution:"), 0,
wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.d_min_info = wx.TextCtrl(self.panel, -1, size=(80,-1),
style=wx.TE_READONLY)
grid_szr.Add(self.d_min_info, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.add_value_widgets(grid_szr)
def process_input_array(self, arr):
array = arr.deep_copy()
work_array = arr
multiplicities = None
try:
if self.merge_equivalents:
array, multiplicities, merge = MergeData(
array, self.settings.show_anomalous_pairs)
settings = self.settings
data = array.data()
#import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) )
self.missing_set = oop.null()
#if (array.is_xray_intensity_array()):
# data.set_selected(data < 0, flex.double(data.size(), 0.))
if (array.is_unique_set_under_symmetry()) and (
settings.map_to_asu):
array = array.map_to_asu()
if (multiplicities is not None):
multiplicities = multiplicities.map_to_asu()
if (settings.d_min is not None):
array = array.resolution_filter(d_min=settings.d_min)
if (multiplicities is not None):
multiplicities = multiplicities.resolution_filter(
d_min=settings.d_min)
self.filtered_array = array.deep_copy()
if (settings.expand_anomalous):
if not array.is_unique_set_under_symmetry():
raise Sorry(
"Error! Cannot generate bijvoet mates of unmerged reflections."
)
array = array.generate_bijvoet_mates()
original_symmetry = array.crystal_symmetry()
if (multiplicities is not None):
multiplicities = multiplicities.generate_bijvoet_mates()
if (self.settings.show_missing):
self.missing_set = array.complete_set().lone_set(array)
if self.settings.show_anomalous_pairs:
self.missing_set = self.missing_set.select(
self.missing_set.centric_flags().data(), negate=True)
if (settings.expand_to_p1):
if not array.is_unique_set_under_symmetry():
raise Sorry(
"Error! Cannot expand unmerged reflections to P1.")
original_symmetry = array.crystal_symmetry()
array = array.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
#array = array.niggli_cell().expand_to_p1()
#self.missing_set = self.missing_set.niggli_cell().expand_to_p1()
self.missing_set = self.missing_set.expand_to_p1(
).customized_copy(crystal_symmetry=original_symmetry)
if (multiplicities is not None):
multiplicities = multiplicities.expand_to_p1(
).customized_copy(crystal_symmetry=original_symmetry)
data = array.data()
self.r_free_mode = False
self.phases = flex.double(data.size(), float('nan'))
self.radians = flex.double(data.size(), float('nan'))
self.ampl = flex.double(data.size(), float('nan'))
self.sigmas = None
if isinstance(data, flex.bool):
self.r_free_mode = True
data_as_float = flex.double(data.size(), 0.0)
data_as_float.set_selected(data == True,
flex.double(data.size(), 1.0))
data = data_as_float
self.data = data #.deep_copy()
else:
if isinstance(data, flex.double):
self.data = data #.deep_copy()
elif isinstance(data, flex.complex_double):
self.data = data #.deep_copy()
self.ampl = flex.abs(data)
self.phases = flex.arg(data) * 180.0 / math.pi
# purge nan values from array to avoid crash in fmod_positive()
#b = flex.bool([bool(math.isnan(e)) for e in self.phases])
b = graphics_utils.IsNansArray(self.phases)
# replace the nan values with an arbitrary float value
self.phases = self.phases.set_selected(b, 42.4242)
# Cast negative degrees to equivalent positive degrees
self.phases = flex.fmod_positive(self.phases, 360.0)
self.radians = flex.arg(data)
# replace the nan values with an arbitrary float value
self.radians = self.radians.set_selected(b, 0.424242)
elif hasattr(array.data(), "as_double"):
self.data = data
else:
raise RuntimeError("Unexpected data type: %r" % data)
if (settings.show_data_over_sigma):
if (array.sigmas() is None):
raise Sorry("sigmas not defined.")
sigmas = array.sigmas()
non_zero_sel = sigmas != 0
array = array.select(non_zero_sel)
array = array.customized_copy(data=array.data() /
array.sigmas())
self.data = array.data()
if (multiplicities is not None):
multiplicities = multiplicities.select(non_zero_sel)
if array.sigmas() is not None:
self.sigmas = array.sigmas()
else:
self.sigmas = None
work_array = array
except Exception as e:
print(to_str(e) + "".join(traceback.format_stack(limit=10)))
raise e
return None, None
work_array.set_info(arr.info())
multiplicities = multiplicities
return work_array, multiplicities
def exercise_floating_origin_restraints(self):
n = self.n_independent_params
eps_zero_rhs = 1e-6
connectivity_table = smtbx.utils.connectivity_table(self.xray_structure)
reparametrisation = constraints.reparametrisation(
structure=self.xray_structure,
constraints=[],
connectivity_table=connectivity_table)
obs = self.fo_sq.as_xray_observations()
ls = least_squares.crystallographic_ls(
obs, reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=oop.null())
ls.build_up()
unrestrained_normal_matrix = ls.normal_matrix_packed_u()
assert len(unrestrained_normal_matrix) == n*(n+1)//2
ev = eigensystem.real_symmetric(
unrestrained_normal_matrix.matrix_packed_u_as_symmetric())
unrestrained_eigenval = ev.values()
unrestrained_eigenvec = ev.vectors()
ls = least_squares.crystallographic_ls(
obs,
reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=
origin_fixing_restraints.homogeneous_weighting)
ls.build_up()
# Let's check that the computed singular directions span the same
# space as the expected ones
singular_test = flex.double()
jac = ls.reparametrisation.jacobian_transpose_matching_grad_fc()
m = 0
for s in ls.origin_fixing_restraint.singular_directions:
assert s.norm() != 0
singular_test.extend(jac*s)
m += 1
for s in self.continuous_origin_shift_basis:
singular_test.extend(flex.double(s))
m += 1
singular_test.reshape(flex.grid(m, n))
assert self.rank(singular_test) == len(self.continuous_origin_shift_basis)
assert ls.opposite_of_gradient()\
.all_approx_equal(0, eps_zero_rhs),\
list(ls.gradient())
restrained_normal_matrix = ls.normal_matrix_packed_u()
assert len(restrained_normal_matrix) == n*(n+1)//2
ev = eigensystem.real_symmetric(
restrained_normal_matrix.matrix_packed_u_as_symmetric())
restrained_eigenval = ev.values()
restrained_eigenvec = ev.vectors()
# The eigendecomposition of the normal matrix
# for the unrestrained problem is:
# A = sum_{0 <= i < n-p-1} lambda_i v_i^T v_i
# where the eigenvalues lambda_i are sorted in decreasing order
# and p is the dimension of the continous origin shift space.
# In particular A v_i = 0, n-p <= i < n.
# In the restrained case, it becomes:
# A' = A + sum_{n-p <= i < n} mu v_i^T v_i
p = len(self.continuous_origin_shift_basis)
assert approx_equal(restrained_eigenval[p:], unrestrained_eigenval[:-p],
eps=1e-12)
assert unrestrained_eigenval[-p]/unrestrained_eigenval[-p-1] < 1e-12
if p > 1:
# eigenvectors are stored by rows
unrestrained_null_space = unrestrained_eigenvec.matrix_copy_block(
i_row=n-p, i_column=0,
n_rows=p, n_columns=n)
assert self.rank(unrestrained_null_space) == p
restrained_space = restrained_eigenvec.matrix_copy_block(
i_row=0, i_column=0,
n_rows=p, n_columns=n)
assert self.rank(restrained_space) == p
singular = flex.double(
self.continuous_origin_shift_basis)
assert self.rank(singular) == p
rank_finder = flex.double(n*3*p)
rank_finder.resize(flex.grid(3*p, n))
rank_finder.matrix_paste_block_in_place(unrestrained_null_space,
i_row=0, i_column=0)
rank_finder.matrix_paste_block_in_place(restrained_space,
i_row=p, i_column=0)
rank_finder.matrix_paste_block_in_place(singular,
i_row=2*p, i_column=0)
assert self.rank(rank_finder) == p
else:
# this branch handles the case p=1
# it's necessary to work around a bug in the svd module
# ( nx1 matrices crashes the code )
assert approx_equal(
restrained_eigenvec[0:n].angle(
unrestrained_eigenvec[-n:]) % math.pi, 0)
assert approx_equal(
unrestrained_eigenvec[-n:].angle(
flex.double(self.continuous_origin_shift_basis[0])) % math.pi, 0)
# Do the floating origin restraints prevent the structure from floating?
xs = self.xray_structure.deep_copy_scatterers()
ls = least_squares.crystallographic_ls(
obs,
reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=
origin_fixing_restraints.atomic_number_weighting
)
barycentre_0 = xs.sites_frac().mean()
while 1:
xs.shake_sites_in_place(rms_difference=0.15)
xs.apply_symmetry_sites()
barycentre_1 = xs.sites_frac().mean()
delta = matrix.col(barycentre_1) - matrix.col(barycentre_0)
moved_far_enough = 0
for singular in self.continuous_origin_shift_basis:
e = matrix.col(singular[:3])
if not approx_equal(delta.dot(e), 0, eps=0.01, out=None):
moved_far_enough += 1
if moved_far_enough: break
# one refinement cycle
ls.build_up()
ls.solve()
shifts = ls.step()
# That's what floating origin restraints are for!
# Note that in the presence of special position, that's different
# from the barycentre not moving along the continuous shift directions.
# TODO: typeset notes about that subtlety.
for singular in self.continuous_origin_shift_basis:
assert approx_equal(shifts.dot(flex.double(singular)), 0, eps=1e-12)
def process_input_array (self) :
from cctbx.array_family import flex
array = self.miller_array.deep_copy()
multiplicities = None
if self.merge_equivalents :
if self.settings.show_anomalous_pairs:
from cctbx import miller
merge = array.merge_equivalents()
multiplicities = merge.redundancies()
asu, matches = multiplicities.match_bijvoet_mates()
mult_plus, mult_minus = multiplicities.hemispheres_acentrics()
anom_mult = flex.int(
min(p, m) for (p, m) in zip(mult_plus.data(), mult_minus.data()))
#flex.min_max_mean_double(anom_mult.as_double()).show()
anomalous_multiplicities = miller.array(
miller.set(asu.crystal_symmetry(),
mult_plus.indices(),
anomalous_flag=False), anom_mult)
anomalous_multiplicities = anomalous_multiplicities.select(
anomalous_multiplicities.data() > 0)
array = anomalous_multiplicities
multiplicities = anomalous_multiplicities
else:
merge = array.merge_equivalents()
array = merge.array()
multiplicities = merge.redundancies()
settings = self.settings
data = array.data()
self.missing_set = oop.null()
if (array.is_xray_intensity_array()) :
data.set_selected(data < 0, flex.double(data.size(), 0.))
if (array.is_unique_set_under_symmetry()) and (settings.map_to_asu) :
array = array.map_to_asu()
if (multiplicities is not None) :
multiplicities = multiplicities.map_to_asu()
if (settings.d_min is not None) :
array = array.resolution_filter(d_min=settings.d_min)
if (multiplicities is not None) :
multiplicities = multiplicities.resolution_filter(
d_min=settings.d_min)
self.filtered_array = array.deep_copy()
if (settings.expand_anomalous) :
array = array.generate_bijvoet_mates()
if (multiplicities is not None) :
multiplicities = multiplicities.generate_bijvoet_mates()
if (self.settings.show_missing) :
self.missing_set = array.complete_set().lone_set(array)
if self.settings.show_anomalous_pairs:
self.missing_set = self.missing_set.select(
self.missing_set.centric_flags().data(), negate=True)
if (settings.expand_to_p1) :
original_symmetry = array.crystal_symmetry()
array = array.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
#array = array.niggli_cell().expand_to_p1()
#self.missing_set = self.missing_set.niggli_cell().expand_to_p1()
self.missing_set = self.missing_set.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
if (multiplicities is not None) :
multiplicities = multiplicities.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
data = array.data()
self.r_free_mode = False
if isinstance(data, flex.bool) :
self.r_free_mode = True
data_as_float = flex.double(data.size(), 0.0)
data_as_float.set_selected(data==True, flex.double(data.size(), 1.0))
data = data_as_float
self.data = data.deep_copy()
else :
if isinstance(data, flex.double) :
self.data = data.deep_copy()
elif isinstance(data, flex.complex_double) :
self.data = flex.abs(data)
elif hasattr(array.data(), "as_double") :
self.data = array.data().as_double()
else:
raise RuntimeError("Unexpected data type: %r" % data)
if (settings.show_data_over_sigma) :
if (array.sigmas() is None) :
raise Sorry("sigmas not defined.")
sigmas = array.sigmas()
non_zero_sel = sigmas != 0
array = array.select(non_zero_sel)
array = array.customized_copy(data=array.data()/array.sigmas())
self.data = array.data()
if (multiplicities is not None) :
multiplicities = multiplicities.select(non_zero_sel)
self.work_array = array
self.multiplicities = multiplicities
def process_input_array(self):
from cctbx.array_family import flex
array = self.miller_array.deep_copy()
multiplicities = None
if self.merge_equivalents:
if self.settings.show_anomalous_pairs:
from cctbx import miller
merge = array.merge_equivalents()
multiplicities = merge.redundancies()
asu, matches = multiplicities.match_bijvoet_mates()
mult_plus, mult_minus = multiplicities.hemispheres_acentrics()
anom_mult = flex.int(
min(p, m)
for (p, m) in zip(mult_plus.data(), mult_minus.data()))
#flex.min_max_mean_double(anom_mult.as_double()).show()
anomalous_multiplicities = miller.array(
miller.set(asu.crystal_symmetry(),
mult_plus.indices(),
anomalous_flag=False), anom_mult)
anomalous_multiplicities = anomalous_multiplicities.select(
anomalous_multiplicities.data() > 0)
array = anomalous_multiplicities
multiplicities = anomalous_multiplicities
else:
merge = array.merge_equivalents()
array = merge.array()
multiplicities = merge.redundancies()
settings = self.settings
data = array.data()
self.missing_set = oop.null()
if (array.is_xray_intensity_array()):
data.set_selected(data < 0, flex.double(data.size(), 0.))
if (array.is_unique_set_under_symmetry()) and (settings.map_to_asu):
array = array.map_to_asu()
if (multiplicities is not None):
multiplicities = multiplicities.map_to_asu()
if (settings.d_min is not None):
array = array.resolution_filter(d_min=settings.d_min)
if (multiplicities is not None):
multiplicities = multiplicities.resolution_filter(
d_min=settings.d_min)
self.filtered_array = array.deep_copy()
if (settings.expand_anomalous):
array = array.generate_bijvoet_mates()
if (multiplicities is not None):
multiplicities = multiplicities.generate_bijvoet_mates()
if (self.settings.show_missing):
self.missing_set = array.complete_set().lone_set(array)
if self.settings.show_anomalous_pairs:
self.missing_set = self.missing_set.select(
self.missing_set.centric_flags().data(), negate=True)
if (settings.expand_to_p1):
original_symmetry = array.crystal_symmetry()
array = array.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
#array = array.niggli_cell().expand_to_p1()
#self.missing_set = self.missing_set.niggli_cell().expand_to_p1()
self.missing_set = self.missing_set.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
if (multiplicities is not None):
multiplicities = multiplicities.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
data = array.data()
self.r_free_mode = False
if isinstance(data, flex.bool):
self.r_free_mode = True
data_as_float = flex.double(data.size(), 0.0)
data_as_float.set_selected(data == True,
flex.double(data.size(), 1.0))
data = data_as_float
self.data = data.deep_copy()
else:
if isinstance(data, flex.double):
self.data = data.deep_copy()
elif isinstance(data, flex.complex_double):
self.data = flex.abs(data)
elif hasattr(array.data(), "as_double"):
self.data = array.data().as_double()
else:
raise RuntimeError("Unexpected data type: %r" % data)
if (settings.show_data_over_sigma):
if (array.sigmas() is None):
raise Sorry("sigmas not defined.")
sigmas = array.sigmas()
non_zero_sel = sigmas != 0
array = array.select(non_zero_sel)
array = array.customized_copy(data=array.data() /
array.sigmas())
self.data = array.data()
if (multiplicities is not None):
multiplicities = multiplicities.select(non_zero_sel)
self.work_array = array
self.multiplicities = multiplicities
def __init__(self,
parent,
figure_size=(8, 6),
font_size=12,
title_font_size=10,
facecolor='white',
transparent=False,
handle_left_click=False,
show_data_points=True,
point_types=('o', '^', '+', 's', 'D'),
title_alignment="right"):
wx.BoxSizer.__init__(self, wx.VERTICAL)
adopt_init_args(self, locals())
self._fonts = {}
self.disabled = False
try:
import matplotlib
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg
from matplotlib.backends.backend_wxagg import FigureManager
import matplotlib.ticker
import matplotlib.cm
import matplotlib.figure
import matplotlib.font_manager
except ImportError as e:
print("")
print("Error loading matplotlib module:")
print(e)
print("")
self.disabled = True
self.canvas = oop.null()
self.figure = oop.null()
self.text_font = oop.null()
self.p = oop.null()
w = int(figure_size[0] * 72)
h = int(figure_size[1] * 72)
panel = wx.Panel(parent=parent, size=(w, h))
panel.SetBackgroundColour((150, 150, 150))
szr = wx.BoxSizer(wx.VERTICAL)
panel.SetSizer(szr)
txt = wx.StaticText(
parent=panel,
label="Plotting disabled due to missing libraries.")
szr.Add(txt, 1, wx.ALL | wx.ALIGN_CENTER, 10)
txt.SetForegroundColour((255, 0, 0))
font = txt.GetFont()
font.SetWeight(wx.FONTWEIGHT_BOLD)
txt.SetFont(font)
txt2 = wx.StaticText(parent=panel, label="Original error:")
txt2.SetForegroundColour((255, 0, 0))
szr.Add(txt2, 1, wx.ALL | wx.ALIGN_CENTER, 10)
txt3 = wx.StaticText(parent=panel, label=str(e))
txt3.SetForegroundColour((255, 0, 0))
szr.Add(txt3, 1, wx.ALL | wx.ALIGN_CENTER, 10)
self.Add(panel, 1, wx.EXPAND | wx.ALL)
self.null_fmt = oop.null()
else:
self.figure = matplotlib.figure.Figure(figure_size,
72,
linewidth=0,
facecolor=facecolor)
if transparent:
self.figure.figurePatch.set_alpha(0.0)
self.canvas = FigureCanvasWxAgg(self.parent, -1, self.figure)
self.canvas.toolbar = oop.null()
self.figmgr = FigureManager(self.canvas, 1, self)
self.Add(self.canvas, 1, wx.EXPAND | wx.ALL)
self.setup_fonts()
self.null_fmt = matplotlib.ticker.NullFormatter()
if self.handle_left_click:
self.canvas.mpl_connect("button_release_event", self.OnClick)
else:
self.canvas.Bind(wx.EVT_CONTEXT_MENU, self.OnRightClick,
self.canvas)
if (wx.Platform == '__WXMAC__'): # FIXME MSW okay, check GTK
self.canvas.Bind(wx.EVT_MOUSEWHEEL, self.OnMouseWheel,
self.canvas)
def __init__(self, command_stream, builder=None):
from libtbx import object_oriented_patterns as oop
if builder is None: builder = oop.null()
parser.__init__(self, command_stream, builder)
self.instructions = {}