def __str__(self):
result = []
for elt, n in self.element_count_pairs:
r = continued_fraction.from_real(n, eps=1e-5).as_rational()
if r.denominator() == 1:
if r.numerator() > 1: m = "%i" % r.numerator()
else: m = ""
elif r.denominator() < 10: m = "%i/%i" % (r.numerator(), r.denominator())
else: m = "%.5f" % n
result.append("%s%s" % (elt, m))
return ' '.join(result)
def derive_change_of_basis_op(from_hkl, to_hkl):
# exclude those reflections that we couldn't index
sel = (to_hkl != (0, 0, 0)) & (from_hkl != (0, 0, 0))
assert sel.count(True) >= 3 # need minimum of 3 equations ?
to_hkl = to_hkl.select(sel)
from_hkl = from_hkl.select(sel)
# for each miller index, solve a system of linear equations to find the
# change of basis operator
h, k, l = to_hkl.as_vec3_double().parts()
r = []
from scitbx.lstbx import normal_eqns
for i in range(3):
eqns = normal_eqns.linear_ls(3)
for index, hkl in zip((h, k, l)[i], from_hkl):
eqns.add_equation(
right_hand_side=index, design_matrix_row=flex.double(hkl), weight=1
)
eqns.solve()
r.extend(eqns.solution())
from scitbx import matrix
from scitbx.math import continued_fraction
denom = 12
r = [
int(denom * continued_fraction.from_real(r_, eps=1e-2).as_rational())
for r_ in r
]
r = matrix.sqr(r).transpose()
# print (1/denom)*r
# now convert into a cctbx change_of_basis_op object
change_of_basis_op = sgtbx.change_of_basis_op(
sgtbx.rt_mx(sgtbx.rot_mx(r, denominator=denom))
).inverse()
print("discovered change_of_basis_op=%s" % (str(change_of_basis_op)))
# sanity check that this is the right cb_op
assert (change_of_basis_op.apply(from_hkl) == to_hkl).count(False) == 0
return change_of_basis_op
def derive_change_of_basis_op(from_hkl, to_hkl):
# exclude those reflections that we couldn't index
sel = (to_hkl != (0,0,0)) & (from_hkl != (0,0,0))
assert sel.count(True) >= 3 # need minimum of 3 equations ?
to_hkl = to_hkl.select(sel)
from_hkl = from_hkl.select(sel)
# for each miller index, solve a system of linear equations to find the
# change of basis operator
h, k, l = to_hkl.as_vec3_double().parts()
r = []
from scitbx.lstbx import normal_eqns
for i in range(3):
eqns = normal_eqns.linear_ls(3)
for index, hkl in zip((h,k,l)[i], from_hkl):
eqns.add_equation(right_hand_side=index,
design_matrix_row=flex.double(hkl),
weight=1)
eqns.solve()
r.extend(eqns.solution())
from scitbx.math import continued_fraction
from scitbx import matrix
denom = 12
r = [int(denom * continued_fraction.from_real(r_, eps=1e-2).as_rational())
for r_ in r]
r = matrix.sqr(r).transpose()
#print (1/denom)*r
# now convert into a cctbx change_of_basis_op object
change_of_basis_op = sgtbx.change_of_basis_op(
sgtbx.rt_mx(sgtbx.rot_mx(r, denominator=denom))).inverse()
print "discovered change_of_basis_op=%s" %(str(change_of_basis_op))
# sanity check that this is the right cb_op
assert (change_of_basis_op.apply(from_hkl) == to_hkl).count(False) == 0
return change_of_basis_op
def filtered_commands(self):
from scitbx.math import continued_fraction
temperature = 20
for command, line in self.command_stream:
cmd, args = command[0], command[-1]
n_args = len(args)
if cmd == 'OMIT':
if n_args == 3 and isinstance(args[0], float):
self.instructions.setdefault('omit_hkl', [])
self.instructions['omit_hkl'].append([int(i) for i in args])
elif n_args == 2 and isinstance(args[0], float):
self.instructions['omit'] = {
's': args[0],
'two_theta': args[1]}
else:
yield command, line
elif cmd == 'SHEL':
if args:
shel = {'lowres': args[0]}
if n_args > 1:
shel['highres'] = args[1]
elif cmd == 'MERG':
if args:
self.instructions['merg'] = args[0]
elif cmd == 'TEMP':
if len(args) > 1:
raise shelx_error("TEMP takes at most 1 argument")
if args: temperature = args[0]
self.instructions['temp'] = temperature
self.builder.temperature_in_celsius = temperature
elif cmd == 'WGHT':
if n_args > 6:
raise shelx_error("Too many argument for %s" % cmd, line)
default_weighting_scheme = { 'a': 0.1,
'b': 0,
'c': 0,
'd': 0,
'e': 0,
'f': 1/3 }
weighting_scheme = dict([
(key, (arg is not None and arg) or default_weighting_scheme[key])
for key, arg in itertools.izip_longest('abcdef', args) ])
self.instructions['wght'] = weighting_scheme
self.builder.make_shelx_weighting_scheme(**weighting_scheme)
elif cmd == 'HKLF':
# only ONE HKLF instruction allowed
assert 'hklf' not in self.instructions
hklf = {'s': 1, 'matrix': sgtbx.rot_mx()}
hklf['n'] = args[0]
if n_args > 1:
hklf['s'] = args[1]
if n_args > 2:
assert n_args > 10
mx = [ continued_fraction.from_real(e, eps=1e-3).as_rational()
for e in args[2:11] ]
den = reduce(rational.lcm, [ r.denominator() for r in mx ])
nums = [ r.numerator()*(den//r.denominator()) for r in mx ]
hklf['matrix'] = sgtbx.rot_mx(nums, den)
if n_args > 11:
hklf['wt'] = args[11]
if n_args == 13:
hklf['m'] = args[12]
self.instructions['hklf'] = hklf
assert not self.builder or ('wt' not in hklf and 'm' not in hklf)
self.builder.create_shelx_reflection_data_source(
format=hklf['n'],
indices_transform=hklf['matrix'],
data_scale=hklf['s'])
if 'basf' in self.instructions and hklf['n'] == 5:
self.builder.make_non_merohedral_twinning_with_transformed_hkl(
fractions=self.instructions['basf'])
elif cmd == 'TWIN':
# only ONE twin instruction allowed
assert 'twin' not in self.instructions
twin = {}
if n_args > 0:
assert n_args >= 9
twin['matrix'] = sgtbx.rt_mx(
sgtbx.rot_mx([int(i) for i in args[0:9]]))
if n_args > 9:
twin['n'] = args[9]
self.instructions['twin'] = twin
if 'basf' in self.instructions: self.issue_merohedral_twinning()
elif cmd == 'BASF':
self.instructions['basf'] = args
if 'twin' in self.instructions: self.issue_merohedral_twinning()
elif cmd == 'EXTI':
if len(args) == 1:
self.instructions['exti'] = args[0]
else:
yield command, line
else:
# All token have been read without errors or early bailout
assert 'hklf' in self.instructions, "Missing HKLF instruction"
def filtered_commands(self):
from scitbx.math import continued_fraction
temperature = 20
for command, line in self.command_stream:
cmd, args = command[0], command[-1]
n_args = len(args)
if cmd == 'OMIT':
if n_args == 3 and isinstance(args[0], float):
self.instructions.setdefault('omit_hkl', [])
self.instructions['omit_hkl'].append([int(i) for i in args])
elif n_args == 2 and isinstance(args[0], float):
self.instructions['omit'] = {
's': args[0],
'two_theta': args[1]}
else:
yield command, line
elif cmd == 'SHEL':
if args:
shel = {'lowres': args[0]}
if n_args > 1:
shel['highres'] = args[1]
elif cmd == 'MERG':
if args:
self.instructions['merg'] = args[0]
elif cmd == 'TEMP':
if len(args) > 1:
raise shelx_error("TEMP takes at most 1 argument")
if args: temperature = args[0]
self.instructions['temp'] = temperature
self.builder.temperature_in_celsius = temperature
elif cmd == 'WGHT':
if n_args > 6:
raise shelx_error("Too many argument for %s" % cmd, line)
default_weighting_scheme = { 'a': 0.1,
'b': 0,
'c': 0,
'd': 0,
'e': 0,
'f': 1/3 }
weighting_scheme = dict([
(key, (arg is not None and arg) or default_weighting_scheme[key])
for key, arg in itertools.izip_longest('abcdef', args) ])
self.instructions['wght'] = weighting_scheme
self.builder.make_shelx_weighting_scheme(**weighting_scheme)
elif cmd == 'HKLF':
# only ONE HKLF instruction allowed
assert 'hklf' not in self.instructions
hklf = {'s': 1, 'matrix': sgtbx.rot_mx()}
hklf['n'] = args[0]
if n_args > 1:
hklf['s'] = args[1]
if n_args > 2:
assert n_args > 10
mx = [ continued_fraction.from_real(e, eps=1e-3).as_rational()
for e in args[2:11] ]
den = reduce(rational.lcm, [ r.denominator() for r in mx ])
nums = [ r.numerator()*(den//r.denominator()) for r in mx ]
hklf['matrix'] = sgtbx.rot_mx(nums, den)
if n_args > 11:
hklf['wt'] = args[11]
if n_args == 13:
hklf['m'] = args[12]
self.instructions['hklf'] = hklf
assert not self.builder or ('wt' not in hklf and 'm' not in hklf)
self.builder.create_shelx_reflection_data_source(
format=hklf['n'],
indices_transform=hklf['matrix'],
data_scale=hklf['s'])
if 'basf' in self.instructions and hklf['n'] == 5:
self.builder.make_non_merohedral_twinning_with_transformed_hkl(
fractions=self.instructions['basf'])
elif cmd == 'TWIN':
# only ONE twin instruction allowed
assert 'twin' not in self.instructions
twin = {}
if n_args > 0:
assert n_args >= 9
twin['matrix'] = sgtbx.rt_mx(
sgtbx.rot_mx([int(i) for i in args[0:9]]))
if n_args > 9:
twin['n'] = args[9]
self.instructions['twin'] = twin
if 'basf' in self.instructions: self.issue_merohedral_twinning()
elif cmd == 'BASF':
self.instructions['basf'] = args
if 'twin' in self.instructions: self.issue_merohedral_twinning()
elif cmd == 'EXTI':
if len(args) == 1:
self.instructions['exti'] = args[0]
else:
yield command, line
else:
# All token have been read without errors or early bailout
assert 'hklf' in self.instructions, "Missing HKLF instruction"