def __init__(self, crystal, beam, detector, goniometer, scan, reflections):
"""Initialise the optimization."""
from scitbx import simplex
# FIXME in here this code is very unstable or actually broken if
# we pass in a few lone images i.e. screening shots - propose need
# for alternative algorithm, in meantime can avoid code death if
# something like this
#
# if scan.get_num_images() == 1:
# self.sigma = 0.5 * scan.get_oscillation_range()[1] * math.pi / 180.0
# return
#
# is used... @JMP please could we discuss? assert best method to get
# sigma_m in that case is actually to look at present / absent
# reflections as per how Mosflm does it...
# Initialise the function used in likelihood estimation.
self._R = FractionOfObservedIntensity(
crystal, beam, detector, goniometer, scan, reflections
)
# Set the starting values to try 1, 3 degrees seems sensible for
# crystal mosaic spread
start = 1 * math.pi / 180
stop = 3 * math.pi / 180
starting_simplex = [flex.double([start]), flex.double([stop])]
# Initialise the optimizer
optimizer = simplex.simplex_opt(
1, matrix=starting_simplex, evaluator=self, tolerance=1e-7
)
# Get the solution
self.sigma = math.exp(optimizer.get_solution()[0])
def simplex(self):
self.n = self.n_params
if (self.x is None):
self.x = flex.double([1] + [0] * (self.n_params - 1))
else:
self.x = self.x.concatenate(
flex.double([0] * (self.n_params - self.n_fst_pass)))
self.pofr = pr_tools.pofr(self.d_max, self.n, self.prior)
self.simplex_scores = []
self.simplex_solutions = []
for ii in xrange(self.simplex_trial):
#make a random simplex
self.starting_simplex = []
for ii in range(self.n):
self.starting_simplex.append((flex.random_double(self.n) * 2 -
1.0) + self.x)
self.starting_simplex.append(self.x)
self.optimizer = simplex.simplex_opt(dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-4)
self.solution = self.optimizer.get_solution()
self.score = self.target(self.solution)
self.simplex_scores.append(self.score)
self.simplex_solutions.append(self.solution)
best_index = flex.min_index(flex.double(self.simplex_scores))
self.solution = self.simplex_solutions[best_index]
#self.cma(m=self.solution)
self.score = self.simplex_scores[best_index]
self.pofr.update(self.solution)
def __init__(self, n_params, d_max, data, n_int=35, alpha=1.0):
self.n = n_params
self.d_max = d_max
self.data = data
self.n_int = n_int
self.alpha = alpha
self.gaussian = 2.0
self.bounds = b.bounds(self.n, "cheb_coef.dat")
if (self.gaussian > 0):
self.bounds.min = self.bounds.mean - self.gaussian * self.bounds.var
self.bounds.max = self.bounds.mean + self.gaussian * self.bounds.var
# make a pofr please
self.pofr = pr_tools.pofr(self.d_max,
self.n,
n_int=self.n_int,
m_int=self.n_int)
#make a random simplex please
self.starting_simplex = []
for ii in range(self.n + 1):
self.starting_simplex.append(flex.random_double(self.n) * 2 - 1)
self.optimizer = simplex.simplex_opt(dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-3)
self.solution = self.optimizer.GetResult()
def __init__(self, values, parameterization, data, indices, bins, seed = None, log=None):
"""
@param values parameterization of the SD terms
@param data ISIGI dictionary of unmerged intensities
@param indices array of miller indices to refine against
@param bins array of flex.bool object specifying the bins to use to calculate the functional
@param log Log to print to (none for stdout)
"""
if log is None:
log = sys.stdout
self.log = log
self.data = data
self.intensity_bin_selections = bins
self.indices = indices
self.parameterization = parameterization
self.n = 3
self.x = flex.double([values.SDFAC, values.SDB, values.SDADD])
self.starting_simplex = []
if seed is None:
random_func = flex.random_double
else:
print("Using random seed %d"%seed, file=self.log)
mt = flex.mersenne_twister(seed)
random_func = mt.random_double
for i in range(self.n+1):
self.starting_simplex.append(random_func(self.n))
self.optimizer = simplex_opt( dimension = self.n,
matrix = self.starting_simplex,
evaluator = self,
tolerance = 1e-1)
self.x = self.optimizer.get_solution()
def __init__(self, frames, z, zeta, sweep):
from scitbx import simplex
from scitbx.array_family import flex
import numpy
self.L = Likelihood(FractionOfObservedIntensity(frames, z, zeta, sweep.get_scan()))
x = 0.1 + numpy.arange(1000) / 2000.0
l = [self.L(xx) for xx in x]
from matplotlib import pylab
pylab.plot(x, l)
pylab.show()
# print 1/0
startA = 0.3
startB = 0.4
# startA = 0.2*3.14159 / 180
# startB = 0.3*3.14159 / 180
print "Start: ", startA, startB
starting_simplex=[flex.double([startA]), flex.double([startB])]
# for ii in range(2):
# starting_simplex.append(flex.double([start]))#flex.random_double(1))
self.optimizer = simplex.simplex_opt(
1, matrix=starting_simplex, evaluator=self, tolerance=1e-7)
def run_simplex(self):
start_matrix=[]
for ii in range(self.n):
start_matrix.append( flex.random_double(self.n)*2.0-1.0 )
start_matrix.append( flex.double(self.n,0) )
self.optimizer = simplex.simplex_opt( dimension=self.n, matrix=start_matrix, evaluator=self, tolerance=1e-5 )
self.x = self.optimizer.get_solution()
def run_simplex(self):
start_matrix=[]
for ii in range(self.n):
start_matrix.append( flex.random_double(self.n)*2.0-1.0 )
start_matrix.append( flex.double(self.n,0) )
self.optimizer = simplex.simplex_opt( dimension=self.n, matrix=start_matrix, evaluator=self, tolerance=1e-5 )
self.x = self.optimizer.get_solution()
def __init__(self, frames, z, zeta, sweep):
from scitbx import simplex
from scitbx.array_family import flex
import numpy
self.L = Likelihood(
FractionOfObservedIntensity(frames, z, zeta, sweep.get_scan()))
x = 0.1 + numpy.arange(1000) / 2000.0
l = [self.L(xx) for xx in x]
from matplotlib import pylab
pylab.plot(x, l)
pylab.show()
# print 1/0
startA = 0.3
startB = 0.4
# startA = 0.2*3.14159 / 180
# startB = 0.3*3.14159 / 180
print("Start: ", startA, startB)
starting_simplex = [flex.double([startA]), flex.double([startB])]
# for ii in range(2):
# starting_simplex.append(flex.double([start]))#flex.random_double(1))
self.optimizer = simplex.simplex_opt(1,
matrix=starting_simplex,
evaluator=self,
tolerance=1e-7)
def simplex(self):
self.simplex_scores = []
self.simplex_solutions = []
for ii in xrange(self.simplex_trial):
#make a random simplex
self.starting_simplex = []
for ii in range(self.n * self.n_refine):
self.starting_simplex.append(
(flex.random_double(self.n * self.n_refine) * 2 - 1.0) *
1.0 + self.x)
self.starting_simplex.append(self.x)
self.optimizer = simplex.simplex_opt(dimension=self.n *
self.n_refine,
matrix=self.starting_simplex,
evaluator=self,
max_iter=500,
tolerance=1e-4)
self.solution = self.optimizer.get_solution()
self.score = self.target(self.solution)
self.simplex_scores.append(self.score)
self.simplex_solutions.append(self.solution)
best_index = flex.min_index(flex.double(self.simplex_scores))
self.solution = self.simplex_solutions[best_index]
self.score = self.target(self.solution)
def __init__(self, n_params, d_max, data, bounds, n_int=25, alpha=1.0):
self.n = n_params
self.d_max = d_max
self.data = data
self.n_int = n_int
self.alpha = alpha
self.gaussian = 0.0
self.bounds = bounds
self.step_size = 2
if (self.gaussian > 0):
self.bounds.min = self.bounds.mean - self.gaussian * self.bounds.var
self.bounds.max = self.bounds.mean + self.gaussian * self.bounds.var
# make a pofr please
self.pofr = pr_tools.pofr(self.d_max,
self.n,
n_int=self.n_int,
m_int=self.n_int)
#make a random simplex please
self.starting_simplex = []
cand = flex.random_double(self.n)
for ii in range(self.n):
self.starting_simplex.append(
flex.double(self.orth(ii, self.n)) * self.step_size + cand)
self.starting_simplex.append(cand)
# self.starting_simplex.append((flex.random_double(self.n)*2-1)*self.step_size)
self.optimizer = simplex.simplex_opt(dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-8)
self.solution = self.optimizer.GetResult()
def simplex(self):
self.simplex_scores = []
self.simplex_solutions = []
for ii in xrange(self.simplex_trial):
#make a random simplex
self.starting_simplex = []
for ii in range(self.n):
self.starting_simplex.append(
random.random() * (flex.random_double(3) * 2 - 1.0) * 2 +
self.x)
self.starting_simplex.append(self.x)
self.optimizer = simplex.simplex_opt(dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
max_iter=50,
tolerance=1e-4)
self.solution = self.optimizer.GetResult()
self.score = self.target(self.solution)
self.simplex_scores.append(self.score)
self.simplex_solutions.append(self.solution)
best_index = flex.min_index(flex.double(self.simplex_scores))
self.score = self.simplex_scores[best_index]
self.solution = self.simplex_solutions[best_index]
if (self.translate):
self.vector = self.solution.deep_copy()
print "translate:", list(self.vector)
else:
self.angle = self.solution.deep_copy()
print "rotate:", list(self.angle)
self.target(self.solution)
def __init__(self, crystal, beam, detector, goniometer, scan, reflections):
'''Initialise the optmization.'''
from scitbx import simplex
from scitbx.array_family import flex
from math import pi, exp
import random
# Initialise the function used in likelihood estimation.
self._R = FractionOfObservedIntensity(crystal, beam, detector, goniometer,
scan, reflections)
# Set the starting values to try
start = random.random() * pi / 180
stop = random.random() * pi / 180
starting_simplex = [flex.double([start]), flex.double([stop])]
# Initialise the optimizer
optimizer = simplex.simplex_opt(
1,
matrix=starting_simplex,
evaluator=self,
tolerance=1e-7)
# Get the solution
self.sigma = exp(optimizer.get_solution()[0])
def optimize(self):
start_matrix = []
for ii in range(self.n + 1):
start_matrix.append((flex.random_double(self.n) - 1.0) * 0.2)
optimizer = simplex.simplex_opt(dimension=self.n,
matrix=start_matrix,
evaluator=self,
tolerance=1e-4)
self.solution = optimizer.get_solution()
self.score = self.target(self.solution)
def __init__(selfOO):
selfOO.starting_simplex=[]
selfOO.n = 2
for ii in range(selfOO.n+1):
selfOO.starting_simplex.append(flex.random_double(selfOO.n))
selfOO.optimizer = simplex_opt( dimension=selfOO.n,
matrix = selfOO.starting_simplex,
evaluator = selfOO,
tolerance=1e-7)
selfOO.x = selfOO.optimizer.get_solution()
def run_simplex(self, start, max_iter=500):
dim = 3
starting_matrix = [start]
for ii in range(dim):
starting_matrix.append(start + (flex.random_double(dim) * 2 - 1) * self.dx)
optimizer = simplex.simplex_opt(
dimension=dim, matrix=starting_matrix, evaluator=self, max_iter=max_iter, tolerance=1e-5
)
result = optimizer.get_solution()
return result
def __init__(selfOO):
selfOO.starting_simplex=[]
selfOO.n = 1
for ii in range(selfOO.n+1):
selfOO.starting_simplex.append(flex.random_double(selfOO.n))
selfOO.optimizer = simplex_opt( dimension=selfOO.n,
matrix = selfOO.starting_simplex,
evaluator = selfOO,
tolerance=1e-4)
selfOO.x = selfOO.optimizer.get_solution()
def __init__(
self,
crystal,
beam,
detector,
goniometer,
scan,
reflections,
n_macro_cycles=10,
):
from dials.array_family import flex
from scitbx import simplex
# Get the oscillation width
dphi2 = scan.get_oscillation(deg=False)[1] / 2.0
# Calculate a list of angles and zeta's
tau, zeta, n, indices = self._calculate_tau_and_zeta(
crystal, beam, detector, goniometer, scan, reflections)
# Calculate zeta * (tau +- dphi / 2) / math.sqrt(2)
self.e1 = (tau + dphi2) * flex.abs(zeta) / math.sqrt(2.0)
self.e2 = (tau - dphi2) * flex.abs(zeta) / math.sqrt(2.0)
self.n = n
self.indices = indices
if len(self.e1) == 0:
raise RuntimeError(
"Something went wrong. Zero pixels selected for estimation of profile parameters."
)
# Compute intensity
self.K = flex.double()
for i0, i1 in zip(self.indices[:-1], self.indices[1:]):
selection = flex.size_t(range(i0, i1))
self.K.append(flex.sum(self.n.select(selection)))
# Set the starting values to try 1, 3 degrees seems sensible for
# crystal mosaic spread
start = math.log(0.1 * math.pi / 180)
stop = math.log(1 * math.pi / 180)
starting_simplex = [flex.double([start]), flex.double([stop])]
# Initialise the optimizer
optimizer = simplex.simplex_opt(1,
matrix=starting_simplex,
evaluator=self,
tolerance=1e-3)
# Get the solution
sigma = math.exp(optimizer.get_solution()[0])
# Save the result
self.sigma = sigma
def run_simplex( self, start, max_iter=500 ):
dim = 3
starting_matrix = [ start ]
for ii in range( dim ):
starting_matrix.append( start + (flex.random_double(dim)*2-1)*self.dx )
optimizer = simplex.simplex_opt( dimension = dim,
matrix = starting_matrix,
evaluator = self,
max_iter = max_iter,
tolerance=1e-5)
result = optimizer.get_solution()
return result
def iterate(self):
if (self.Niter > 0): # need to build PDB object from the last PDB file
iter_name = self.root + str(self.Niter) + ".pdb"
t1 = time.time()
self.pdb = PDB(iter_name, method=self.method)
self.nmode = self.pdb.Hessian(self.cutoff, self.nmode_init,
self.scale_factor) - 1
self.time_nm += (time.time() - t1)
self.n1 = self.nmodes + 1
score = []
candidates = []
for kk in range(self.nmode_init - self.nmodes):
self.modes = flex.int(range(self.nmodes)) + 7
self.modes.append(kk + 7 + self.nmodes)
self.starting_simplex = []
cand = flex.double(self.n1, 0)
for ii in range(self.n1):
self.starting_simplex.append(
flex.double(self.orth(ii, self.n1)) * self.step_size +
cand)
self.starting_simplex.append(cand)
self.optimizer = simplex.simplex_opt(dimension=self.n1,
matrix=self.starting_simplex,
evaluator=self,
monitor_cycle=4,
tolerance=1e-1)
self.x = self.optimizer.get_solution()
candidates.append(self.x.deep_copy())
score.append(self.optimizer.get_score())
minscore = min(score[0:self.topn])
print self.Niter, minscore, self.counter
if ((self.Niter % self.optNum) > 1):
self.stopCheck(minscore)
self.updateScore(minscore)
minvec = candidates[score.index(minscore)]
new_coord = flex.vec3_double(self.pdb.NMPerturb(self.modes, minvec))
self.Niter = self.Niter + 1
iter_name = self.root + str(self.Niter) + ".pdb"
self.pdb.writePDB(new_coord, iter_name)
if (self.Niter % self.optNum == 0):
processed_pdb, pdb_inp = self.pdb_processor.process_pdb_files(
pdb_file_names=[iter_name])
new_coord = geo_opt(processed_pdb, self.log)
self.pdb.writePDB(new_coord, iter_name)
if (not self.stop):
# if(self.Niter < 50):
self.iterate()
def __init__(self, name):
self.n = 2
self.x = start.deep_copy()
self.name = name
self.starting_simplex = []
self.fcount = 0
for ii in range(self.n + 1):
self.starting_simplex.append((flex.random_double(self.n) / 2 - 1) * 0.0003 + self.x)
self.optimizer = simplex.simplex_opt(
dimension=self.n, matrix=self.starting_simplex, evaluator=self, tolerance=1e-10
)
self.x = self.optimizer.get_solution()
print "SIMPLEX ITRATIONS", self.optimizer.count, self.fcount, "SOLUTION", list(self.x), self.target(self.x)
def __init__(self, wide_search_offset):
self.n = 2
self.wide_search_offset = wide_search_offset
self.optimizer = simplex_opt(
dimension=self.n,
matrix=[flex.random_double(self.n) for _ in range(self.n + 1)],
evaluator=self,
tolerance=1e-7,
)
self.x = self.optimizer.get_solution()
self.offset = self.x[0] * 0.2 * beamr1 + self.x[1] * 0.2 * beamr2
if self.wide_search_offset is not None:
self.offset += self.wide_search_offset
def __init__(selfOO, wide_search_offset=None):
selfOO.starting_simplex=[]
selfOO.n = 2
selfOO.wide_search_offset = wide_search_offset
for ii in range(selfOO.n+1):
selfOO.starting_simplex.append(flex.random_double(selfOO.n))
selfOO.optimizer = simplex_opt(dimension=selfOO.n,
matrix=selfOO.starting_simplex,
evaluator=selfOO,
tolerance=1e-7)
selfOO.x = selfOO.optimizer.get_solution()
selfOO.offset = selfOO.x[0]*0.2*beamr1 + selfOO.x[1]*0.2*beamr2
if selfOO.wide_search_offset is not None:
selfOO.offset += selfOO.wide_search_offset
def __init__(self):
"""
"""
self.n = 2
self.x = flex.double([0.5,0.0])
self.starting_simplex = []
for i in xrange(self.n+1):
self.starting_simplex.append(flex.random_double(self.n))
self.optimizer = simplex_opt( dimension = self.n,
matrix = self.starting_simplex,
evaluator = self,
tolerance = 1e-1)
self.x = self.optimizer.get_solution()
def __init__(selfOO, wide_search_offset=None):
selfOO.starting_simplex=[]
selfOO.n = 2
selfOO.wide_search_offset = wide_search_offset
for ii in range(selfOO.n+1):
selfOO.starting_simplex.append(flex.random_double(selfOO.n))
selfOO.optimizer = simplex_opt(dimension=selfOO.n,
matrix=selfOO.starting_simplex,
evaluator=selfOO,
tolerance=1e-7)
selfOO.x = selfOO.optimizer.get_solution()
selfOO.offset = selfOO.x[0]*0.2*beamr1 + selfOO.x[1]*0.2*beamr2
if selfOO.wide_search_offset is not None:
selfOO.offset += selfOO.wide_search_offset
def __init__(self):
"""
"""
self.n = 2
self.x = flex.double([0.5, 0.0])
self.starting_simplex = []
for i in xrange(self.n + 1):
self.starting_simplex.append(flex.random_double(self.n))
self.optimizer = simplex_opt(dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-1)
self.x = self.optimizer.get_solution()
def __init__(self, values, offset, evaluator, max_iter, tolerance=1e-10):
"""
Init the simplex
"""
self.n = len(values)
self.x = values
self.starting_simplex = self.generate_start(values, offset)
optimizer = simplex.simplex_opt(
dimension=self.n,
matrix=self.starting_simplex,
evaluator=evaluator,
tolerance=tolerance,
max_iter=max_iter,
)
self.x = optimizer.get_solution()
def run(self, initial_simplex):
"""Calculate scaling"""
# Optimise the simplex
self.optimised = simplex.simplex_opt(dimension=len(initial_simplex[0]),
matrix=initial_simplex,
evaluator=self)
# Extract solution
self.optimised_values = self.optimised.get_solution()
# Scaled input values
self.out_values = self.transform(values=self.scl_values)
# Calculate rmsds
self.unscaled_rmsd = self.rmsd_to_ref(values=self.scl_values)
self.scaled_rmsd = self.rmsd_to_ref(values=self.out_values)
return self.optimised_values
def __init__(self, values, offset, evaluator, max_iter):
self.n = len(values)
self.x = values
self.starting_simplex = generate_start(values, offset)
self.fcount = 0
optimizer = simplex.simplex_opt(
dimension=self.n,
matrix=self.starting_simplex,
evaluator=evaluator,
tolerance=1e-10,
max_iter=max_iter,
)
self.x = optimizer.get_solution()
return
def __init__(self, name):
self.n = 2
self.x = start.deep_copy()
self.name = name
self.starting_simplex = []
self.fcount = 0
for ii in range(self.n + 1):
self.starting_simplex.append((flex.random_double(self.n) / 2 - 1) *
0.0003 + self.x)
self.optimizer = simplex.simplex_opt(dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-10)
self.x = self.optimizer.get_solution()
print("SIMPLEX ITRATIONS", self.optimizer.count, self.fcount,
"SOLUTION", list(self.x), self.target(self.x))
def optimize_further(self):
self.solutions=[]
self.scores= flex.double()
for candi in self.candidates:
starting_simplex = []
for ii in range(self.dimension+1):
starting_simplex.append(flex.random_double(self.dimension)*self.simplex_scale + candi)
optimizer = simplex.simplex_opt( dimension=self.dimension,
matrix = starting_simplex,
evaluator = self.evaluator,
tolerance=self.tolerance
)
self.solutions.append( optimizer.get_solution() )
self.scores.append( optimizer.get_score() )
min_index = flex.min_index( self.scores )
self.best_solution = self.solutions[ min_index ]
self.best_score = self.scores[ min_index ]
def optimize_further(self):
self.solutions=[]
self.scores= flex.double()
for candi in self.candidates:
starting_simplex = []
for ii in range(self.dimension+1):
starting_simplex.append(flex.random_double(self.dimension)*self.simplex_scale + candi)
optimizer = simplex.simplex_opt( dimension=self.dimension,
matrix = starting_simplex,
evaluator = self.evaluator,
tolerance=self.tolerance
)
self.solutions.append( optimizer.get_solution() )
self.scores.append( optimizer.get_score() )
min_index = flex.min_index( self.scores )
self.best_solution = self.solutions[ min_index ]
self.best_score = self.scores[ min_index ]
def __init__(self, reflections, sweep):
'''Initialise the optmization.'''
from scitbx import simplex
from scitbx.array_family import flex
from math import pi
import random
# Initialise the function used in likelihood estimation.
self._R = FractionOfObservedIntensity(reflections, sweep)
# Set the starting values to try
start = 0.1 * random.random() * pi / 180
stop = 0.1 * random.random() * pi / 180
starting_simplex = [flex.double([start]), flex.double([stop])]
# Initialise the optimizer
self._optimizer = simplex.simplex_opt(1, matrix=starting_simplex,
evaluator=self, tolerance=1e-7)
def __init__(
self,
experiments,
reflections,
initial_mosaic_parameters,
wavelength_func,
refine_bandpass=False,
):
"""Initialize the minimizer and perform the minimization
@param experiments ExperimentList
@param reflections flex.reflection_table
@param initial_mosaic_parameters Tuple of domain size (angstroms) and half mosaic angle (degrees)
@param wavelength_func Function to compute wavelengths
@param refine_bandpass If True, refine band pass for each experiment.
"""
self.experiments = experiments
self.reflections = reflections
self.wavelength_func = wavelength_func
self.refine_bandpass = refine_bandpass
self.x = flex.double(initial_mosaic_parameters)
self.n = 2
if refine_bandpass:
for expt_id, expt in enumerate(experiments):
refls = reflections.select(reflections["id"] == expt_id)
wavelength_min, wavelength_max = estimate_bandpass(refls)
expt.crystal.bandpass = wavelength_min, wavelength_max
# actually refine the midpoint and the width. That ensures the two values don't cross over.
self.x.append(wavelength_max - wavelength_min)
self.x.append((wavelength_min + wavelength_max) / 2)
self.n += 2
self.starting_simplex = []
for i in xrange(self.n + 1):
self.starting_simplex.append(
(0.9 + (flex.random_double(self.n) / 10)) * self.x)
self.optimizer = simplex_opt(
dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-1,
)
self.x = self.optimizer.get_solution()
def __init__(self, r, x, seed=None, plot=False):
from dials.array_family import flex
self.plot = plot
assert seed is not None, 'seed should not be None'
self.n = r.focus()[0] * 2 # Number of parameters
self.x = x
self.r = r
self.starting_simplex = []
mt = flex.mersenne_twister(seed)
random_scale = .5
self.n_datapoints = r.focus()[0]
self.data = r
for i in range(self.n + 1):
self.starting_simplex.append(random_scale * ((
(mt.random_double(self.n)) / 2.0) - 1.0) + self.x)
self.optimizer = simplex_opt(dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-3)
self.x = self.optimizer.get_solution()
def __init__(selfOO, alt_crystal, Ncells_abc, host_runner, PP, n_cycles,
s_cycles):
selfOO.n_cycles = n_cycles
selfOO.PP = PP
selfOO.crnm = host_runner
# count the full number of parameters
selfOO.n = 0
selfOO.iteration = 0
selfOO.alt_crystal = alt_crystal
selfOO.Ncells_abc = Ncells_abc
initial_values = flex.double()
selfOO.starting_simplex = [initial_values]
bounding_values = flex.double()
for key in selfOO.crnm.ref_params:
selfOO.crnm.ref_params[key].accept()
for label in selfOO.crnm.ref_params[key].display_labels:
selfOO.n += 1
print(label, selfOO.crnm.ref_params[key].chain[label][-1])
initial_values.append(
selfOO.crnm.ref_params[key].chain[label][-1])
vals = selfOO.crnm.ref_params[key].generate_simplex_interval()
for il, label in enumerate(
selfOO.crnm.ref_params[key].display_labels):
print(label, vals[il])
bounding_values.append(vals[il])
#print("there are %d parameters"%selfOO.n)
selfOO.crnm.plot_all(selfOO.iteration + 1, of=n_cycles)
for ii in range(selfOO.n):
vertex = copy.deepcopy(initial_values)
vertex[ii] = bounding_values[ii]
selfOO.starting_simplex.append(vertex)
print(selfOO.starting_simplex)
selfOO.optimizer = simplex_opt(dimension=selfOO.n,
matrix=selfOO.starting_simplex,
evaluator=selfOO,
monitor_cycle=20,
max_iter=s_cycles - 1,
tolerance=1e-7)
selfOO.x = selfOO.optimizer.get_solution()
def __init__(self, crystal, beam, detector, goniometer, scan, reflections):
'''Initialise the optmization.'''
from scitbx import simplex
from scitbx.array_family import flex
from math import pi, exp
# FIXME in here this code is very unstable or actually broken if
# we pass in a few lone images i.e. screening shots - propose need
# for alternative algorithm, in meantime can avoid code death if
# something like this
#
# if scan.get_num_images() == 1:
# self.sigma = 0.5 * scan.get_oscillation_range()[1] * pi / 180.0
# return
#
# is used... @JMP please could we discuss? assert best method to get
# sigma_m in that case is actually to look at present / absent
# reflections as per how Mosflm does it...
# Initialise the function used in likelihood estimation.
self._R = FractionOfObservedIntensity(crystal, beam, detector, goniometer,
scan, reflections)
# Set the starting values to try 1, 3 degrees seems sensible for
# crystal mosaic spread
start = 1 * pi / 180
stop = 3 * pi / 180
starting_simplex = [flex.double([start]), flex.double([stop])]
# Initialise the optimizer
optimizer = simplex.simplex_opt(
1,
matrix=starting_simplex,
evaluator=self,
tolerance=1e-7)
# Get the solution
self.sigma = exp(optimizer.get_solution()[0])
def scale(self):
'''Find scale factors s, b that minimise target function.'''
from scitbx.direct_search_simulated_annealing import dssa
from scitbx.simplex import simplex_opt
from scitbx.array_family import flex
# only scale second and subsequent scale factors - first ones are
# constrained to 0.0
self.n = 2 * len(self._frame_sizes) - 2
self.x = flex.double(self._scales_s[1:] + self._scales_b[1:])
self.starting_matrix = [self.x + flex.random_double(self.n) \
for j in range(self.n + 1)]
if False:
self.optimizer = dssa(dimension = self.n,
matrix = self.starting_matrix,
evaluator = self,
tolerance = 1.e-6,
further_opt = True)
else:
self.optimizer = simplex_opt(dimension = self.n,
matrix = self.starting_matrix,
evaluator = self,
tolerance = 1.e-3)
# save the best scale factors
self.x = self.optimizer.get_solution()
self._scales_s = flex.double(1, 0.0)
self._scales_s.extend(self.x[:len(self._frame_sizes) - 1])
self._scales_b = flex.double(1, 0.0)
self._scales_b.extend(self.x[len(self._frame_sizes) - 1:])
# scale the raw intensity data for later reference
scaled_intensities = []
j = 0
for f, fs in enumerate(self._frame_sizes):
for k in range(fs):
hkl = self._indices[j]
g_hl = self.scale_factor(f, hkl)
scaled_intensities.append((self._intensities[j] / g_hl))
j += 1
self._scaled_intensities = scaled_intensities
# now compute reflections with > 1 observation as starting point for
# computing the Rmerge
from collections import defaultdict
multiplicity = defaultdict(list)
for j, i in enumerate(self._indices):
multiplicity[i].append(j)
rmerge_n = 0.0
rmerge_d = 0.0
import math
for i in multiplicity:
if len(multiplicity[i]) == 1:
continue
imean = self._imean[i]
for j in multiplicity[i]:
rmerge_n += math.fabs(scaled_intensities[j] - imean)
rmerge_d += imean
return rmerge_n / rmerge_d
def __init__(self,
miller_obs,
miller_calc,
min_d_star_sq=0.0,
max_d_star_sq=2.0,
n_points=2000,
level=6.0):
assert miller_obs.indices().all_eq(miller_calc.indices())
if (miller_obs.is_xray_amplitude_array()):
miller_obs = miller_obs.f_as_f_sq()
if (miller_calc.is_xray_amplitude_array()):
miller_calc = miller_calc.f_as_f_sq()
self.obs = miller_obs.deep_copy()
self.calc = miller_calc.deep_copy()
self.mind = min_d_star_sq
self.maxd = max_d_star_sq
self.m = n_points
self.n = 2
self.level = level
norma_obs = absolute_scaling.kernel_normalisation(
miller_array=self.obs, auto_kernel=True, n_bins=45, n_term=17)
norma_calc = absolute_scaling.kernel_normalisation(
miller_array=self.calc, auto_kernel=True, n_bins=45, n_term=17)
obs_d_star_sq = norma_obs.d_star_sq_array
calc_d_star_sq = norma_calc.d_star_sq_array
sel_calc_obs = norma_calc.bin_selection.select(norma_obs.bin_selection)
sel_obs_calc = norma_obs.bin_selection.select(norma_calc.bin_selection)
sel = ((obs_d_star_sq > low_lim) & (obs_d_star_sq < high_lim) &
(norma_obs.mean_I_array > 0))
sel = sel.select(sel_calc_obs)
self.obs_d_star_sq = obs_d_star_sq.select(sel)
self.calc_d_star_sq = calc_d_star_sq.select(sel_obs_calc).select(sel)
self.mean_obs = norma_obs.mean_I_array.select(sel)
self.mean_calc = norma_calc.mean_I_array.select(sel_obs_calc).select(
sel)
self.var_obs = norma_obs.var_I_array.select(sel)
self.var_calc = norma_calc.var_I_array.select(sel_obs_calc).select(sel)
# make an interpolator object please
self.interpol = scale_curves.curve_interpolator(
self.mind, self.maxd, self.m)
# do the interpolation
tmp_obs_d_star_sq , self.mean_obs,self.obs_a , self.obs_b = \
self.interpol.interpolate(self.obs_d_star_sq,self.mean_obs)
self.obs_d_star_sq , self.var_obs,self.obs_a , self.obs_b = \
self.interpol.interpolate(self.obs_d_star_sq, self.var_obs)
tmp_calc_d_star_sq , self.mean_calc,self.calc_a, self.calc_b = \
self.interpol.interpolate(self.calc_d_star_sq,self.mean_calc)
self.calc_d_star_sq, self.var_calc,self.calc_a , self.calc_b = \
self.interpol.interpolate(self.calc_d_star_sq,self.var_calc)
self.mean_ratio_engine = chebyshev_polynome(mean_coefs.size(),
low_lim - 1e-3,
high_lim + 1e-3,
mean_coefs)
self.std_ratio_engine = chebyshev_polynome(std_coefs.size(),
low_lim - 1e-3,
high_lim + 1e-3, std_coefs)
self.x = flex.double([0, 0])
self.low_lim_for_scaling = 1.0 / (4.0 * 4.0) #0.0625
selection = (self.calc_d_star_sq > self.low_lim_for_scaling)
if (selection.count(True) == 0):
raise Sorry(
"No reflections within required resolution range after " +
"filtering.")
self.weight_array = selection.as_double() / (2.0 * self.var_obs)
assert (not self.weight_array.all_eq(0.0))
self.mean = flex.double(
[1.0 / (flex.sum(self.mean_calc) / flex.sum(self.mean_obs)), 0.0])
self.sigmas = flex.double([0.5, 0.5])
s = 1.0 / (flex.sum(self.weight_array * self.mean_calc) /
flex.sum(self.weight_array * self.mean_obs))
b = 0.0
self.sart_simplex = [
flex.double([s, b]),
flex.double([s + 0.1, b + 1.1]),
flex.double([s - 0.1, b - 1.1])
]
self.opti = simplex.simplex_opt(2, self.sart_simplex, self)
sol = self.opti.get_solution()
self.scale = abs(sol[0])
self.b_value = sol[1]
self.modify_weights()
self.all_bad_z_scores = self.weight_array.all_eq(0.0)
if (not self.all_bad_z_scores):
s = 1.0 / (flex.sum(self.weight_array * self.mean_calc) /
flex.sum(self.weight_array * self.mean_obs))
b = 0.0
self.sart_simplex = [
flex.double([s, b]),
flex.double([s + 0.1, b + 1.1]),
flex.double([s - 0.1, b - 1.1])
]
self.opti = simplex.simplex_opt(2, self.sart_simplex, self)
def __init__(self,
miller_obs,
miller_calc,
min_d_star_sq=0.0,
max_d_star_sq=2.0,
n_points=2000,
level=6.0):
assert miller_obs.indices().all_eq(miller_calc.indices())
if (miller_obs.is_xray_amplitude_array()) :
miller_obs = miller_obs.f_as_f_sq()
if (miller_calc.is_xray_amplitude_array()) :
miller_calc = miller_calc.f_as_f_sq()
self.obs = miller_obs.deep_copy()
self.calc = miller_calc.deep_copy()
self.mind = min_d_star_sq
self.maxd = max_d_star_sq
self.m = n_points
self.n = 2
self.level = level
norma_obs = absolute_scaling.kernel_normalisation(
miller_array=self.obs,
auto_kernel=True,
n_bins=45,
n_term=17)
norma_calc = absolute_scaling.kernel_normalisation(
miller_array=self.calc,
auto_kernel=True,
n_bins=45,
n_term=17)
obs_d_star_sq = norma_obs.d_star_sq_array
calc_d_star_sq = norma_calc.d_star_sq_array
sel_calc_obs = norma_calc.bin_selection.select(norma_obs.bin_selection)
sel_obs_calc = norma_obs.bin_selection.select(norma_calc.bin_selection)
sel = ((obs_d_star_sq > low_lim) & (obs_d_star_sq < high_lim) &
(norma_obs.mean_I_array > 0))
sel = sel.select(sel_calc_obs)
self.obs_d_star_sq = obs_d_star_sq.select( sel )
self.calc_d_star_sq = calc_d_star_sq.select( sel_obs_calc ).select(sel)
self.mean_obs = norma_obs.mean_I_array.select(sel)
self.mean_calc = norma_calc.mean_I_array.select(
sel_obs_calc).select(sel)
self.var_obs = norma_obs.var_I_array.select(sel)
self.var_calc = norma_calc.var_I_array.select(
sel_obs_calc).select(sel)
# make an interpolator object please
self.interpol = scale_curves.curve_interpolator( self.mind, self.maxd,
self.m)
# do the interpolation
tmp_obs_d_star_sq , self.mean_obs,self.obs_a , self.obs_b = \
self.interpol.interpolate(self.obs_d_star_sq,self.mean_obs)
self.obs_d_star_sq , self.var_obs,self.obs_a , self.obs_b = \
self.interpol.interpolate(self.obs_d_star_sq, self.var_obs)
tmp_calc_d_star_sq , self.mean_calc,self.calc_a, self.calc_b = \
self.interpol.interpolate(self.calc_d_star_sq,self.mean_calc)
self.calc_d_star_sq, self.var_calc,self.calc_a , self.calc_b = \
self.interpol.interpolate(self.calc_d_star_sq,self.var_calc)
self.mean_ratio_engine = chebyshev_polynome( mean_coefs.size(),
low_lim-1e-3, high_lim+1e-3,mean_coefs)
self.std_ratio_engine = chebyshev_polynome( std_coefs.size(),
low_lim-1e-3, high_lim+1e-3,std_coefs)
self.x = flex.double([0,0])
self.low_lim_for_scaling = 1.0/(4.0*4.0) #0.0625
selection = (self.calc_d_star_sq > self.low_lim_for_scaling)
if (selection.count(True) == 0) :
raise Sorry("No reflections within required resolution range after "+
"filtering.")
self.weight_array = selection.as_double() / (2.0 * self.var_obs)
assert (not self.weight_array.all_eq(0.0))
self.mean = flex.double( [1.0/(flex.sum(self.mean_calc) /
flex.sum(self.mean_obs)), 0.0 ] )
self.sigmas = flex.double( [0.5, 0.5] )
s = 1.0/(flex.sum(self.weight_array*self.mean_calc)/
flex.sum(self.weight_array*self.mean_obs))
b = 0.0
self.sart_simplex = [ flex.double([s,b]), flex.double([s+0.1,b+1.1]),
flex.double([s-0.1,b-1.1]) ]
self.opti = simplex.simplex_opt( 2, self.sart_simplex, self)
sol = self.opti.get_solution()
self.scale = abs(sol[0])
self.b_value = sol[1]
self.modify_weights()
self.all_bad_z_scores = self.weight_array.all_eq(0.0)
if (not self.all_bad_z_scores) :
s = 1.0/(flex.sum(self.weight_array*self.mean_calc) /
flex.sum(self.weight_array*self.mean_obs))
b = 0.0
self.sart_simplex = [ flex.double([s,b]), flex.double([s+0.1,b+1.1]),
flex.double([s-0.1,b-1.1]) ]
self.opti = simplex.simplex_opt( 2, self.sart_simplex, self)
def iterate(self):
self.n1 = self.nmodes
if (self.Niter > 0): # need to build PDB object from the last PDB file
iter_name = self.root + str(self.Niter) + ".pdb"
self.pdb = PDB(iter_name, method=self.method)
self.pdb.Hessian(self.cutoff, self.nmode_init, self.scale_factor)
# Generate random normal modes
self.modes = flex.int(range(self.nmodes - 1)) + 7
self.modes.append(
int(random.random() * (self.nmode_init - self.nmodes)) + 7 +
self.nmodes)
self.scale = 0
candidates = []
score = []
for kk in range(self.topn * 10):
if (kk == 0):
vec = flex.random_double(self.nmodes) * 0
else:
vec = (flex.random_double(self.nmodes) -
0.5) * 2 * self.step_size
result = self.target(vec)
insert = 0
for ii in range(len(score)):
if (score[ii] > result):
score.insert(ii, result)
candidates.insert(ii, vec)
insert = 1
break
if (insert == 0):
score.append(result)
candidates.append(vec)
for kk in range(self.topn):
self.starting_simplex = []
cand = candidates[kk]
for ii in range(self.n1):
self.starting_simplex.append(
flex.double(self.orth(ii, self.n1)) * self.step_size +
cand)
self.starting_simplex.append(cand)
self.optimizer = simplex.simplex_opt(dimension=self.n1,
matrix=self.starting_simplex,
evaluator=self,
monitor_cycle=5,
tolerance=1e-2)
self.x = self.optimizer.get_solution()
candidates[kk] = self.x.deep_copy()
score[kk] = self.optimizer.get_score()
minscore = min(score[0:self.topn])
print self.Niter, minscore, self.counter
print >> self.chi, self.Niter, minscore
if ((self.Niter % self.optNum) > 1):
self.stopCheck(minscore)
self.updateScore(minscore)
minvec = candidates[score.index(minscore)]
new_coord = self.pdb.NMPerturb(self.modes, minvec)
print list(minvec)
self.Niter = self.Niter + 1
iter_base = self.root + str(self.Niter)
iter_name = iter_base + ".pdb"
self.pdb.writePDB(new_coord, iter_name)
if (self.Niter % self.optNum == 0):
print self.pulchra
run_command(command=self.pulchra + ' ' + iter_name)
run_command(command='mv ' + iter_base + '.rebuilt.pdb ' +
iter_name)
#processed_pdb, pdb_inp = self.pdb_processor.process_pdb_files( pdb_file_names=[iter_name] )
#new_coord = geo_opt(processed_pdb, self.log)
#self.pdb.writePDB(new_coord,iter_name)
# if(not self.stop):
if (self.Niter < 40):
self.iterate()
def optimize(self):
self.candidate = flex.random_double(self.Nb)
candidates = []
score = []
for kk in range(self.topn * 10):
if (kk == 0):
ab_s = self.candidate
else:
ab_s = (flex.random_double(self.Nb) * self.step_size +
self.candidate)
result = self.target(ab_s)
insert = 0
for ii in range(len(score)):
if (score[ii] > result):
score.insert(ii, result)
candidates.insert(ii, ab_s)
insert = 1
break
if (insert == 0):
score.append(result)
candidates.append(ab_s)
for kk in range(self.topn):
self.starting_simplex = []
cand = candidates[kk]
for ii in range(self.Nb):
self.starting_simplex.append(
flex.double(self.orth(ii, self.Nb)) * self.step_size +
cand)
self.starting_simplex.append(cand)
self.optimizer = simplex.simplex_opt(dimension=self.Nb,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-10)
self.x = self.optimizer.GetResult()
candidates[kk] = self.x.deep_copy()
score[kk] = self.target(self.x)
minscore = min(score[0:self.topn])
minvec = candidates[score.index(minscore)]
self.fpr.load_coefs(minvec[0:])
k1 = minvec[0]
new_I = pr2I(self.N_pr, self.fpr, self.q, k1)
print '&', list(minvec), "coef", minscore
for r, n in zip(self.q, new_I): #,self.calc_I):
print r, n
self.candidate = minvec.deep_copy()
self.calc_I = new_I.deep_copy()
self.Niter = self.Niter + 1
print '&'
for r, n in zip(self.q, self.expt_I): #,self.calc_I):
print r, n
r = flex.double(range(-50, 50)) / 50.0 + 1e-7
pr = self.fpr.get_p_of_r(r)
sum_pr = flex.sum(pr) * self.dMax
pr = pr / sum_pr * 100
r = (r + 1) * self.dMax / 2.0
print '&'
for ri, pri in zip(r, pr):
print ri, pri
self.prior = pr.deep_copy()
self.Nb = self.Nb + self.Nb
self.fpr = function(self.Nb, self.N_pr, 1.0, self.dMax)
if (self.Niter < 2):
self.optimize()
def estimate(self, num_reflections):
"""
Estimate the model parameters
"""
from scitbx import simplex
from copy import deepcopy
from dials.array_family import flex
from random import uniform
# Select the reflections
reflections = self._select_reflections(self.reflections,
num_reflections)
# The number of parameters
num_parameters = len(self.history.names)
# Setup the starting simplex
if self.simplex is None:
self.simplex = []
for i in range(num_parameters + 1):
self.simplex.append(
flex.log(
flex.double([
uniform(0.0001, 0.01)
for j in range(num_parameters)
])))
class Evaluator(object):
"""
Evaluator to simplex
"""
def __init__(
self,
history,
experiment,
reflections,
num_integral,
use_mosaic_block_angular_spread,
use_wavelength_spread,
):
"""
Initialise
"""
from dials_scratch.jmp.profile_modelling import MLTarget3D
self.func = MLTarget3D(
experiment,
reflections,
num_integral=num_integral,
use_mosaic_block_angular_spread=
use_mosaic_block_angular_spread,
use_wavelength_spread=use_wavelength_spread,
)
self.count = 1
self.history = history
self.logL = None
def target(self, log_parameters):
"""
Compute the negative log likelihood
"""
from dials.array_family import flex
parameters = flex.exp(log_parameters)
self.logL = self.func.log_likelihood(parameters)
logL = flex.sum(self.logL)
self.count += 1
print(self.count, list(parameters), logL)
self.history.append(parameters, logL)
# Return negative log likelihood
return -logL
# Setup the simplex optimizer
optimizer = simplex.simplex_opt(
num_parameters,
matrix=self.simplex,
evaluator=Evaluator(
self.history,
self.experiments[0],
reflections,
num_integral=self.num_integral,
use_mosaic_block_angular_spread=self.
use_mosaic_block_angular_spread,
use_wavelength_spread=self.use_wavelength_spread,
),
tolerance=1e-7,
)
# Get the solution
self.parameters = flex.exp(optimizer.get_solution())
# Get the final simplex
self.simplex = optimizer.matrix
# Save the likelihood for each reflection
self.log_likelihood = optimizer.evaluator.logL
def __init__(self,
n_params,
n_fst_pass,
d_max,
data,
n_int=35,
simplex_trial=5):
self.n = n_fst_pass
self.n_coeff = n_params
self.delta = self.n_coeff - self.n
self.data = data
self.d_max = max(self.data.q)
self.n_int = n_int
self.x = None
self.ent = entropic_restraints.entropy_restraint()
# make a pofr please
self.pofr = pr_tools.pofr(self.d_max,
self.n,
n_int=self.n_int,
m_int=self.n_int)
self.q_weight = flex.bool(self.data.q < 0.1).as_double()
self.weight = 1.0
# first we do a global optimisation using a diferentail evolution search
self.domain = []
for ii in range(self.n):
self.domain.append((-0.1, 0.1))
self.optimizer = de.differential_evolution_optimizer(
self,
population_size=self.n,
n_cross=1,
f=0.85,
eps=1e-5,
monitor_cycle=50,
show_progress=False)
self.q_weight = self.q_weight * 0.0 + 1.0
self.x = self.x.concatenate(flex.double([0] * self.delta))
self.n = self.n + self.delta
self.pofr = pr_tools.pofr(self.d_max,
self.n,
n_int=self.n_int,
m_int=self.n_int)
self.simplex_trial = simplex_trial
self.simplex_scores = []
self.simplex_solutions = []
for ii in xrange(self.simplex_trial):
#make a random simplex please
self.weight = 1.0
self.starting_simplex = []
for ii in range(self.n + 1):
self.starting_simplex.append(
0.10 * (flex.random_double(self.n) * 2 - 1.0) + self.x)
self.optimizer = simplex.simplex_opt(dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
tolerance=1e-3)
self.solution = self.optimizer.get_solution()
self.score = self.target(self.solution)
self.simplex_scores.append(self.score)
self.simplex_solutions.append(self.solution)
best_simplex_score = self.simplex_scores[0]
this_simplex = 0
for ii in xrange(self.simplex_trial):
if self.simplex_scores[ii] < best_simplex_score:
best_simplex_score = self.simplex_scores[ii]
this_simplex = ii
self.solution = self.simplex_solutions[this_simplex]
#self.optimizer = simulated_annealing.sa_optimizer( self, self.solution, flex.double( self.n*[0.0051] ), start_t=2.1, end_t=0.001, burn_in=100, burn_out=50000, steps=5000 , show_progress=True)
#self.solution, self.score = self.optimizer.get_solution()
self.pofr.update(self.solution)
self.calc_data = self.pofr.f(self.data.q)
