def run_dssa(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 = dssa.dssa( dimension=self.n, matrix=start_matrix, evaluator=self, tolerance=1e-5, further_opt=True )
self.x = self.optimizer.get_solution()
def run_dssa(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 = dssa.dssa( dimension=self.n, matrix=start_matrix, evaluator=self, tolerance=1e-5, further_opt=True )
self.x = self.optimizer.get_solution()
def __init__(self, name):
self.name = name
self.fcount = 0
self.n = 2
self.x = start.deep_copy()
self.starting_simplex = []
for ii in range(self.n + 1):
self.starting_simplex.append(3.1 * (flex.random_double(self.n) / 2 - 1) + self.x)
self.optimizer = direct_search_simulated_annealing.dssa(
dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
further_opt=True,
coolfactor=0.5,
simplex_scale=1,
)
self.x = self.optimizer.get_solution()
print "DSSA ITERATIONS", self.optimizer.count, self.fcount, "SOLUTION", list(self.x), self.target(self.x)
def run_dssa(self):
self.starting_simplex = []
for ii in range(self.n):
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)
dssa_optimizer = direct_search_simulated_annealing.dssa(
dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
max_iter=5000,
further_opt=True,
tolerance=1e-4)
candidates = dssa_optimizer.get_candi()
self.solution = dssa_optimizer.get_solution()
self.score = self.target(self.solution)
def __init__(self, name):
self.name = name
self.fcount = 0
self.n = 2
self.x = start.deep_copy()
self.starting_simplex = []
for ii in range(self.n + 1):
self.starting_simplex.append(3.1 *
(flex.random_double(self.n) / 2 - 1) +
self.x)
self.optimizer = direct_search_simulated_annealing.dssa(
dimension=self.n,
matrix=self.starting_simplex,
evaluator=self,
further_opt=True,
coolfactor=0.5,
simplex_scale=1)
self.x = self.optimizer.get_solution()
print("DSSA ITERATIONS", self.optimizer.count, self.fcount, "SOLUTION",
list(self.x), self.target(self.x))
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