def run_refinement(projectf, mixture_index, options):
"""
Runs a refinement setup for
- projectf: project data
- mixture_index: what mixture in the project to use
- options: refinement options
"""
if projectf is not None:
from pyxrd.data import settings
settings.CACHE = None
settings.apply_runtime_settings()
from pyxrd.generic import pool
pool.get_pool()
from pyxrd.project.models import Project
type(Project).object_pool.clear()
project = Project.load_object(None, data=projectf)
del projectf
import gc
gc.collect()
mixture = project.mixtures[mixture_index]
mixture.update_refinement_treestore()
mixture.refiner.setup_context(store=False) # we already have a dumped project
context = mixture.refiner.context
context.options = options
mixture.refiner.refine(stop=pool.pool_stop)
return list(context.best_solution), context.best_residual, (context.record_header, context.records) #@UndefinedVariable
def setup_project(projectf):
# Only import these at this point, the cause a considerable increase in
# memory usage, so if no projectf was passed to improve_solutions, this
# module does not use more then it needs.
from pyxrd.data import settings
settings.apply_runtime_settings()
from pyxrd.project.models import Project
type(Project).object_pool.clear()
f = StringIO()
f.write(projectf)
project = Project.load_object(f)
f.close()
return project
# coding=UTF-8
# ex:ts=4:sw=4:et=on
# Copyright (c) 2013, Mathijs Dumon
# All rights reserved.
# Complete license can be found in the LICENSE file.
import time
from itertools import izip
import numpy as np
from scipy.optimize import fmin_l_bfgs_b
from pyxrd.data import settings
settings.apply_runtime_settings()
import logging
logger = logging.getLogger(__name__)
from .specimen import calculate_phase_intensities, get_summed_intensities
from .exceptions import wrap_exceptions
from .statistics import Rp, Rpw, Rpder
__residual_method_map = {
"Rp" : Rp,
"Rpw" : Rpw,
"Rpder": Rpder
}
def parse_solution(x, mixture):
fractions = np.asanyarray(x[:mixture.m])
scales = np.asanyarray(x[mixture.m:mixture.m + mixture.n])
