def improve_solution(projectf, mixture_index, solution, residual, l_bfgs_b_kwargs={}):
if projectf is not None:
from pyxrd.data import settings
settings.initialize()
# Retrieve project and mixture:
project = setup_project(projectf)
del projectf
mixture = project.mixtures[mixture_index]
with mixture.data_changed.ignore():
# Setup context again:
mixture.update_refinement_treestore()
refiner = mixture.refinement.get_refiner()
# Refine solution
vals = fmin_l_bfgs_b(
refiner.get_residual,
solution,
approx_grad=True,
bounds=refiner.ranges,
**l_bfgs_b_kwargs
)
new_solution, new_residual = tuple(vals[0:2])
# Return result
return new_solution, new_residual
else:
return solution, residual
def improve_solution(projectf, mixture_index, solution, residual, l_bfgs_b_kwargs={}):
if projectf is not None:
from pyxrd.data import settings
settings.initialize()
# Retrieve project and mixture:
project = setup_project(projectf)
del projectf
mixture = project.mixtures[mixture_index]
with mixture.data_changed.ignore():
# Setup context again:
mixture.update_refinement_treestore()
refiner = mixture.refinement.get_refiner()
# Refine solution
vals = fmin_l_bfgs_b(
refiner.get_residual,
solution,
approx_grad=True,
bounds=refiner.ranges,
**l_bfgs_b_kwargs
)
new_solution, new_residual = tuple(vals[0:2])
# Return result
return new_solution, new_residual
else:
return solution, residual
def _worker_initializer(pool_stop, debug, *args):
# Spoof command line arguments so settings are loaded with correct
# debugging flag
if debug and not "-d" in sys.argv:
sys.argv.insert(1, "-d")
if not debug and "-d" in sys.argv:
sys.argv.remove("-d")
# Load settings
from pyxrd.data import settings
settings.initialize()
if settings.DEBUG:
from pyxrd import stacktracer
stacktracer.trace_start(
"trace-worker-%s.html" % multiprocessing.current_process().name,
interval=5, auto=True) # Set auto flag to always update file!
logger.info("Worker process initialized, DEBUG=%s" % debug)
pass
def __init__(self):
from pyxrd.data import settings
settings.initialize()
logger.warning("Creating pool, DEBUG=%s" % settings.DEBUG)
self.pool_stop = multiprocessing.Event()
self.pool_stop.clear()
maxtasksperchild = 10 if 'nt' == os.name else None
self.pool = multiprocessing.Pool(initializer=_worker_initializer,
maxtasksperchild=maxtasksperchild,
initargs=(
self.pool_stop,
settings.DEBUG,
))
# register the shutdown
settings.FINALIZERS.append(self.shutdown)
def _worker_initializer(pool_stop, debug, *args):
# Spoof command line arguments so settings are loaded with correct
# debugging flag
if debug and not "-d" in sys.argv:
sys.argv.insert(1, "-d")
if not debug and "-d" in sys.argv:
sys.argv.remove("-d")
# Load settings
from pyxrd.data import settings
settings.initialize()
if settings.DEBUG:
from pyxrd import stacktracer
stacktracer.trace_start(
"trace-worker-%s.html" % multiprocessing.current_process().name,
interval=5,
auto=True) # Set auto flag to always update file!
logger.info("Worker process initialized, DEBUG=%s" % debug)
pass
def reload_settings(clear_script=True):
"""
This will reload the PyXRD settings after clearing the script path from
the command line arguments. This allows to run the GUI when needed.
"""
import sys
from copy import copy
# Make a copy to prevent errors
args = copy(sys.argv)
for i, arg in enumerate(args):
if arg == "-s":
# Clear the next key (contains the script name
del sys.argv[i + 1]
# Clear the flag
del sys.argv[i]
# Exit the loop
break
from pyxrd.data import settings
settings.SETTINGS_APPLIED = False # clear this flag to reload settings
settings.initialize() # reload settings
def __init__(self):
from pyxrd.data import settings
settings.initialize()
logger.warning("Creating pool, DEBUG=%s" % settings.DEBUG)
self.pool_stop = multiprocessing.Event()
self.pool_stop.clear()
maxtasksperchild = 10 if 'nt' == os.name else None
self.pool = multiprocessing.Pool(
initializer=_worker_initializer,
maxtasksperchild=maxtasksperchild,
initargs=(
self.pool_stop,
settings.DEBUG,
)
)
# register the shutdown
settings.FINALIZERS.append(self.shutdown)
def reload_settings(clear_script=True):
"""
This will reload the PyXRD settings after clearing the script path from
the command line arguments. This allows to run the GUI when needed.
"""
import sys
from copy import copy
# Make a copy to prevent errors
args = copy(sys.argv)
for i, arg in enumerate(args):
if arg == "-s":
# Clear the next key (contains the script name
del sys.argv[i + 1]
# Clear the flag
del sys.argv[i]
# Exit the loop
break
from pyxrd.data import settings
settings.SETTINGS_APPLIED = False # clear this flag to reload settings
settings.initialize() # reload settings
def run_refinement(projectf, mixture_index):
"""
Runs a refinement setup for
- projectf: project data
- mixture_index: what mixture in the project to use
"""
if projectf is not None:
from pyxrd.data import settings
settings.initialize()
# Retrieve project and mixture:
project = setup_project(projectf)
del projectf
import gc
gc.collect()
mixture = project.mixtures[mixture_index]
mixture.refinement.update_refinement_treestore()
refiner = mixture.refinement.get_refiner()
refiner.refine()
return list(refiner.history.best_solution), refiner.history.best_residual
def run_refinement(projectf, mixture_index):
"""
Runs a refinement setup for
- projectf: project data
- mixture_index: what mixture in the project to use
"""
if projectf is not None:
from pyxrd.data import settings
settings.initialize()
# Retrieve project and mixture:
project = setup_project(projectf)
del projectf
import gc
gc.collect()
mixture = project.mixtures[mixture_index]
mixture.refinement.update_refinement_treestore()
refiner = mixture.refinement.get_refiner()
refiner.refine()
return list(refiner.history.best_solution), refiner.history.best_residual
def run_main():
"""
Parsers command line arguments and launches PyXRD accordingly.
"""
# Make sure the current path is used for loading PyXRD modules:
mod = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
if not mod in sys.path:
sys.path.insert(1, mod)
# Init settings, first import will trigger initialization
from pyxrd.data import settings
settings.initialize()
# Setup basic logging
from pyxrd.logs import setup_logging
setup_logging(basic=True)
if settings.DEBUG:
from pyxrd import stacktracer
stacktracer.trace_start(
"trace.html",
interval=5, auto=True) # Set auto flag to always update file!
try:
if settings.ARGS.script:
# Run the specified user script:
_run_user_script()
else:
# Run the GUI:
_run_gui()
except:
raise # re-raise the error
finally:
for finalizer in settings.FINALIZERS:
finalizer()
if settings.DEBUG: stacktracer.trace_stop()
def run_main():
"""
Parsers command line arguments and launches PyXRD accordingly.
"""
# Make sure the current path is used for loading PyXRD modules:
mod = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
if not mod in sys.path:
sys.path.insert(1, mod)
# Init settings, first import will trigger initialization
from pyxrd.data import settings
settings.initialize()
# Setup basic logging
from pyxrd.logs import setup_logging
setup_logging(basic=True)
if settings.DEBUG:
from pyxrd import stacktracer
stacktracer.trace_start(
"trace.html", interval=5,
auto=True) # Set auto flag to always update file!
try:
if settings.ARGS.script:
# Run the specified user script:
_run_user_script()
else:
# Run the GUI:
_run_gui()
except:
raise # re-raise the error
finally:
for finalizer in settings.FINALIZERS:
finalizer()
if settings.DEBUG: stacktracer.trace_stop()
def setUp(self):
settings.initialize()
self.phase = Phase(R=0, G=1)
def mock_settings():
from pyxrd.data import settings
settings._parse_args = mock.Mock(return_value=_mocked_parse_args())
settings.initialize()
def setUp(self):
settings.initialize()
self.phase = Phase(R=0, G=1)