def __init__(self, *args, **kwargs):
my_kwargs = self.pop_kwargs(kwargs,
"refine_method_index", "refine_method", "refine_options"
)
super(Refinement, self).__init__(*args, **kwargs)
kwargs = my_kwargs
# Setup the refinables treestore
self.refinables = TreeNode()
self.update_refinement_treestore()
# Setup the refine methods
try:
self.refine_method_index = int(self.get_kwarg(kwargs, None, "refine_method_index", "refine_method"))
except ValueError:
self.refine_method_index = self.refine_method_index
pass # ignore faulty values, these indices change from time to time.
self.refine_methods = RefineMethodManager.initialize_methods(
self.get_kwarg(kwargs, None, "refine_options")
)
def __init__(self, *args, **kwargs):
my_kwargs = self.pop_kwargs(kwargs,
"refine_method", "refine_options"
)
super(Refiner, self).__init__(*args, **kwargs)
kwargs = my_kwargs
# Setup the refinables treestore
self.refinables = TreeNode()
# Setup the refine methods
try:
self.refine_method = int(self.get_kwarg(kwargs, None, "refine_method"))
except ValueError:
self.refine_method = self.refine_method
pass # ignore faulty values, these indices change from time to time.
self.refine_methods = self.create_refine_methods(self.get_kwarg(kwargs, None, "refine_options"))
self.update_refinement_treestore()
class Refinement(ChildModel):
"""
A simple model that plugs onto the Mixture model. It provides
the functionality related to refinement of parameters.
"""
# MODEL INTEL:
class Meta(ChildModel.Meta):
properties = [ # TODO add labels
PropIntel(name="refinables", label="", has_widget=True, data_type=object, is_column=True, widget_type="object_tree_view", class_type=RefinableWrapper),
PropIntel(name="refine_options", label="", data_type=dict, is_column=False),
OptionPropIntel(name="refine_method_index", label="Refinement method index", has_widget=True, data_type=int, options={ key: method.name for key, method in RefineMethodManager.get_all_methods().items() }),
PropIntel(name="make_psp_plots", label="", data_type=bool, is_colum=False, has_widget=True, storable=False),
]
store_id = "Refinement"
mixture = property(ChildModel.parent.fget, ChildModel.parent.fset)
#: Flag, True if after refinement plots should be generated of the parameter space
make_psp_plots = False
#: TreeNode containing the refinable properties
refinables = None
#: A dict containing an instance of each refinement method
refine_methods = None
_refine_method_index = 0
@property
def refine_method_index(self):
""" An integer describing which method to use for the refinement """
return self._refine_method_index
@refine_method_index.setter
def refine_method_index(self, value): self._refine_method_index = int(value)
#: A dict containing the current refinement options
@property
def refine_options(self):
return self.get_refinement_method().get_options()
#: A dict containing all refinement options
@property
def all_refine_options(self):
return {
method.index : method.get_options()
for method in list(self.refine_methods.values())
}
def __init__(self, *args, **kwargs):
my_kwargs = self.pop_kwargs(kwargs,
"refine_method_index", "refine_method", "refine_options"
)
super(Refinement, self).__init__(*args, **kwargs)
kwargs = my_kwargs
# Setup the refinables treestore
self.refinables = TreeNode()
self.update_refinement_treestore()
# Setup the refine methods
try:
self.refine_method_index = int(self.get_kwarg(kwargs, None, "refine_method_index", "refine_method"))
except ValueError:
self.refine_method_index = self.refine_method_index
pass # ignore faulty values, these indices change from time to time.
self.refine_methods = RefineMethodManager.initialize_methods(
self.get_kwarg(kwargs, None, "refine_options")
)
# ------------------------------------------------------------
# Refiner methods
# ------------------------------------------------------------
def get_refiner(self):
"""
This returns a Refiner object which can be used to refine the
selected properties using the selected algorithm.
Just call 'refine(stop)' on the returned object, with stop a
threading.Event or multiprocessing.Event which you can use to stop
the refinement before completion.
The Refiner object also has a RefineHistory and RefineStatus object
that can be used to track the status and history of the refinement.
"""
return Refiner(
method = self.get_refinement_method(),
residual_callback = get_optimized_residual,
data_callback = lambda: self.mixture.data_object,
refinables = self.refinables,
event_cmgr = EventContextManager(self.mixture.needs_update, self.mixture.data_changed),
)
# ------------------------------------------------------------
# Refinement Methods Management
# ------------------------------------------------------------
def get_refinement_method(self):
"""
Returns the actual refinement method by translating the
`refine_method` attribute
"""
return self.refine_methods[self.refine_method_index]
# ------------------------------------------------------------
# Refinables Management
# ------------------------------------------------------------
# TODO set a restrict range attribute on the PropIntels, so we can use custom ranges for each property
def auto_restrict(self):
"""
Convenience function that restricts the selected properties
automatically by setting their minimum and maximum values.
"""
with self.mixture.needs_update.hold():
for node in self.refinables.iter_children():
ref_prop = node.object
if ref_prop.refine and ref_prop.refinable:
ref_prop.value_min = ref_prop.value * 0.8
ref_prop.value_max = ref_prop.value * 1.2
def randomize(self):
"""
Convenience function that randomize the selected properties.
Respects the current minimum and maximum values.
Executes an optimization after the randomization.
"""
with self.mixture.data_changed.hold_and_emit():
with self.mixture.needs_update.hold_and_emit():
for node in self.refinables.iter_children():
ref_prop = node.object
if ref_prop.refine and ref_prop.refinable:
ref_prop.value = random.uniform(ref_prop.value_min, ref_prop.value_max)
def update_refinement_treestore(self):
"""
This creates a tree store with all refinable properties and their
minimum, maximum and current value.
"""
if self.parent is not None: # not linked so no valid phases!
self.refinables.clear()
def add_property(parent_node, obj, prop, is_grouper):
rp = RefinableWrapper(obj=obj, prop=prop, parent=self.mixture, is_grouper=is_grouper)
return parent_node.append(TreeNode(rp))
def parse_attribute(obj, prop, root_node):
"""
obj: the object
attr: the attribute of obj or None if obj contains attributes
root_node: the root TreeNode new iters should be put under
"""
if prop is not None:
if hasattr(obj, "get_uninherited_property_value"):
value = obj.get_uninherited_property_value(prop)
else:
value = getattr(obj, prop.name)
else:
value = obj
if isinstance(value, RefinementValue): # AtomRelation and UnitCellProperty
new_node = add_property(root_node, value, prop, False)
elif hasattr(value, "__iter__"): # List or similar
for new_obj in value:
parse_attribute(new_obj, None, root_node)
elif isinstance(value, RefinementGroup): # Phase, Component, Probability
if len(value.refinables) > 0:
new_node = add_property(root_node, value, prop, True)
for prop in value.refinables:
parse_attribute(value, prop, new_node)
else: # regular values
new_node = add_property(root_node, obj, prop, False)
for phase in self.mixture.project.phases:
if phase in self.mixture.phase_matrix:
parse_attribute(phase, None, self.refinables)
pass # end of class
def add_property(parent_node, obj, prop, is_grouper):
rp = RefinableWrapper(obj=obj, prop=prop, parent=self.mixture, is_grouper=is_grouper)
return parent_node.append(TreeNode(rp))
class Refiner(ChildModel):
"""
A simple model that plugs onto the Mixture model. It provides
the functionality related to refinement of parameters.
"""
# MODEL INTEL:
class Meta(ChildModel.Meta):
properties = [ # TODO add labels
PropIntel(name="refinables", label="", has_widget=True, data_type=object, is_column=True, widget_type="object_tree_view", class_type=RefinableWrapper),
PropIntel(name="refine_options", label="", data_type=dict, is_column=False),
OptionPropIntel(name="refine_method", label="Refinement method", has_widget=True, data_type=int, options={ key: method.name for key, method in get_all_refine_methods().iteritems() }),
PropIntel(name="make_psp_plots", label="", data_type=bool, is_colum=False, has_widget=True, storable=False),
]
store_id = "Refiner"
mixture = property(ChildModel.parent.fget, ChildModel.parent.fset)
#: Refinement context
context = None
#: Refinement thread (or None if not running)
thread = None
#: Flag, True if after refinement plots should be generated of the parameter space
make_psp_plots = False
#: TreeNode containing the refinable properties
refinables = None
#: A dict containing an instance of each refinement method
refine_methods = None
_refine_method = 0
@property
def refine_method(self):
""" An integer describing which method to use for the refinement (see
refinement.methods.get_all_refine_methods) """
return self._refine_method
@refine_method.setter
def refine_method(self, value): self._refine_method = int(value)
#: A dict containing the current refinement options
@property
def refine_options(self):
method = self.get_refinement_method()
return { name: getattr(method, name) for name in method.options }
#: A dict containing all refinement options
@property
def all_refine_options(self):
return {
method.index : { name: getattr(method, name) for name in method.options }
for method in self.refine_methods.values()
}
def __init__(self, *args, **kwargs):
my_kwargs = self.pop_kwargs(kwargs,
"refine_method", "refine_options"
)
super(Refiner, self).__init__(*args, **kwargs)
kwargs = my_kwargs
# Setup the refinables treestore
self.refinables = TreeNode()
# Setup the refine methods
try:
self.refine_method = int(self.get_kwarg(kwargs, None, "refine_method"))
except ValueError:
self.refine_method = self.refine_method
pass # ignore faulty values, these indices change from time to time.
self.refine_methods = self.create_refine_methods(self.get_kwarg(kwargs, None, "refine_options"))
self.update_refinement_treestore()
# ------------------------------------------------------------
# Methods & Functions
# ------------------------------------------------------------
def setup_context(self, store=False):
"""
Creates a RefineContext object filled with parameters based on the
current state of the Mixture object.
"""
self.context = RefineContext(
parent=self.parent,
options=self.parent.refine_options,
store=store
)
def delete_context(self):
"""
Clears the RefineContext from this model
"""
self.context = None
def _inner_refine(self, refine_method, context, stop=None, **kwargs):
# Suppress updates:
with self.mixture.needs_update.hold():
with self.mixture.data_changed.hold():
# If something has been selected: continue...
if len(context.ref_props) > 0:
# Make sure the stop signal is not set from a previous run:
if stop is not None:
stop.clear()
# Log some information:
logger.info("-"*80)
logger.info("Starting refinement with this setup:")
msg_frm = "%22s: %s"
logger.info(msg_frm % ("refinement method", refine_method))
logger.info(msg_frm % ("number of parameters", len(context.ref_props)))
logger.info(msg_frm % ("GUI mode", settings.GUI_MODE))
# Record start time
t1 = time.time()
try: # Run until it ends or it raises an exception:
refine_method(context, stop=stop)
except any as error:
logger.exception("Unhandled run-time error when refining: %s" % error)
context.status = "error"
context.status_message = "Error occurred..."
else: # No errors occurred:
if stop is not None and stop.is_set():
context.status = "stopped"
context.status_message = "Stopped ..."
logger.info("Refinement was stopped prematurely")
else:
context.status = "finished"
context.status_message = "Finished"
logger.info("Refinement ended successfully")
# Record end time
t2 = time.time()
# Log some more information:
logger.info('%s took %0.3f ms' % ("Total refinement", (t2 - t1) * 1000.0))
logger.info('Best solution found was:')
for line in context.best_solution_to_string().split('\n'):
logger.info(line)
logger.info("-"*80)
else: # nothing selected for refinement
context.status = "error"
context.status_message = "No parameters selected!"
# Return the context to whatever called this
return context
def refine(self, threaded=False, on_complete=None, **kwargs):
"""
This refines the selected properties using the selected algorithm.
This can be run asynchronously when threaded is set to True.
"""
refine_method = partial(self._inner_refine,
self.get_refinement_method(), self.context, **kwargs)
if not threaded:
context = refine_method()
if callable(on_complete):
on_complete(context)
else:
def thread_completed(context):
#Assuming this is GTK-thread safe (i.e. wrapped in @run_when_idle)
on_complete(context)
self.thread = None
self.thread = CancellableThread(refine_method, thread_completed)
self.thread.start()
def cancel(self):
"""
Cancels a threaded refinement,
and will call the on_complete callback passed to `refine`
"""
if self.thread is not None:
logger.info("Refinement cancelled")
self.thread.cancel()
else:
logger.info("Cannot cancel, no refinement running")
self.thread = None
def stop(self):
""" Stops a threaded refinement, not returning any result """
if self.thread is not None:
logger.info("Refinement stopped")
self.thread.stop()
else:
logger.info("Cannot stop, no refinement running")
self.thread = None
# ------------------------------------------------------------
# Refinement Methods Management
# ------------------------------------------------------------
@staticmethod
def get_all_refine_methods():
return get_all_refine_methods()
@staticmethod
def create_refine_methods(refine_options):
"""
Returns a dict of refine methods as values and their index as key
with the passed refine_options dict applied.
"""
# 1. Create a list of refinement instances:
refine_methods = {}
for index, method in get_all_refine_methods().iteritems():
refine_methods[index] = method()
# 2. Create dict of default options
default_options = {}
for method in refine_methods.values():
default_options[method.index] = {
name: getattr(type(method), name).default for name in method.options
}
# 3. Apply the refine options to the methods
if not refine_options == None:
for index, options in zip(refine_options.keys(), refine_options.values()):
index = int(index)
if index in refine_methods:
method = refine_methods[index]
for arg, value in zip(options.keys(), options.values()):
if hasattr(method, arg):
setattr(method, arg, value)
return refine_methods
def get_refinement_method(self):
"""
Returns the actual refinement method by translating the
`refine_method` attribute
"""
return self.refine_methods[self.refine_method]
def get_refinement_option(self, option):
return getattr(type(self.get_refinement_method()), option)
def get_refinement_option_value(self, option):
return getattr(self.get_refinement_method(), option)
def set_refinement_option_value(self, option, value):
return setattr(self.get_refinement_method(), option, value)
# ------------------------------------------------------------
# Refinables Management
# ------------------------------------------------------------
# TODO set a restrict range attribute on the PropIntels, so we can use custom ranges for each property
def auto_restrict(self):
"""
Convenience function that restricts the selected properties
automatically by setting their minimum and maximum values.
"""
with self.mixture.needs_update.hold():
for node in self.refinables.iter_children():
ref_prop = node.object
if ref_prop.refine and ref_prop.refinable:
ref_prop.value_min = ref_prop.value * 0.8
ref_prop.value_max = ref_prop.value * 1.2
def randomize(self):
"""
Convenience function that randomize the selected properties.
Respects the current minimum and maximum values.
Executes an optimization after the randomization.
"""
with self.mixture.data_changed.hold_and_emit():
with self.mixture.needs_update.hold_and_emit():
for node in self.refinables.iter_children():
ref_prop = node.object
if ref_prop.refine and ref_prop.refinable:
ref_prop.value = random.uniform(ref_prop.value_min, ref_prop.value_max)
def update_refinement_treestore(self):
"""
This creates a tree store with all refinable properties and their
minimum, maximum and current value.
"""
if self.parent is not None: # not linked so no valid phases!
self.refinables.clear()
def add_property(parent_node, obj, prop, is_grouper):
rp = RefinableWrapper(obj=obj, prop=prop, parent=self.mixture, is_grouper=is_grouper)
return parent_node.append(TreeNode(rp))
def parse_attribute(obj, prop, root_node):
"""
obj: the object
attr: the attribute of obj or None if obj contains attributes
root_node: the root TreeNode new iters should be put under
"""
if prop is not None:
if hasattr(obj, "get_uninherited_property_value"):
value = obj.get_uninherited_property_value(prop)
else:
value = getattr(obj, prop.name)
else:
value = obj
if isinstance(value, RefinementValue): # AtomRelation and UnitCellProperty
new_node = add_property(root_node, value, prop, False)
elif hasattr(value, "__iter__"): # List or similar
for new_obj in value:
parse_attribute(new_obj, None, root_node)
elif isinstance(value, RefinementGroup): # Phase, Component, Probability
if len(value.refinables) > 0:
new_node = add_property(root_node, value, prop, True)
for prop in value.refinables:
parse_attribute(value, prop, new_node)
else: # regular values
new_node = add_property(root_node, obj, prop, False)
for phase in self.mixture.project.phases:
if phase in self.mixture.phase_matrix:
parse_attribute(phase, None, self.refinables)
pass # end of class
class Refinement(ChildModel):
"""
A simple model that plugs onto the Mixture model. It provides
the functionality related to refinement of parameters.
"""
# MODEL INTEL:
class Meta(ChildModel.Meta):
store_id = "Refinement"
mixture = property(ChildModel.parent.fget, ChildModel.parent.fset)
#: Flag, True if after refinement plots should be generated of the parameter space
make_psp_plots = BoolProperty(
default=False, text="Make parameter space plots",
tabular=False, visible=True, persistent=True
)
#: TreeNode containing the refinable properties
refinables = ListProperty(
default=None, text="Refinables",
tabular=True, persistent=False, visible=True,
data_type=RefinableWrapper,
cast_to=None, widget_type="object_tree_view"
)
#: A dict containing an instance of each refinement method
refine_methods = None
#: An integer describing which method to use for the refinement
refine_method_index = IntegerChoiceProperty(
default=0, text="Refinement method index",
tabular=True, persistent=True, visible=True,
choices={ key: method.name for key, method in RefineMethodManager.get_all_methods().items() }
)
#: A dict containing the current refinement options
@LabeledProperty(
default=None, text="Refine options",
persistent=False, visible=False,
mix_with=(ReadOnlyMixin,)
)
def refine_options(self):
return self.get_refinement_method().get_options()
#: A dict containing all refinement options
@property
def all_refine_options(self):
return {
method.index : method.get_options()
for method in list(self.refine_methods.values())
}
def __init__(self, *args, **kwargs):
my_kwargs = self.pop_kwargs(kwargs,
"refine_method_index", "refine_method", "refine_options"
)
super(Refinement, self).__init__(*args, **kwargs)
kwargs = my_kwargs
# Setup the refinables treestore
self.refinables = TreeNode()
self.update_refinement_treestore()
# Setup the refine methods
try:
self.refine_method_index = int(self.get_kwarg(kwargs, None, "refine_method_index", "refine_method"))
except ValueError:
self.refine_method_index = self.refine_method_index
pass # ignore faulty values, these indices change from time to time.
self.refine_methods = RefineMethodManager.initialize_methods(
self.get_kwarg(kwargs, None, "refine_options")
)
# ------------------------------------------------------------
# Refiner methods
# ------------------------------------------------------------
def get_refiner(self):
"""
This returns a Refiner object which can be used to refine the
selected properties using the selected algorithm.
Just call 'refine(stop)' on the returned object, with stop a
threading.Event or multiprocessing.Event which you can use to stop
the refinement before completion.
The Refiner object also has a RefineHistory and RefineStatus object
that can be used to track the status and history of the refinement.
"""
return Refiner(
method = self.get_refinement_method(),
data_callback = lambda: self.mixture.data_object,
refinables = self.refinables,
event_cmgr = EventContextManager(self.mixture.needs_update, self.mixture.data_changed),
metadata = dict(
phases = self.mixture.phases,
num_specimens = len(self.mixture.specimens),
)
)
# ------------------------------------------------------------
# Refinement Methods Management
# ------------------------------------------------------------
def get_refinement_method(self):
"""
Returns the actual refinement method by translating the
`refine_method` attribute
"""
return self.refine_methods[self.refine_method_index]
# ------------------------------------------------------------
# Refinables Management
# ------------------------------------------------------------
# TODO set a restrict range attribute on the PropIntels, so we can use custom ranges for each property
def auto_restrict(self):
"""
Convenience function that restricts the selected properties
automatically by setting their minimum and maximum values.
"""
with self.mixture.needs_update.hold():
for node in self.refinables.iter_children():
ref_prop = node.object
if ref_prop.refine and ref_prop.refinable:
ref_prop.value_min = ref_prop.value * 0.8
ref_prop.value_max = ref_prop.value * 1.2
def randomize(self):
"""
Convenience function that randomize the selected properties.
Respects the current minimum and maximum values.
Executes an optimization after the randomization.
"""
with self.mixture.data_changed.hold_and_emit():
with self.mixture.needs_update.hold_and_emit():
for node in self.refinables.iter_children():
ref_prop = node.object
if ref_prop.refine and ref_prop.refinable:
ref_prop.value = random.uniform(ref_prop.value_min, ref_prop.value_max)
def update_refinement_treestore(self):
"""
This creates a tree store with all refinable properties and their
minimum, maximum and current value.
"""
if self.parent is not None: # not linked so no valid phases!
self.refinables.clear()
def add_property(parent_node, obj, prop, is_grouper):
rp = RefinableWrapper(obj=obj, prop=prop, parent=self.mixture, is_grouper=is_grouper)
return parent_node.append(TreeNode(rp))
def parse_attribute(obj, prop, root_node):
"""
obj: the object
attr: the attribute of obj or None if obj contains attributes
root_node: the root TreeNode new iters should be put under
"""
if prop is not None:
if isinstance(prop, InheritableMixin):
value = prop.get_uninherited(obj)
else:
value = getattr(obj, prop.label)
else:
value = obj
if isinstance(value, RefinementValue): # AtomRelation and UnitCellProperty
new_node = add_property(root_node, value, prop, False)
elif hasattr(value, "__iter__"): # List or similar
for new_obj in value:
parse_attribute(new_obj, None, root_node)
elif isinstance(value, RefinementGroup): # Phase, Component, Probability
if len(value.refinables) > 0:
new_node = add_property(root_node, value, prop, True)
for prop in value.refinables:
parse_attribute(value, prop, new_node)
else: # regular values
new_node = add_property(root_node, obj, prop, False)
for phase in self.mixture.project.phases:
if phase in self.mixture.phase_matrix:
parse_attribute(phase, None, self.refinables)
pass # end of class