def get_previous_value(self, context=None):
# temporary method until previous values are integrated for all parameters
value = self.parameters.previous_value._get(context)
if value is None:
value = self.parameters.previous_value._get(Context())
return value
def __init__(self,
composition,
execution_ids=[None],
*,
additional_tags=frozenset()):
super().__init__(buffers=[
'state_struct', 'param_struct', 'data_struct', 'conditions'
])
self._composition = composition
self._execution_contexts = [
Context(execution_id=eid) for eid in execution_ids
]
self.__bin_exec_func = None
self.__bin_exec_multi_func = None
self.__bin_func = None
self.__bin_run_func = None
self.__bin_run_multi_func = None
self.__debug_env = debug_env
self.__frozen_vals = None
self.__tags = frozenset(additional_tags)
# TODO: Consolidate these
if len(execution_ids) > 1:
self.__state_struct = None
self.__param_struct = None
self.__data_struct = None
self.__conds = None
self._ct_len = ctypes.c_int(len(execution_ids))
def _add_system(self, system, role: str):
super()._add_system(system, role)
if isinstance(self.modulated_mechanisms,
str) and self.modulated_mechanisms is ALL:
# Call with ContextFlags.COMPONENT so that OutputPorts are replaced rather than added
self._instantiate_output_ports(context=Context(
source=ContextFlags.COMPONENT))
def __init__(self, component, execution_ids=[None], *, tags=frozenset()):
super().__init__()
self._bin_func = pnlvm.LLVMBinaryFunction.from_obj(component,
tags=tags)
self._execution_contexts = [
Context(execution_id=eid) for eid in execution_ids
]
self._component = component
self.__debug_env = debug_env
par_struct_ty, ctx_struct_ty, vi_ty, vo_ty = self._bin_func.byref_arg_types
if len(execution_ids) > 1:
self._bin_multirun = self._bin_func.get_multi_run()
self._ct_len = ctypes.c_int(len(execution_ids))
vo_ty = vo_ty * len(execution_ids)
vi_ty = vi_ty * len(execution_ids)
self.__param_struct = None
self.__state_struct = None
self._vo_ty = vo_ty
self._ct_vo = vo_ty()
self._vi_ty = vi_ty
self._vi_dty = _element_dtype(vi_ty)
if "stat" in self.__debug_env:
print("Input struct size:", _pretty_size(ctypes.sizeof(vi_ty)),
"for", self._component.name)
print("Output struct size:", _pretty_size(ctypes.sizeof(vo_ty)),
"for", self._component.name)
def __init__(self, composition, device, context=None):
if not torch_available:
raise Exception('Pytorch python module (torch) is not installed. Please install it with '
'`pip install torch` or `pip3 install torch`')
super(PytorchModelCreator, self).__init__()
# Maps Mechanism -> PytorchMechanismWrapper
self.nodes = []
self.component_map = {}
# Maps Projections -> PytorchProjectionWrappers
self.projections = []
self.projection_map = {}
self.params = nn.ParameterList()
self.device = device
self._composition = composition
# Instantiate pytorch mechanisms
for node in set(composition.nodes) - set(composition.get_nodes_by_role(NodeRole.LEARNING)):
pytorch_node = PytorchMechanismWrapper(node, self._composition._get_node_index(node), device, context=context)
self.component_map[node] = pytorch_node
self.nodes.append(pytorch_node)
# Instantiate pytorch projections
for projection in composition.projections:
if projection.sender.owner in self.component_map and projection.receiver.owner in self.component_map:
proj_send = self.component_map[projection.sender.owner]
proj_recv = self.component_map[projection.receiver.owner]
port_idx = projection.sender.owner.output_ports.index(projection.sender)
new_proj = PytorchProjectionWrapper(projection, list(self._composition._inner_projections).index(projection), port_idx, device, sender=proj_send, receiver=proj_recv, context=context)
proj_send.add_efferent(new_proj)
proj_recv.add_afferent(new_proj)
self.projection_map[projection] = new_proj
self.projections.append(new_proj)
self.params.append(new_proj.matrix)
c = Context()
try:
composition.scheduler._init_counts(execution_id=c.execution_id, base_execution_id=context.execution_id)
except graph_scheduler.SchedulerError:
# called from LLVM, no base context is provided
composition.scheduler._init_counts(execution_id=c.execution_id)
# Setup execution sets
# 1) Remove all learning-specific nodes
self.execution_sets = [x - set(composition.get_nodes_by_role(NodeRole.LEARNING)) for x in composition.scheduler.run(context=c)]
# 2) Convert to pytorchcomponent representation
self.execution_sets = [{self.component_map[comp] for comp in s if comp in self.component_map} for s in self.execution_sets]
# 3) Remove empty execution sets
self.execution_sets = [x for x in self.execution_sets if len(x) > 0]
composition.scheduler._delete_counts(c.execution_id)
def evaluate(self,
feature_values,
control_allocation,
num_estimates,
base_context=Context(execution_id=None),
context=None):
"""Return `target <FunctionAppproximator.target>` predicted by `function <FunctionAppproximator.function> for
**input**, using current set of `prediction_parameters <FunctionAppproximator.prediction_parameters>`.
"""
# FIX: AUGMENTTO USE num_estimates
return self.function(feature_values,
control_allocation,
context=context)
def __init__(self,
default_variable=None,
sample: tc.optional(
tc.any(OutputPort, Mechanism_Base, dict, is_numeric,
str)) = None,
target: tc.optional(
tc.any(OutputPort, Mechanism_Base, dict, is_numeric,
str)) = None,
function=LinearCombination(weights=[[-1], [1]]),
output_ports: tc.optional(tc.any(str, Iterable)) = None,
params=None,
name=None,
prefs: is_pref_set = None,
**kwargs):
input_ports = kwargs.pop(INPUT_PORTS, {})
if input_ports:
input_ports = {INPUT_PORTS: input_ports}
input_ports = self._merge_legacy_constructor_args(
sample, target, default_variable, input_ports)
# Default output_ports is specified in constructor as a tuple rather than a list
# to avoid "gotcha" associated with mutable default arguments
# (see: bit.ly/2uID3s3 and http://docs.python-guide.org/en/latest/writing/gotchas/)
if isinstance(output_ports, (str, tuple)):
output_ports = list(output_ports)
# IMPLEMENTATION NOTE: The following prevents the default from being updated by subsequent assignment
# (in this case, to [OUTCOME, {NAME= MSE}]), but fails to expose default in IDE
# output_ports = output_ports or [OUTCOME, MSE]
super().__init__(
monitor=input_ports,
function=function,
output_ports=
output_ports, # prevent default from getting overwritten by later assign
params=params,
name=name,
prefs=prefs,
**kwargs)
# Require Projection to TARGET InputPort (already required for SAMPLE as primary InputPort)
self.input_ports[1].parameters.require_projection_in_composition._set(
True, Context())
def __init__(self, component, execution_ids=[None]):
super().__init__()
self._bin_func = pnlvm.LLVMBinaryFunction.from_obj(component)
self._execution_contexts = [
Context(execution_id=eid) for eid in execution_ids
]
self._component = component
par_struct_ty, ctx_struct_ty, vi_ty, vo_ty = self._bin_func.byref_arg_types
if len(execution_ids) > 1:
self._bin_multirun = self._bin_func.get_multi_run()
self._ct_len = ctypes.c_int(len(execution_ids))
vo_ty = vo_ty * len(execution_ids)
vi_ty = vi_ty * len(execution_ids)
self.__param_struct = None
self.__state_struct = None
self._ct_vo = vo_ty()
self._vi_ty = vi_ty
def execute(
self,
inputs=None,
autodiff_stimuli=None,
scheduler=None,
termination_processing=None,
call_before_time_step=None,
call_before_pass=None,
call_after_time_step=None,
call_after_pass=None,
context=None,
base_context=Context(execution_id=None),
clamp_input=SOFT_CLAMP,
runtime_params=None,
skip_initialization=False,
bin_execute=False,
):
if isinstance(inputs, list):
inputs = {
self.get_mechanisms_by_role(NodeRole.ORIGIN).pop(): inputs
}
output = super(PathwayComposition, self).execute(
inputs,
scheduler=scheduler,
termination_processing=termination_processing,
call_before_time_step=call_before_time_step,
call_before_pass=call_before_pass,
call_after_time_step=call_after_time_step,
call_after_pass=call_after_pass,
context=context,
clamp_input=clamp_input,
runtime_params=runtime_params,
skip_initialization=skip_initialization,
bin_execute=bin_execute,
)
return output
def run(self,
termination_conds=None,
context=None,
base_context=Context(execution_id=None),
skip_trial_time_increment=False):
"""
run is a python generator, that when iterated over provides the next `TIME_STEP` of
executions at each iteration
:param termination_conds: (dict) - a mapping from `TimeScale`\\s to `Condition`\\s that when met
terminate the execution of the specified `TimeScale`
"""
self._validate_run_state()
if termination_conds is None:
termination_conds = self.termination_conds
else:
termination_conds = self.update_termination_conditions(
Scheduler._parse_termination_conditions(termination_conds))
if context is None:
context = Context(execution_id=self.default_execution_id)
self._init_counts(context.execution_id, base_context.execution_id)
self._reset_counts_useable(context.execution_id)
self._reset_counts_total(TimeScale.TRIAL, context.execution_id)
while (not termination_conds[TimeScale.TRIAL].is_satisfied(
scheduler=self, context=context)
and not termination_conds[TimeScale.RUN].is_satisfied(
scheduler=self, context=context)):
self._reset_counts_total(TimeScale.PASS, context.execution_id)
execution_list_has_changed = False
cur_index_consideration_queue = 0
while (cur_index_consideration_queue < len(
self.consideration_queue)
and not termination_conds[TimeScale.TRIAL].is_satisfied(
scheduler=self, context=context)
and not termination_conds[TimeScale.RUN].is_satisfied(
scheduler=self, context=context)):
# all nodes to be added during this time step
cur_time_step_exec = set()
# the current "layer/group" of nodes that MIGHT be added during this time step
cur_consideration_set = self.consideration_queue[
cur_index_consideration_queue]
try:
iter(cur_consideration_set)
except TypeError as e:
raise SchedulerError(
'cur_consideration_set is not iterable, did you ensure that this Scheduler was instantiated with an actual toposort output for param toposort_ordering? err: {0}'
.format(e))
# do-while, on cur_consideration_set_has_changed
# we check whether each node in the current consideration set is allowed to run,
# and nodes can cause cascading adds within this set
while True:
cur_consideration_set_has_changed = False
for current_node in cur_consideration_set:
# only add each node once during a single time step, this also serves
# to prevent infinitely cascading adds
if current_node not in cur_time_step_exec:
if self.conditions.conditions[
current_node].is_satisfied(
scheduler=self, context=context):
cur_time_step_exec.add(current_node)
execution_list_has_changed = True
cur_consideration_set_has_changed = True
for ts in TimeScale:
self.counts_total[context.execution_id][
ts][current_node] += 1
# current_node's node is added to the execution queue, so we now need to
# reset all of the counts useable by current_node's node to 0
for n in self.counts_useable[
context.execution_id]:
self.counts_useable[context.execution_id][
n][current_node] = 0
# and increment all of the counts of current_node's node useable by other
# nodes by 1
for n in self.counts_useable[
context.execution_id]:
self.counts_useable[context.execution_id][
current_node][n] += 1
# do-while condition
if not cur_consideration_set_has_changed:
break
# add a new time step at each step in a pass, if the time step would not be empty
if len(cur_time_step_exec) >= 1:
self.execution_list[context.execution_id].append(
cur_time_step_exec)
yield self.execution_list[context.execution_id][-1]
self.get_clock(context)._increment_time(
TimeScale.TIME_STEP)
cur_index_consideration_queue += 1
# if an entire pass occurs with nothing running, add an empty time step
if not execution_list_has_changed:
self.execution_list[context.execution_id].append(set())
yield self.execution_list[context.execution_id][-1]
self.get_clock(context)._increment_time(TimeScale.TIME_STEP)
self.get_clock(context)._increment_time(TimeScale.PASS)
if not skip_trial_time_increment:
self.get_clock(context)._increment_time(TimeScale.TRIAL)
if termination_conds[TimeScale.RUN].is_satisfied(scheduler=self,
context=context):
self.date_last_run_end = datetime.datetime.now()
return self.execution_list[context.execution_id]
def execute(
self,
inputs=None,
num_trials=None,
minibatch_size=1,
do_logging=False,
scheduler=None,
termination_processing=None,
call_before_minibatch=None,
call_after_minibatch=None,
call_before_time_step=None,
call_before_pass=None,
call_after_time_step=None,
call_after_pass=None,
reset_stateful_functions_to=None,
context=None,
base_context=Context(execution_id=None),
clamp_input=SOFT_CLAMP,
targets=None,
runtime_params=None,
execution_mode: pnlvm.ExecutionMode = pnlvm.ExecutionMode.Python,
skip_initialization=False,
report_output: ReportOutput = ReportOutput.OFF,
report_params: ReportOutput = ReportParams.OFF,
report_progress: ReportProgress = ReportProgress.OFF,
report_simulations: ReportSimulations = ReportSimulations.OFF,
report_to_devices: ReportDevices = None,
report=None,
report_num=None,
):
self._assign_execution_ids(context)
context.composition = self
context.source = ContextFlags.COMPOSITION
if scheduler is None:
scheduler = self.scheduler
if self._is_learning(context):
# TBI: How are we supposed to use base_context and statefulness here?
# TBI: can we call _build_pytorch_representation in _analyze_graph so that pytorch
# model may be modified between runs?
autodiff_inputs = self._infer_input_nodes(inputs)
autodiff_targets = self._infer_output_nodes(inputs)
report(
self,
LEARN_REPORT,
# EXECUTE_REPORT,
report_num=report_num,
scheduler=scheduler,
content='trial_start',
context=context)
self._build_pytorch_representation(context)
output = self.autodiff_training(autodiff_inputs, autodiff_targets,
context, scheduler)
# FIX 5/28/20:
# context.add_flag(ContextFlags.PROCESSING)
execution_phase = context.execution_phase
context.execution_phase = ContextFlags.PROCESSING
self.output_CIM.execute(output, context=context)
# FIX 5/28/20:
context.execution_phase = execution_phase
report(
self,
# [LEARN_REPORT],
[EXECUTE_REPORT, PROGRESS_REPORT],
report_num=report_num,
scheduler=scheduler,
content='trial_end',
context=context)
scheduler.get_clock(context)._increment_time(TimeScale.TRIAL)
return output
return super(AutodiffComposition, self).execute(
inputs=inputs,
scheduler=scheduler,
termination_processing=termination_processing,
call_before_time_step=call_before_time_step,
call_before_pass=call_before_pass,
call_after_time_step=call_after_time_step,
call_after_pass=call_after_pass,
reset_stateful_functions_to=reset_stateful_functions_to,
context=context,
base_context=base_context,
clamp_input=clamp_input,
runtime_params=runtime_params,
execution_mode=execution_mode,
report=report,
report_num=report_num)
def execute(
self,
inputs=None,
num_trials=None,
minibatch_size=1,
do_logging=False,
scheduler=None,
termination_processing=None,
call_before_minibatch=None,
call_after_minibatch=None,
call_before_time_step=None,
call_before_pass=None,
call_after_time_step=None,
call_after_pass=None,
reset_stateful_functions_to=None,
context=None,
base_context=Context(execution_id=None),
clamp_input=SOFT_CLAMP,
targets=None,
runtime_params=None,
bin_execute=False,
skip_initialization=False,
):
self._assign_execution_ids(context)
context.composition = self
context.source = ContextFlags.COMPOSITION
if scheduler is None:
scheduler = self.scheduler
if self._is_learning(context):
# TBI: How are we supposed to use base_context and statefulness here?
# TBI: can we call _build_pytorch_representation in _analyze_graph so that pytorch
# model may be modified between runs?
autodiff_inputs = self._infer_input_nodes(inputs)
autodiff_targets = self._infer_output_nodes(inputs)
self._build_pytorch_representation(context)
output = self.autodiff_training(autodiff_inputs, autodiff_targets,
context, scheduler)
# FIX 5/28/20:
# context.add_flag(ContextFlags.PROCESSING)
execution_phase = context.execution_phase
context.execution_phase = ContextFlags.PROCESSING
self.output_CIM.execute(output, context=context)
# FIX 5/28/20:
context.execution_phase = execution_phase
scheduler.get_clock(context)._increment_time(TimeScale.TRIAL)
return output
return super(AutodiffComposition, self).execute(
inputs=inputs,
scheduler=scheduler,
termination_processing=termination_processing,
call_before_time_step=call_before_time_step,
call_before_pass=call_before_pass,
call_after_time_step=call_after_time_step,
call_after_pass=call_after_pass,
reset_stateful_functions_to=reset_stateful_functions_to,
context=context,
base_context=base_context,
clamp_input=clamp_input,
runtime_params=runtime_params,
bin_execute=bin_execute,
)