pypet
What is pypet all about?
Main Features
Getting Started!
Install
What to do with pypet?
Basic Work Flow
Quick Working Example
Cookbook
Naming Convention
More about the Environment
More on Trajectories and Single Runs
Interaction with Trajectories after an Experiment
Annotations
More on Parameters and Results
How to Structure your Simulations
Using BRIAN with pypet
Examples
01 First Steps
02 Natural Naming, Storage and Loading
03 Merging of Trajectories
04 Multiprocessing
05 Custom Parameter (Strange Attractor Inside!)
06 Parameter Presetting
07 Short BRIAN Example
08 Using the f_find_idx Function
09 Storing and Loading Large Results (or just parts of them)
10 Accessing Results from All Runs at Once
11 Large scale BRIAN simulation
FAQs and Known Issues
Library Reference
The Environment
The Trajectory, Single Runs and Group Nodes
Parameters and Results
Annotations
Utils
Exceptions
Global Constants
Storage Services
Brian Parameters, Results and Monitors
Brian Network Framework
pypet
Docs
»
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Index
_
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A
|
B
|
C
|
D
|
E
|
F
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H
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L
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N
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O
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P
|
Q
|
R
|
S
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T
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V
_
__class__ (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
__delattr__ (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
__dict__ (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
__format__() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
__getattribute__ (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
__getitem__() (pypet.parameter.BaseParameter method)
__getstate__() (pypet.brian.network.NetworkManager method)
(pypet.brian.network.NetworkRunner method)
__hash__ (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
__init__() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
__len__() (pypet.parameter.BaseParameter method)
__module__ (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
__new__() (pypet.parameter.BaseParameter static method)
(pypet.parameter.BaseResult static method)
__reduce__() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
__reduce_ex__() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
__repr__ (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
__setattr__ (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
__setstate__() (pypet.brian.network.NetworkManager method)
(pypet.brian.network.NetworkRunner method)
__sizeof__() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
__str__() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
__subclasshook__() (pypet.parameter.BaseParameter static method)
(pypet.parameter.BaseResult static method)
__weakref__ (pypet.brian.network.NetworkManager attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
_equal_values() (pypet.parameter.BaseParameter method)
_execute_network_run() (pypet.brian.network.NetworkRunner method)
_expand() (pypet.parameter.BaseParameter method)
_explore() (pypet.parameter.BaseParameter method)
_extract_subruns() (pypet.brian.network.NetworkRunner method)
_load() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
_rename() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
_restore_default() (pypet.parameter.BaseParameter method)
_run_network() (pypet.brian.network.NetworkManager method)
_set_logger() (pypet.brian.network.NetworkManager method)
_set_parameter_access() (pypet.parameter.BaseParameter method)
_shrink() (pypet.parameter.BaseParameter method)
_store() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
_store_flags() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
_values_of_same_type() (pypet.parameter.BaseParameter method)
A
add_parameters() (pypet.brian.network.NetworkComponent method)
(pypet.brian.network.NetworkManager method)
add_to_network() (pypet.brian.network.NetworkComponent method)
analyse() (pypet.brian.network.NetworkAnalyser method)
Annotations (class in pypet.annotations)
ArrayParameter (class in pypet.parameter)
B
BaseParameter (class in pypet.parameter)
BaseResult (class in pypet.parameter)
BrianDurationParameter (class in pypet.brian.parameter)
BrianMonitorResult (class in pypet.brian.parameter)
BrianParameter (class in pypet.brian.parameter)
BrianResult (class in pypet.brian.parameter)
build() (pypet.brian.network.NetworkComponent method)
(pypet.brian.network.NetworkManager method)
C
cartesian_product() (in module pypet.utils.explore)
ConfigGroup (class in pypet.naturalnaming)
D
DerivedParameterGroup (class in pypet.naturalnaming)
E
Environment (class in pypet.environment)
execute_network_pre_run() (pypet.brian.network.NetworkRunner method)
execute_network_run() (pypet.brian.network.NetworkRunner method)
F
f_add_config() (pypet.naturalnaming.ConfigGroup method)
f_add_config_group() (pypet.naturalnaming.ConfigGroup method)
f_add_derived_parameter() (pypet.naturalnaming.DerivedParameterGroup method)
f_add_derived_parameter_group() (pypet.naturalnaming.DerivedParameterGroup method)
f_add_parameter() (pypet.naturalnaming.ParameterGroup method)
f_add_parameter_group() (pypet.naturalnaming.ParameterGroup method)
f_add_result() (pypet.naturalnaming.ResultGroup method)
f_add_result_group() (pypet.naturalnaming.ResultGroup method)
f_add_to_dynamic_imports() (pypet.trajectory.Trajectory method)
f_ann_to_str() (pypet.annotations.Annotations method)
(pypet.naturalnaming.NNGroupNode method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_ann_to_string() (pypet.naturalnaming.NNGroupNode method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_as_run() (pypet.trajectory.Trajectory method)
f_backup() (pypet.trajectory.Trajectory method)
f_children() (pypet.naturalnaming.NNGroupNode method)
f_contains() (pypet.naturalnaming.NNGroupNode method)
f_continue_run() (pypet.environment.Environment method)
f_empty() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_expand() (pypet.trajectory.Trajectory method)
f_explore() (pypet.trajectory.Trajectory method)
f_find_idx() (pypet.trajectory.Trajectory method)
f_get() (pypet.annotations.Annotations method)
(pypet.naturalnaming.NNGroupNode method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_get_annotations() (pypet.naturalnaming.NNGroupNode method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_get_array() (pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
f_get_children() (pypet.naturalnaming.NNGroupNode method)
f_get_class_name() (pypet.naturalnaming.NNGroupNode method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_get_config() (pypet.trajectory.SingleRun method)
f_get_derived_parameters() (pypet.trajectory.SingleRun method)
f_get_explored_parameters() (pypet.trajectory.SingleRun method)
f_get_from_runs() (pypet.trajectory.Trajectory method)
f_get_parameters() (pypet.trajectory.SingleRun method)
f_get_range() (pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
f_get_results() (pypet.trajectory.SingleRun method)
f_get_run_information() (pypet.trajectory.Trajectory method)
f_get_run_names() (pypet.trajectory.Trajectory method)
f_has_children() (pypet.naturalnaming.NNGroupNode method)
f_has_range() (pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
f_idx_to_run() (pypet.trajectory.Trajectory method)
f_is_array() (pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
f_is_completed() (pypet.trajectory.Trajectory method)
f_is_empty() (pypet.annotations.Annotations method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
(pypet.trajectory.Trajectory method)
f_is_root() (pypet.naturalnaming.NNGroupNode method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_iter_leaves() (pypet.naturalnaming.NNGroupNode method)
f_iter_nodes() (pypet.naturalnaming.NNGroupNode method)
f_load() (pypet.trajectory.Trajectory method)
f_load_child() (pypet.naturalnaming.NNGroupNode method)
f_load_item() (pypet.trajectory.Trajectory method)
f_load_items() (pypet.trajectory.Trajectory method)
f_lock() (pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
f_lock_derived_parameters() (pypet.trajectory.Trajectory method)
f_lock_parameters() (pypet.trajectory.Trajectory method)
f_merge() (pypet.trajectory.Trajectory method)
f_preset_config() (pypet.trajectory.Trajectory method)
f_preset_parameter() (pypet.trajectory.Trajectory method)
f_remove_child() (pypet.naturalnaming.NNGroupNode method)
f_remove_item() (pypet.trajectory.Trajectory method)
f_remove_items() (pypet.trajectory.Trajectory method)
f_restore_default() (pypet.trajectory.Trajectory method)
f_run() (pypet.environment.Environment method)
f_set() (pypet.annotations.Annotations method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_set_annotations() (pypet.naturalnaming.NNGroupNode method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_set_single() (pypet.annotations.Annotations method)
(pypet.brian.parameter.BrianMonitorResult method)
(pypet.brian.parameter.BrianResult method)
(pypet.parameter.PickleResult method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_shrink() (pypet.trajectory.Trajectory method)
f_store() (pypet.trajectory.SingleRun method)
(pypet.trajectory.Trajectory method)
f_store_child() (pypet.naturalnaming.NNGroupNode method)
f_store_item() (pypet.trajectory.SingleRun method)
f_store_items() (pypet.trajectory.SingleRun method)
f_supports() (pypet.brian.parameter.BrianParameter method)
(pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
(pypet.parameter.PickleParameter method)
(pypet.parameter.SparseParameter method)
f_supports_fast_access() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
f_switch_off_all_overview() (pypet.environment.Environment method)
f_switch_off_large_overview() (pypet.environment.Environment method)
f_switch_off_small_overview() (pypet.environment.Environment method)
f_to_dict() (pypet.annotations.Annotations method)
(pypet.naturalnaming.NNGroupNode method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
(pypet.trajectory.SingleRun method)
f_unlock() (pypet.parameter.BaseParameter method)
(pypet.parameter.Parameter method)
f_update_skeleton() (pypet.trajectory.Trajectory method)
f_val_to_str() (pypet.parameter.BaseParameter method)
(pypet.parameter.BaseResult method)
(pypet.parameter.Parameter method)
(pypet.parameter.Result method)
(pypet.parameter.SparseResult method)
H
HDF5StorageService (class in pypet.storageservice)
L
LazyStorageService (class in pypet.storageservice)
load() (pypet.storageservice.HDF5StorageService method)
(pypet.storageservice.LazyStorageService method)
(pypet.storageservice.LockWrapper method)
LockWrapper (class in pypet.storageservice)
N
nested_equal() (in module pypet.utils.comparisons)
NetworkAnalyser (class in pypet.brian.network)
NetworkComponent (class in pypet.brian.network)
NetworkManager (class in pypet.brian.network)
NetworkRunner (class in pypet.brian.network)
NNGroupNode (class in pypet.naturalnaming)
NoSuchServiceError
NotUniqueNodeError
O
ObjectTable (class in pypet.parameter)
P
Parameter (class in pypet.parameter)
ParameterGroup (class in pypet.naturalnaming)
ParameterLockedException
parameters_equal() (in module pypet.utils.comparisons)
PickleParameter (class in pypet.parameter)
PickleResult (class in pypet.parameter)
pre_build() (pypet.brian.network.NetworkComponent method)
(pypet.brian.network.NetworkManager method)
pre_run_network() (pypet.brian.network.NetworkManager method)
PresettingError
pypet.brian.network (module)
pypet.brian.parameter (module)
pypet.environment (module)
pypet.parameter (module)
pypet.pypetconstants (module)
pypet.pypetexceptions (module)
pypet.utils.comparisons (module)
pypet.utils.explore (module)
Q
QueueStorageServiceSender (class in pypet.storageservice)
QueueStorageServiceWriter (class in pypet.storageservice)
R
remove_from_network() (pypet.brian.network.NetworkComponent method)
Result (class in pypet.parameter)
ResultGroup (class in pypet.naturalnaming)
results_equal() (in module pypet.utils.comparisons)
run() (pypet.storageservice.QueueStorageServiceWriter method)
run_network() (in module pypet.brian.network)
(pypet.brian.network.NetworkManager method)
S
send_done() (pypet.storageservice.QueueStorageServiceSender method)
set_logger() (pypet.brian.network.NetworkRunner method)
SingleRun (class in pypet.trajectory)
SparseParameter (class in pypet.parameter)
SparseResult (class in pypet.parameter)
store() (pypet.storageservice.HDF5StorageService method)
(pypet.storageservice.LazyStorageService method)
(pypet.storageservice.LockWrapper method)
(pypet.storageservice.QueueStorageServiceSender method)
T
TooManyGroupsError
Trajectory (class in pypet.trajectory)
V
v_annotations (pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_as_run (pypet.trajectory.Trajectory attribute)
v_check_uniqueness (pypet.trajectory.SingleRun attribute)
v_comment (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
(pypet.trajectory.Trajectory attribute)
v_creator_name (pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_depth (pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_environment_hexsha (pypet.trajectory.SingleRun attribute)
v_environment_name (pypet.trajectory.SingleRun attribute)
v_fast_access (pypet.trajectory.SingleRun attribute)
v_fast_accessible (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_full_copy (pypet.parameter.BaseParameter attribute)
(pypet.parameter.Parameter attribute)
(pypet.trajectory.Trajectory attribute)
v_full_name (pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_hexsha (pypet.environment.Environment attribute)
v_idx (pypet.trajectory.SingleRun attribute)
(pypet.trajectory.Trajectory attribute)
v_is_leaf (pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_is_parameter (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_is_root (pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_leaf (pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_location (pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_locked (pypet.parameter.BaseParameter attribute)
(pypet.parameter.Parameter attribute)
v_monitor_type (pypet.brian.parameter.BrianMonitorResult attribute)
v_name (pypet.environment.Environment attribute)
(pypet.naturalnaming.NNGroupNode attribute)
(pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_no_data_string (pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_parameter (pypet.parameter.BaseParameter attribute)
(pypet.parameter.BaseResult attribute)
(pypet.parameter.Parameter attribute)
(pypet.parameter.Result attribute)
(pypet.parameter.SparseResult attribute)
v_protocol (pypet.parameter.PickleParameter attribute)
(pypet.parameter.PickleResult attribute)
v_search_strategy (pypet.trajectory.SingleRun attribute)
v_standard_parameter (pypet.trajectory.SingleRun attribute)
v_standard_result (pypet.trajectory.SingleRun attribute)
v_storage_mode (pypet.brian.parameter.BrianMonitorResult attribute)
(pypet.brian.parameter.BrianParameter attribute)
(pypet.brian.parameter.BrianResult attribute)
v_storage_service (pypet.trajectory.SingleRun attribute)
(pypet.trajectory.Trajectory attribute)
v_stored (pypet.trajectory.SingleRun attribute)
v_time (pypet.environment.Environment attribute)
(pypet.trajectory.SingleRun attribute)
v_timestamp (pypet.environment.Environment attribute)
(pypet.trajectory.SingleRun attribute)
v_trajectory (pypet.environment.Environment attribute)
v_trajectory_name (pypet.trajectory.SingleRun attribute)
v_trajectory_time (pypet.trajectory.SingleRun attribute)
v_trajectory_timestamp (pypet.trajectory.SingleRun attribute)
v_version (pypet.trajectory.Trajectory attribute)
VersionMismatchError
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v: 0.1b.3
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