init

data_base.db_initializers.load_simrun_general.init(db, simresult_path, core=True, synapse_activation=True, dendritic_voltage_traces=True, parameterfiles=True, spike_times=True, repartition=True, scheduler=None, rewrite_in_optimized_format=True, dendritic_spike_times=True, dendritic_spike_times_threshold=-30.0, client=None, check_health=False, n_chunks=5000, voltage_traces=None, burst_times=None, dumper=None, paramfile_copy_config=None)

Initialize a database with simulation data.

Use this function to load simulation data generated with the simrun module into a DataBase.

Most configuration options you would want to change on a init-by-init basis are given here as keyword arguments. Additional options can be configured in data_base.db_initializers.load_simrun_general.config

Parameters:
db : DataBase

The database to store the simulation results in.

core : bool, optional

Parse and write the core data to the database: voltage traces, metadata, sim_trial_index and filelist.

spike_times : bool, optional

Parse and write the spike times into the database. See also: data_base.analyze.spike_detection.spike_detection()

dendritic_voltage_traces : bool, optional

Parse and write the dendritic voltage traces to the database.

dendritic_spike_times : bool, optional

Parse and write the dendritic spike times to the database.

dendritic_spike_times_threshold : float, optional

Threshold for the dendritic spike times in \(mV\). Default is \(-30 mV\).

synapse_activation : bool, optional

Parse and write the synapse activation data to the database.

parameterfiles : bool, optional

Resolve and copy the parameterfiles used in each simulation to the database. Since this copies all parameterfiels required to rerun simulations, this makes the database self-containing and portable. You could then remove the original raw simulation data, provided you have selected all desired results in the keyword arguments here.

rewrite_in_optimized_format : bool, optional

If True (default): data is converted to a high performance binary format If False: the db only contains links (pickled objects) to the actual simulation data folder and will not work if the data folder is deleted or moved or transferred to another machine.

repartition : bool|int

If int, the voltage trace dataframes will be partitioned to be of this length (approximately). If True, the voltage trace dataframes will be partitioned to be of a default length: DEFAULT_VT_PARTITION_SIZE If False, the voltage trace dataframe will not be repartitioned, and the dask dataframe will be one .csv file per partition.

n_chunks : int, optional

Amount of partitions to split the Synapse activation and Presynaptic spike times dataframes into. Default is \(5000\).

paramfile_copy_config : dict, optional

Dictionary containing configuration on how to organise parameterfiles in the database. Options are:

  • copy_method (str): Which copy strategy to use. Must be either "hash_rename" or "remount". "hash_rename" will rename all parameterfiles to a hash of their content. Useful when you want all parameter files in one folder and avoid fielname clashes. "remount" will preserve the relative directory structure of the parameterfiles per file category (see below). Useful when parameterfiles are already organized.

  • ”neup” (str): Target directory name of neuron_params_format. Default is "parameterfiles_folder"

  • ”netp” (str): Target directory name of network_params_format. Default is "parameterfiles_folder"

  • ”hoc” (str): Target directory name of .hoc files. Default is "parameterfiles_folder"

  • ”syn” (str): Target directory name of .syn files. Default is "parameterfiles_folder"

  • ”con” (str): Target directory name of .con files. Default is "parameterfiles_folder"

  • ”recsites” (str): Target directory name of recordingsites (.landmarkAscii). Default is "parameterfiles_folder"

client : distributed.Client

Distributed Client object for parallel parsing of anything that isn’t a dask dataframe.

scheduler : distributed.Client

Scheduler to use for parallellized parsing of dask dataframes. can e.g. be simply the distributed.Client.get method. Default is None.

Note

Note the difference between amount of partitions (n_chunks) and target partition size (repartition)

New in version 0.5.0: The keyword argument repartition now accepts integers in addition to booleans. Integers reflect the target size of each voltage trace dataframe partition. Booleans reflect either True for a default lenght, or False for no repartitioning (i.e. one .csv file per partition)

Deprecated since version 0.2.0: The burst_times argument is deprecated and will be removed in a future version.

Deprecated since version 0.5.0: The dumper argument is deprecated and will be removed in a future version. Dumpers are configured in the centralized config module.

Deprecated since version 0.5.0: The voltage_traces is deprecated and will be removed in a future version. Voltage traces are always built when core is True.