e_model_packager.synaptic_plasticity.extractors

Functions to extract data needed for the glusynapse package.

Functions

extract_all(basedirs, output_dir, pregid, ...)	Extract everything.
extract_config(output_dir, circuit, postgid, ...)	Extract and write config and fit_params.
extract_cpre_and_cpost(output_dir, basedir, ...)	Extract c_pre and c_post.
extract_morph_data(output_dir, circuit, ...)	Extract morphology.
extract_protocols(output_dir, bc_dicts[, ...])	Extract Pulse Stimuli from BlueConfig.
extract_syn_extra_params(output_dir, ssim, ...)	Extract synapse extra params.
extract_synapses_data(output_dir, bcpath[, ...])	Extract synapse data.
extract_synprop(output_dir, basedir[, ...])	Extract model properties to be stored in simulation output.
fix_Dep_and_Fac_TM(basedir, syn_extra_params)	Take Dep_TM and Fac_TM values from original simulation.
fix_tuple_keys_for_json(dict_to_fix)	Replace tuple keys by str: (a,b) -> '(a,b)'.
get_blueconfig_dict(bcpath)	Get BlueConfig configuration data as a dict.
get_fit_params(basedir)	Parse simulation.batch to get the fit_params.

extract_all(basedirs, output_dir, pregid, postgid, circuitpath, extra_recipe, recipes_path)

Extract everything.

extract_config(output_dir, circuit, postgid, pregid, bc_dicts, recipes_path, outfile_basename='config', out_fit_params_file='fit_params.json', out_const_dir='config', celsius=34, v_init=-65, fastforward=None, invivo=False, fit_params=None, default_synrec=None, base_stimuli_name='stimuli', base_spiketrain_name='spiketrain')

Extract and write config and fit_params.

extract_cpre_and_cpost(output_dir, basedir, fit_params, invivo=False, syn_dir='synapses', output_file='cpre_cpost.json')

Extract c_pre and c_post.

extract_morph_data(output_dir, circuit, simulation, postgid, output_morph_dir='morphology')

Extract morphology.

extract_protocols(output_dir, bc_dicts, prot_dir='protocols', base_output_name='stimuli')

Extract Pulse Stimuli from BlueConfig.

extract_syn_extra_params(output_dir, ssim, circuitpath, extra_recipe, basedir, syn_dir='synapses', output_file='syn_extra_params.json')

Extract synapse extra params.

extract_synapses_data(output_dir, bcpath, syn_dir='synapses')

Extract synapse data.

extract_synprop(output_dir, basedir, syn_dir='synapses', output_file='synapse_properties.json')

Extract model properties to be stored in simulation output.

fix_Dep_and_Fac_TM(basedir, syn_extra_params)

Take Dep_TM and Fac_TM values from original simulation.

fix_tuple_keys_for_json(dict_to_fix)

Replace tuple keys by str: (a,b) -> ‘(a,b)’.

get_blueconfig_dict(bcpath)

Get BlueConfig configuration data as a dict.

get_fit_params(basedir)

Parse simulation.batch to get the fit_params.