diff --git a/demos/python/EffectiveNetworkInference/net_inf.py b/demos/python/EffectiveNetworkInference/net_inf.py index 73cd878..3520120 100755 --- a/demos/python/EffectiveNetworkInference/net_inf.py +++ b/demos/python/EffectiveNetworkInference/net_inf.py @@ -9,23 +9,39 @@ import pickle import copy import sys +# net_type_name is useful if you are iterating over multiple files with different network types. +# Looking at the definition of SPIKES_FILE_NAME and OUTPUT_FILE_PREFIX will imply what the purpose of +# these command line arguments is. net_type_name = sys.argv[1] num_spikes_string = sys.argv[2] repeat_num_string = sys.argv[3] target_index_string = sys.argv[4] +# The number of surrogates to create for each significance test of a TE value NUM_SURROGATES_PER_TE_VAL = 100 +# The p level below which the null hypothesis will be rejected. P_LEVEL = 0.05 +# The number of nearest neighbours to consider in the TE estimation. KNNS = 10 +# The number of random sample points laid down will be NUM_SAMPLES_MULTIPLIER * length_of_target_train NUM_SAMPLES_MULTIPLIER = 5.0 #SURROGATE_NUM_SAMPLES_MULTIPLIER = 5.0 +# As above, but for the creation of surrogates SURROGATE_NUM_SAMPLES_MULTIPLIER = 5.0 +# The number of nearest neighbours to consider when using the local permutation method to create surrogates K_PERM = 20 +# The level of the noise to add to the random sample points used in creating surrogates JITTERING_LEVEL = 2000 +# When MAX_NUM_SECOND_INTERVALS sources have 2 or more history intervals added into the conditioning set, the inference stops MAX_NUM_SECOND_INTERVALS = 2 +# Exclude target spikes beyond this number MAX_NUM_TARGET_SPIKES = int(num_spikes_string) +# The spikes file with the below name is expected to contain a single pickled Python list. This list contains numpy arrays. Each +# numpy array contains the spike times of each candidate target. SPIKES_FILE_NAME = "spikes_LIF_" + net_type_name + "_" + repeat_num_string + ".pk" +# The ground truth file of the below name is expected to contain a single pickled Python list. This list contains tuples of the format(source, target). +# source and target are integers of the indices of true connections. GROUND_TRUTH_FILE_NAME = "connections_LIF_"+ net_type_name + "_" + repeat_num_string + ".pk" OUTPUT_FILE_PREFIX = "results/inferred_sources_target_2_" + net_type_name + "_" + num_spikes_string + "_" + repeat_num_string + "_" + target_index_string LOG_FILE_NAME = "logs/" + net_type_name + "_" + num_spikes_string + "_" + repeat_num_string + "_" + target_index_string + ".log"