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Update net_inf.py 

Comments to the net_inf.py file.
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dpshorten 2022-08-25 16:12:35 +09:30 committed by GitHub
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demos/python/EffectiveNetworkInference/net_inf.py
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@ -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"