<commit_before><commit_msg>created initial outline of tools script<commit_after>

def get_subject_timeseries():
    """get txt files in aal dir, remove vermis and cerebellum"""
    pass


def calc_cost_thresh(edges):
    """ return list of lists
    list[0] sorted thresholds
    list[1] associated cost
    """
    pass

def calc_partial_correl(aal_timeseries):
    """ use pcorr from fslnets to get partial correlations"""
    pass

def theshold_matrix(matrix, threshold):
    """return binary matrix size of matrix thresholded at threshold"""
    pass

def get_mod_value(bin_matrix):
    """ make graph, run newman, 
    return modularity value"""
    pass

def write_costs_mods():
    """ save the modularity at each cost in numpy array
    size 2 X ncosts
    0, : -> modularity
    1, : -> real cost
    """
    pass

def integrate_graph_metrics():
    """
    start with modularity, 
    add others
    shortest path (with some nan)
    largest component 
    betweenness centrality
    number of disconnections
    number of participation coeff """
    pass
    

{'fraction_non_alphanumeric': 0.08216619981325864, 'fraction_numerical': 0.004668534080298786, 'mean_word_length': 3.1550387596899223, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1900943', 'n_tokens_mistral': 322, 'n_tokens_neox': 305, 'n_words': 111}