24_deb_pkg_gov/text_analysis/topicModel.py

import re
import numpy as np
import pandas as pd
import glob
import copy
from statistics import mean, median
from strip_markdown import strip_markdown
import joblib

from getMetadata import metadata_for_file

# Gensim
import gensim
import gensim.corpora as corpora
from gensim.utils import simple_preprocess
from gensim.models import CoherenceModel
from gensim.models.phrases import Phrases

from sklearn.decomposition import LatentDirichletAllocation
from sklearn.model_selection import GridSearchCV
from sklearn.feature_extraction.text import CountVectorizer, TfidfVectorizer

from statistics import mode

# spacy and nltk for lemmatization
import nltk 
#nltk.download('stopwords')
import spacy
from nltk.corpus import stopwords
from nltk.stem.wordnet import WordNetLemmatizer

stopwords = stopwords.words('english')
#https://nlp.stanford.edu/IR-book/html/htmledition/dropping-common-terms-stop-words-1.html

#loading data in, getting misc descriptors
def get_data_from_dir(directory):
    files = glob.glob(f"{directory}/*")
    data_list = []
    word_counts = []
    avg_word_lengths = []
    file_list = []
    for file in files:
        text = open(file, encoding='utf-8').read()
        #here's some of the descriptive text analysis
        word_count, avg_word_length = metadata_for_file(text)
        word_counts.append(word_count)
        avg_word_lengths.append(avg_word_length)
        #adding the data to the list of text
        data_list.append(text)
        #adding filename
        file_list.append(file)
    return data_list, word_counts, avg_word_lengths, file_list

#preprocessing text data
def preprocess(corpus_list):
    #extending stopwords 
    specific_stopwords = ["http", "com", "www", "org", "file", "code", "time", "software", "use", "user", "set", "line", "run", "source", "github",
    "lineno", "python", "php", "ruby", "api"]
    stopwords.extend(specific_stopwords)
    D = copy.copy(corpus_list)
    #stripping markdown from documents
    D = [strip_markdown(doc) for doc in D]
    #strip html 
    D = [re.sub(r'<!--.*?-->', '', doc, flags=re.DOTALL) for doc in D]
    #mvp right now, can certainly be expanded as iterations of text analysis are done
    D = [[token for token in simple_preprocess(doc) if token not in stopwords and len(token) > 2]for doc in D]
    lemmatizer = WordNetLemmatizer()
    D_lemma = [" ".join([lemmatizer.lemmatize(token) for token in doc]) for doc in D]
    return D_lemma

#preparing processed data for model usage
def text_preparation(lemmatized_text):
    #bigrams
    D_bigrams = copy.copy(lemmatized_text)
    bigram = Phrases(D_bigrams, min_count=2)
    for i in range(len(lemmatized_text)):
        for token in bigram[D_bigrams[i]]:
            if '_' in token:
                D_bigrams[i].append(token)
    #id2word
    id2word = corpora.Dictionary(D_bigrams)
    id2word.filter_extremes(no_below=5, no_above=0.5)
    #bow representation 
    bag_of_words = [id2word.doc2bow(doc) for doc in D_bigrams]
    return bag_of_words, id2word

#TODO: identify best LDA model here
def lda_model_identification(data_vectorized):
    lda = LatentDirichletAllocation()
    search_params = {'n_components': [8], 'learning_decay': [.5, .7, .9], 'batch_size' : [128, 256]  }
    model = GridSearchCV(lda, param_grid=search_params, verbose=10)
    model.fit(data_vectorized)
    best_lda_model = model.best_estimator_
    print("Best Model's Params: ", model.best_params_)
    print("Best Log Likelihood Score: ", model.best_score_)
    print("Model Perplexity: ", best_lda_model.perplexity(data_vectorized))

#TODO: implement best LDA model here 
def best_lda_model(data_vectorized, vocab):
    #Best Log Likelihood Score:  -502085.9749390023
    #Model Perplexity:  1689.0943431883845
    lda = LatentDirichletAllocation(n_components=8, learning_decay = 0.9, batch_size = 128, max_iter = 50)
    id_topic = lda.fit_transform(data_vectorized)
    topic_words = {}
    for topic, comp in enumerate(lda.components_):
        word_idx = np.argsort(comp)[::-1][:10]
        topic_words[topic] = [vocab[i] for i in word_idx]
    for topic, words in topic_words.items():
        print('Topic: %d' % topic)
        print('  %s' % ', '.join(words))
    #lda.print_topics(num_words=10)
    joblib.dump(lda, '0509_lda.jl')
    #lda = joblib.load('0509_lda.jl')
    return id_topic

def get_most_prevalent(distributions, documents):
    most_prevalent = {0: [0, ""],1: [0, ""], 2: [0, ""], 3: [0, ""], 4: [0, ""], 5: [0, ""], 6: [0, ""],  7: [0, ""]}
    for i, topic_distribution in enumerate(distributions):
        for j in range(8):
            if topic_distribution[j] > most_prevalent[j][0]:
                most_prevalent[j] = [topic_distribution[j], documents[i]]
    print(most_prevalent)
    return most_prevalent

def prevalent_topics(vect_documents, file_list):
    lda = joblib.load('0509_readme_lda.jl')
    distributions = lda.transform(vect_documents)
    #figuring out what the max distribution is and then figuring out the mode
    top_topic = []
    count_of_multiple = 0
    topic_arrays = []
    for i, topic_distribution in enumerate(distributions):
        max_dist = max(topic_distribution)
        indexes = np.where(topic_distribution == max_dist)[0]
        if len(indexes) == 1:
            top_topic.append(indexes[0])
        else:
            count_of_multiple += 1
        topic_arrays.append(topic_distribution)
    #most_frequent(top_topic)
    print(count_of_multiple)
    df = pd.DataFrame(topic_arrays)
    #print(df.sort_values(by=['0']).head(5))
    for i in range(8):
        print("-----------------------Topic " + str(i) + " --------------------------------")
        top5 = df.nlargest(10, i)
        top_indices = top5.index.to_list()
        print(top5)
        for index in top_indices:
            print(file_list[index])
        bottom5 = df.nsmallest(10, i)
        bottom_indices = bottom5.index.to_list()
        print(bottom5)
        for index in bottom_indices:
            print(file_list[index])
    #averages = df.mean()
    #print(averages)
    
def most_frequent(topic_prevalence):
    most_frequent_array = []
    for j in range(8):
        topic = mode(topic_prevalence)
        most_frequent_array.append(topic)
        topic_prevalence = [i for i in topic_prevalence if i != topic]
    print(most_frequent_array)



if __name__ == "__main__":
    readme_directory = "/data/users/mgaughan/kkex/time_specific_files/readme3"
    contributing_directory = "/data/users/mgaughan/kkex/time_specific_files/partitioned_contributing/p2"
    listed_corpus, wordcounts, wordlengths, file_list = get_data_from_dir(readme_directory)
    print("Mean wordcount: ", mean(wordcounts))
    print("Median wordcount: ", median(wordcounts))
    print("Mean wordlength: ", mean(wordlengths))
    print("Median wordlength: ", median(wordlengths))
    lemmatized_corpus = preprocess(listed_corpus)
    '''
    vectorizer = CountVectorizer(analyzer='word',       
                             min_df=2,                        
                             stop_words='english',             
                             lowercase=True,                   
                             token_pattern='[a-zA-Z0-9]{2,}',  
                            )
    data_vectorized = vectorizer.fit_transform(lemmatized_corpus)
    '''
    vectorizer = joblib.load('readme_vectorizer.jl')
    data_vectorized = vectorizer.transform(lemmatized_corpus)                
    #lda_model_identification(data_vectorized)
    #topic_distributions = best_lda_model(data_vectorized, vectorizer.get_feature_names_out())
    #get_most_prevalent(topic_distributions, file_list)
    prevalent_topics(data_vectorized, file_list)