run_tsne_on_all_sale_documents.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "fc6630f2",
   "metadata": {},
   "source": [
    "# Imports and Functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "91ac757e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import re\n",
    "import pandas as pd\n",
    "from tqdm import tqdm\n",
    "import csv\n",
    "from sklearn.feature_extraction.text import CountVectorizer, TfidfVectorizer\n",
    "from scipy.spatial.distance import pdist, squareform\n",
    "from sklearn.decomposition import PCA\n",
    "from sklearn.manifold import TSNE\n",
    "import plotly.express as px\n",
    "import plotly.io as pio"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "e3b0c3ad",
   "metadata": {},
   "outputs": [],
   "source": [
    "# text processing functions\n",
    "def upload_corpus_csv(path):\n",
    "    \"\"\"\n",
    "    Function to upload CSV files containing the texts and converting them into a dataframe\n",
    "    :return: a list of dataframes\n",
    "    \"\"\"\n",
    "    texts = os.listdir(path)\n",
    "    corpus = []\n",
    "    for text in texts:\n",
    "        try:\n",
    "            df = pd.read_csv(f\"{path}/{text}\", encoding=\"utf-8\").fillna(\"\")\n",
    "            corpus.append(df)\n",
    "        except Exception as e:\n",
    "            print(f\"can't process {text}:\\n{e}\")\n",
    "    return corpus\n",
    "\n",
    "def split_df_by_column_value(df, column):\n",
    "    \"\"\"\n",
    "    Function to split the text dataframes according to a column. Used to separate text to lines\n",
    "    :param df: dataframe containing one word in each row.\n",
    "    :param column: the column by which to split the dfs, perferably `text` or `line`.\n",
    "    :return: a list of dataframes split according to the value given to the column parameter.\n",
    "    \"\"\"\n",
    "    dfs = []\n",
    "    column_values = df[column].unique()\n",
    "    for value in column_values:\n",
    "        split_df = df[df[column]==value]\n",
    "        dfs.append(split_df)\n",
    "    return dfs\n",
    "\n",
    "def df2str(df, column, break_perc=1, mask=True, segmentation=True):\n",
    "    \"\"\"\n",
    "    Function to convert the values from the text dataframe to a string of text with line breaks.\n",
    "    :param df: the text dataframe\n",
    "    :param column: the chosen column from the dataframe to construct the text from (preferably Unicode, cf, or lemma)\n",
    "    :param break_perc: a parameter which dictates whether to include broken words depending on the percentage of how broken they are. Compares this value to the `break_perc` column in the dataframe. Parameter is set to 1 (i.e. all words, whether broken or not, are included); can be any float between 0 and 1.\n",
    "    :param mask: boolean whether to mask named entities or not; set to True.\n",
    "    :return: a string which includes all the words in the texts according to the column chosen. Extra spaces that were between broken words or empty lines are removed.\n",
    "    \"\"\"\n",
    "    # check if column exists in dataframe. If not, return empty text.\n",
    "    if column not in df.columns:\n",
    "        return (\"\", 0, 0)\n",
    "    else: \n",
    "        # remove rows that include duplicate values for compound words\n",
    "        if column not in [\"norm\", \"cf\", \"sense\", \"pos\"]:\n",
    "            df = df.drop_duplicates(\"ref\").copy()\n",
    "        # if column entry is empty string, replace with UNK (can happen with normalization or lemmatization)\n",
    "        mask_empty = df[column]==\"\"\n",
    "        df[column] = df[column].where(~mask_empty, other=\"UNK\")\n",
    "        # mask proper nouns\n",
    "        if mask and \"pos\" in df.columns:\n",
    "            mask_bool = df[\"pos\"].isin([\"PN\", \"RN\", \"DN\", \"GN\", \"MN\", \"SN\", \"n\"])\n",
    "            df[column] = df[column].where(~mask_bool, other=df[\"pos\"])\n",
    "        # change number masking from `n` to `NUM`\n",
    "        if mask:\n",
    "            mask_num = df[column]==\"n\"\n",
    "            df[column] = df[column].where(~mask_num, other=\"NUM\")\n",
    "            # add masking to male PNs based on determinative\n",
    "            has_determinative = df[column].str[0]==\"𒁹\"\n",
    "            df[column] = df[column].where(~has_determinative, other=\"PN\")\n",
    "        # remove rows without break_perc\n",
    "        if \"\" in df[\"break_perc\"].unique().tolist():\n",
    "            df = df[df[\"break_perc\"]!=\"\"].copy()\n",
    "        # filter according to break_perc\n",
    "        mask_break = df[\"break_perc\"] <= break_perc\n",
    "        df[column] = df[column].where(mask_break, other=\"X\")\n",
    "        # calculate text length with and without UNK and x tokens\n",
    "        text_length_full = df.shape[0]\n",
    "        mask_partial = df[column].isin([\"UNK\", \"X\", \"x\"])\n",
    "        text_length_partial = text_length_full - sum(mask_partial)\n",
    "        # create text lines\n",
    "        text = \"\"\n",
    "        df_lines = split_df_by_column_value(df, \"line\")\n",
    "        for line in df_lines:\n",
    "            word_list = list(filter(None, line[column].to_list()))\n",
    "            if word_list != []:\n",
    "                text += \" \".join(map(str, word_list)).replace(\"x\", \"X\").strip() + \"\\n\"\n",
    "\n",
    "        if segmentation == False:\n",
    "            # remove all white spaces (word segmentation and line breaks)\n",
    "            text = re.sub(r\"[\\s\\u00A0]+\", \"\", text)\n",
    "            \n",
    "        # double check length of words in text matches number of rows:\n",
    "        len_text = len([word for word in text.replace(\"\\n\", \" \").split(\" \") if word != \"\"])\n",
    "        if len_text != text_length_full:\n",
    "            print(f\"Number of words in text ({len_text}) does not match number of rows in dataframe ({text_length_full})!\\nSee {df.loc[0, 'text']}\")\n",
    "\n",
    "        return (text, text_length_full, text_length_partial)\n",
    "    \n",
    "def get_segmented_unicode_texts(corpus, break_perc=1, mask=True):\n",
    "    \"\"\"\n",
    "    Function to convert the dataframes into strings of segmented unicode texts.\n",
    "    :param corpus: a list of dataframes\n",
    "    :param break_perc: a parameter which dictates whether to include broken words depending on the percentage of how broken they are. Compares this value to the `break_perc` column in the dataframe. Parameter is set to 1 (i.e. all words, whether broken or not, are included); can be any float between 0 and 1.\n",
    "    :param mask: boolean whether to mask named entities or not; set to True.\n",
    "    :return: a dictionary where the keys are the text IDs and the values are the segmented unicode texts\n",
    "    \"\"\"\n",
    "    texts_dict = {}\n",
    "    for df in corpus:\n",
    "        # get the text number from the dataframe \"text\" column\n",
    "        key = df.loc[0, \"text\"]\n",
    "        text, text_length_full, text_length_partial = df2str(df, \"unicode_word\", break_perc, mask)\n",
    "        texts_dict[key] = (text, text_length_full, text_length_partial)\n",
    "    return texts_dict\n",
    "\n",
    "def add_texts_dict_to_dataframe(df, text_dict):\n",
    "    text_df = pd.DataFrame(text_dict).transpose().rename(columns={0: \"Text\",\n",
    "                                                                  1: f\"Text_length_full\",\n",
    "                                                                  2: f\"Text_length_partial\"})\n",
    "    new_df = df.join(text_df)\n",
    "    return new_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "8a7e0672",
   "metadata": {},
   "outputs": [],
   "source": [
    "# vectorization and tsne functions\n",
    "# vectorizing texts\n",
    "\n",
    "def vectorize(vectorizer, corpus, analyzer=\"word\", ngram_range=(1,1), max_df=1.0, min_df=1, max_features=None, stop_words=[\"UNK\", \"X\"]):\n",
    "    \"\"\"\n",
    "    Converts a list of texts into a term-document matrix based on TF-IDF scores.\n",
    "    Full full documentation of the variables of TfidfVectorizer from sklearn, see:\n",
    "    https://scikit-learn.org/stable/modules/generated/sklearn.feature_extraction.text.TfidfVectorizer.html#sklearn.feature_extraction.text.TfidfVectorizer\n",
    "    :param corpus: a dataframe in which the texts are in a `\"Text\"` column and the dataframe's index is the text ids.\n",
    "    :param analyzer: whether the feature should be made of word or character n-grams.\n",
    "                     use `\"word\"` for word features, `\"char_wb\"` for character n-grams within word boundaries,\n",
    "                     or `\"char\"` for character n-grams without word boundaries.\n",
    "    :param ngram_range: the lower and upper boundary of the range of n-values for different n-grams to be extracted.\n",
    "    :param max_df: threshold to ignore terms that have a document frequency above a certain value.\n",
    "                   If the threshold is a float, it represent a proportion of the documents.\n",
    "                   If the threshold is an integer, it represents absolute counts of number of documents in which the terms appears.\n",
    "    :param min_df: threshold to ignore terms that have a document frequency below a certain value.\n",
    "                   If the threshold is a float, it represent a proportion of the documents.\n",
    "                   If the threshold is an integer, it represents absolute counts of number of documents in which the terms appears.\n",
    "    :param max_features: if not `None`, build a vocabulary that only considers the top max_features ordered by term frequency across the corpus.\n",
    "    :param stop_words: if `None`, no stop words are used. Otherwise, can be a list with words to be removed from resulting tokens.\n",
    "    :return: `counts` the raw counts of the vectorizer,\n",
    "             `counts_df` a dataframe of the counts where the index is the text ids and the columns are the tokens,\n",
    "             `stop_words` an updated list of stop words\n",
    "    \"\"\"\n",
    "\n",
    "    if vectorizer == \"tfidf\":\n",
    "        vectorizer = TfidfVectorizer(input=\"content\", lowercase=False, analyzer=analyzer,\n",
    "                                 token_pattern=r\"(?u)\\b\\w+\\b\", ngram_range=ngram_range,\n",
    "                                 max_df=max_df, min_df=min_df, max_features=max_features, stop_words=stop_words)\n",
    "    elif vectorizer == \"count\":\n",
    "        vectorizer = CountVectorizer(input=\"content\", lowercase=False, analyzer=analyzer,\n",
    "                                 token_pattern=r\"(?u)\\b\\w+\\b\", ngram_range=ngram_range,\n",
    "                                 max_df=max_df, min_df=min_df, max_features=max_features, stop_words=stop_words,\n",
    "                                 binary=True)\n",
    "\n",
    "    counts = vectorizer.fit_transform(corpus[\"Text\"].tolist()).toarray()\n",
    "    stop_words = vectorizer.stop_words_\n",
    "\n",
    "    # saving the vocab used for vectorization, and switching the dictionary so that the feature index is the key\n",
    "    vocab = vectorizer.vocabulary_\n",
    "    switched_vocab = {value: key for key, value in vocab.items()}\n",
    "    # adding the vocab words to the counts dataframe for easier viewing.\n",
    "    column_names = []\n",
    "    x = 0\n",
    "    while x < len(switched_vocab):\n",
    "        column_names.append(switched_vocab[x])\n",
    "        x += 1\n",
    "\n",
    "    counts_df = pd.DataFrame(counts, index=corpus.index, columns=column_names)\n",
    "\n",
    "    return (counts, counts_df, stop_words)\n",
    "\n",
    "# calculating distances between vectorized documents\n",
    "\n",
    "def distance_calculator(counts, metric, text_ids):\n",
    "    \"\"\"\n",
    "    Converts a term-document matrix to a text similarity matrix.\n",
    "    :param counts: the raw counts from the `vectorize` function.\n",
    "    :param metric: the metric by which to calculate the distances between the texts in the corpus.\n",
    "                   Valid metrics are:\n",
    "                   ‘braycurtis’, ‘canberra’, ‘chebyshev’, ‘cityblock’, ‘correlation’, ‘cosine’,\n",
    "                   ‘dice’, ‘euclidean’, ‘hamming’, ‘jaccard’, ‘jensenshannon’, ‘kulczynski1’,\n",
    "                   ‘mahalanobis’, ‘matching’, ‘minkowski’, ‘rogerstanimoto’, ‘russellrao’,\n",
    "                   ‘seuclidean’, ‘sokalmichener’, ‘sokalsneath’, ‘sqeuclidean’, ‘yule’.\n",
    "    :param text_ids: list of unique text_ids.\n",
    "    :return: a dataframe matrix of distance between texts.\n",
    "    \"\"\"\n",
    "    return pd.DataFrame(squareform(pdist(counts, metric=metric)), index=text_ids, columns=text_ids)\n",
    "\n",
    "# reducing dimensions with pca or tsne\n",
    "\n",
    "def reduce_dimensions_pca(df, metadata):\n",
    "    \"\"\"\n",
    "    Reduces multidimensional data into two dimensions using PCA.\n",
    "    :param df: dataframe holding the dimensions to reduce. All columns should include numerical values only.\n",
    "               The dataframe's index should hold the unique text ids.\n",
    "    :param metadata: the rest of the metadata in the corpus, to help visualize the resulting clusters in meaningful ways.\n",
    "                     The metadata's index should hold the unique text ids.\n",
    "    :return: a dataframe with the coordinates of the two remaining dimensions on all other columns from the metadata.\n",
    "    \"\"\"\n",
    "    pca = PCA(n_components=2)\n",
    "    reduced_data = pca.fit_transform(df)\n",
    "    reduced_df = pd.DataFrame(data=reduced_data, index=df.index, columns=[\"component 1\", \"component 2\"])\n",
    "    reduced_df_metadata = metadata.join(reduced_df)\n",
    "    return reduced_df_metadata\n",
    "\n",
    "def reduce_dimensions_tsne(df, perplexity, n_iter, metric, metadata):\n",
    "    \"\"\"\n",
    "    Reduces multidimensional data into two dimensions using TSNE.\n",
    "    See full documentation of sklearn's TSNE on:\n",
    "    https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html\n",
    "    :param df: dataframe holding the dimensions to reduce. All columns should include numerical values only.\n",
    "               The dataframe's index should hold the unique text ids.\n",
    "    :param perplexity: perplexity is a measure the weighs the importance of nearby versus distant points when creating a lower-dimension mapping.\n",
    "                       t-SNE first converts the distances between points into conditional probabilities that represent similarities,\n",
    "                       using Gaussian probability distributions.\n",
    "                       The perplexity parameter influences the variance used to compute these probabilities.\n",
    "                       A higher perplexity leads to a broader Gaussian that considers a larger number of neighbors when assessing similarity.\n",
    "                       Lower perplexity puts more focus on the local structure and considers fewer neighbors.\n",
    "                       A good perplexity depends greatly on dataset size and density.\n",
    "                       The documentation recommends a value between 5 and 50.\n",
    "                       We recommend to start with the square root of the length of the corpus.\n",
    "    :param n_iter: maximum number of iterations for optimization.\n",
    "    :param metric: the metric to be used when calculating distances between vectors.\n",
    "                   Valid metrics are:\n",
    "                   ‘braycurtis’, ‘canberra’, ‘chebyshev’, ‘cityblock’, ‘correlation’, ‘cosine’,\n",
    "                   ‘dice’, ‘euclidean’, ‘hamming’, ‘jaccard’, ‘jensenshannon’, ‘kulczynski1’,\n",
    "                   ‘mahalanobis’, ‘matching’, ‘minkowski’, ‘rogerstanimoto’, ‘russellrao’,\n",
    "                   ‘seuclidean’, ‘sokalmichener’, ‘sokalsneath’, ‘sqeuclidean’, ‘yule’.\n",
    "    :param metadata: the rest of the metadata in the corpus, to help visualize the resulting clusters in meaningful ways.\n",
    "                     The metadata's index should hold the unique text ids.\n",
    "    :return: a dataframe with the coordinates of the two remaining dimensions on all other columns from the metadata.\n",
    "    \"\"\"\n",
    "    tsne = TSNE(n_components=2, perplexity=perplexity, n_iter=n_iter, metric=metric, init=\"pca\", random_state=42)\n",
    "    reduced_data = tsne.fit_transform(df)\n",
    "    reduced_df = pd.DataFrame(data=reduced_data, index=df.index, columns=[\"component 1\", \"component 2\"])\n",
    "    reduced_df_metadata = metadata.join(reduced_df)\n",
    "    return reduced_df_metadata"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9d1e4c71",
   "metadata": {},
   "source": [
    "# Main"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "5c95f5ab",
   "metadata": {},
   "outputs": [],
   "source": [
    "# upload text CSVs\n",
    "corpus = upload_corpus_csv(\"land_sale_annotated\")\n",
    "corpus.extend(upload_corpus_csv(\"slave_sale_annotated\"))\n",
    "corpus.extend(upload_corpus_csv(\"unknown_sale_annotated\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "6296c6fc",
   "metadata": {},
   "outputs": [],
   "source": [
    "# create metadata file with a new column for visualizing the type of sale document\n",
    "land_sale = ['lease document',\n",
    "             'lease document (field)',\n",
    "             'sales document (field)',\n",
    "             'sales document (field, person)',\n",
    "             'sales document (garden)',\n",
    "             'sales document (house)',\n",
    "             'sales document (inheritance)',\n",
    "             'sales document (plot)']\n",
    "slave_sale = ['sales document (duplicate)',\n",
    "              'sales document (person)',\n",
    "              'sales document (person, marriage?)',\n",
    "              'sales document (person, restricted)']\n",
    "unknown_sale = ['sales document']\n",
    "\n",
    "df = pd.read_csv(\"NA_archival_texts_metadata_050724.csv\",\n",
    "                 encoding=\"utf-8\",\n",
    "                 index_col=\"ID\").fillna(\"\")\n",
    "\n",
    "df[\"sale_type\"] = df[\"subgenre\"].where(~df[\"subgenre\"].isin(land_sale), other=\"Land Sale\")\n",
    "df[\"sale_type\"] = df[\"sale_type\"].where(~df[\"subgenre\"].isin(slave_sale), other=\"Slave Sale\")\n",
    "df[\"sale_type\"] = df[\"sale_type\"].where(~df[\"subgenre\"].isin(unknown_sale), other=\"Unknown Sale\")\n",
    "\n",
    "# add processed texts to metadata\n",
    "text_dict = get_segmented_unicode_texts(corpus, break_perc=.25, mask=True)\n",
    "df = add_texts_dict_to_dataframe(df, text_dict)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "3d4421be",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\user\\anaconda3\\envs\\stylometry\\lib\\site-packages\\sklearn\\manifold\\_t_sne.py:810: FutureWarning: The default learning rate in TSNE will change from 200.0 to 'auto' in 1.2.\n",
      "  warnings.warn(\n",
      "C:\\Users\\user\\anaconda3\\envs\\stylometry\\lib\\site-packages\\sklearn\\manifold\\_t_sne.py:996: FutureWarning: The PCA initialization in TSNE will change to have the standard deviation of PC1 equal to 1e-4 in 1.2. This will ensure better convergence.\n",
      "  warnings.warn(\n"
     ]
    }
   ],
   "source": [
    "# vectorize and reduce dimensions\n",
    "final_df = df[df[\"Text_length_partial\"]>=3]\n",
    "counts, counts_df, stop_words = vectorize(vectorizer=\"tfidf\", corpus=final_df)\n",
    "matrix = distance_calculator(counts, \"cosine\", final_df.index)\n",
    "reduced_tsne = reduce_dimensions_tsne(matrix,\n",
    "                                      perplexity=matrix.shape[0]**0.5,\n",
    "                                      n_iter=5000,\n",
    "                                      metric=\"euclidean\",\n",
    "                                      metadata=final_df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "1c627d49",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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Sale Document Corpus\"}},                        {\"responsive\": true}                    ).then(function(){\n",
       "                            \n",
       "var gd = document.getElementById('c2712ef3-d85a-4b21-8d41-a8bf183f466a');\n",
       "var x = new MutationObserver(function (mutations, observer) {{\n",
       "        var display = window.getComputedStyle(gd).display;\n",
       "        if (!display || display === 'none') {{\n",
       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
       "            observer.disconnect();\n",
       "        }}\n",
       "}});\n",
       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
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       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
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      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# create figure\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "import matplotlib.colors as mcolors\n",
    "\n",
    "# Get colormap\n",
    "cmap = plt.get_cmap('tab20')  # This is a colormap with 10 colors\n",
    "\n",
    "# Create a list of colors from the colormap\n",
    "colors = [mcolors.rgb2hex(cmap(i)) for i in range(cmap.N)]\n",
    "\n",
    "region_order = [\"Kuyunjik (Nineveh)\", \"Nimrud (Kalhu)\", \"Qalat Sherqat (Assur)\",\n",
    "                \"Balawat (Imgur-Enlil)\", \"Dur-Katlimmu\", \"Western periphery\"]\n",
    "reduced_tsne['region-tsne'] = pd.Categorical(reduced_tsne['region-tsne'], categories=region_order, ordered=True)\n",
    "reduced_tsne = reduced_tsne.sort_values(by='region-tsne')\n",
    "\n",
    "colors = ['#A25FAC', '#5F8AEE', '#64D380', '#FFF56A', '#FF8D00', '#E50000']\n",
    "\n",
    "fig = px.scatter(reduced_tsne, x=\"component 1\", y=\"component 2\",\n",
    "                 color=\"region-tsne\", #symbol=\"sale_type\",\n",
    "                 color_discrete_sequence=colors, size=reduced_tsne[\"Text_length_partial\"].astype(int),\n",
    "                 title=\"NA Sale Document Corpus\",\n",
    "                 hover_data=[\"subgenre\", \"project\", \"date_for_viz\", reduced_tsne.index, \"Text_length_partial\", \"Text_length_full\"]\n",
    "                 )\n",
    "fig.update_traces(marker=dict(line=dict(width=1, color='black')))\n",
    "\n",
    "fig.update_layout(\n",
    "    legend_title_text='Provenience',  # Change the legend heading\n",
    "    xaxis_title='',  # Remove x-axis label\n",
    "    yaxis_title=''   # Remove y-axis label\n",
    ")\n",
    "\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "16ba6b4d",
   "metadata": {},
   "outputs": [],
   "source": []
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