Upload Prepare_original_data.ipynb

Prepare_original_data.ipynb

@@ -0,0 +1,427 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1fc75ebf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "## datasets==2.0.0 pandas==1.4.2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c9cc126c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "import re\n",
+    "from tqdm import tqdm\n",
+    "from datasets import Dataset, DatasetDict\n",
+    "import pickle\n",
+    "import json"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2adeaf52",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_list_values(text):\n",
+    "    return text.split()\n",
+    "\n",
+    "def replc_t_n(text):\n",
+    "    return re.sub(\"\\t|\\n\", \" \", text).strip()\n",
+    "\n",
+    "def read_file(filepath, readlines=False):\n",
+    "    with open(filepath, \"r\") as f:\n",
+    "        if readlines:\n",
+    "            txt = f.readlines()\n",
+    "        else:\n",
+    "            txt = f.read()\n",
+    "    return txt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26a51547",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def split_text_on_labeled_tokens(text, labels):\n",
+    "    \"\"\"\n",
+    "    Split text on labeled token\n",
+    "\n",
+    "    :param text: input text\n",
+    "    :type text: string\n",
+    "    :param labels: token labels with position in text \n",
+    "    :type labels: list\n",
+    "    :return: list of splited text on tokens, list of entity label for each token\n",
+    "    :rtype: list, list\n",
+    "    \"\"\"\n",
+    "    ### inner function\n",
+    "    def chunk_text_labeling(text, start, end, is_ner = False):\n",
+    "        \"\"\"\n",
+    "        Labeling part of text by text position\n",
+    "\n",
+    "        :param text: input text\n",
+    "        :type text: string\n",
+    "        :param start: start position of entity in text \n",
+    "        :type start: int\n",
+    "        :param end: end position of entity in text \n",
+    "        :type end: int\n",
+    "        :param is_ner: part of text is named entity or not \n",
+    "        :type is_ner: bool\n",
+    "        \"\"\"\n",
+    "        chunk_iter = 0\n",
+    "        ner_chunk = text[start: end].split()\n",
+    "        for part_of_chunk in ner_chunk:\n",
+    "            split_text.append(part_of_chunk)\n",
+    "            if is_ner:\n",
+    "                if chunk_iter == 0:\n",
+    "                    ner_label.append(\"B-\"+ner)\n",
+    "                else:\n",
+    "                    ner_label.append(\"I-\"+ner)\n",
+    "                chunk_iter += 1\n",
+    "            else:\n",
+    "                ner_label.append(\"O\") \n",
+    "    ### inner function\n",
+    "                \n",
+    "    init_start = 0\n",
+    "    split_text = []\n",
+    "    ner_label = []\n",
+    "    for ner, start, end in labels:\n",
+    "\n",
+    "        if start > init_start:\n",
+    "\n",
+    "            chunk_text_labeling(text, init_start, start)        \n",
+    "            chunk_text_labeling(text, start, end, True)\n",
+    "            init_start = end\n",
+    "        else:\n",
+    "            chunk_text_labeling(text, start, end, True)\n",
+    "            init_start = end\n",
+    "    \n",
+    "    return split_text, ner_label"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0ba5da7e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def grouped_and_sort_labeled_data(annotation_file):\n",
+    "    \"\"\"\n",
+    "    Get list of entities with corresponding position in text\n",
+    "\n",
+    "    :param annotation_file: List of entities\n",
+    "    :type annotation_file: list\n",
+    "    :return: list entitiens sorted by start position in text\n",
+    "    :rtype: list\n",
+    "    \"\"\"\n",
+    "    df_ann = pd.DataFrame([get_list_values(replc_t_n(i)) for i in annotation_file if \";\" not in i]) \n",
+    "    df_ann[2] = df_ann[2].astype(\"int\")\n",
+    "    df_ann[3] = df_ann[3].astype(\"int\")\n",
+    "    grouped = df_ann.groupby([1, 2])[3].min().reset_index()\n",
+    "    \n",
+    "    return grouped.sort_values(by=2)[[1,2,3]].values"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "46fdb74b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def check_isalnum(text):\n",
+    "    return any(i.isalnum() for i in text)\n",
+    "\n",
+    "def keep_only_alnum(text):\n",
+    "    return \"\".join([i if i.isalnum() else \" \" for i in text]).strip()\n",
+    "\n",
+    "def drop_punct(seq, labels):\n",
+    "    \"\"\"\n",
+    "    Drop punctuation from labeled data\n",
+    "\n",
+    "    :param seq: List of tokens\n",
+    "    :type seq: list\n",
+    "    :param labels: List of entities\n",
+    "    :type labels: list\n",
+    "    \"\"\"\n",
+    "    new_seq = []\n",
+    "    new_labels = []\n",
+    "    for i in range(len(seq)):\n",
+    "        if seq[i].isalnum():\n",
+    "            new_seq.append(seq[i])\n",
+    "            new_labels.append(labels[i])   \n",
+    "    return new_seq, new_labels\n",
+    "\n",
+    "def drop_duplicate_tokens(seq, labels):\n",
+    "    new_seq = []\n",
+    "    new_labels = []\n",
+    "    for i in range(len(seq)):\n",
+    "        if (i != 0) & (seq[i-1] == seq[i]):\n",
+    "            continue\n",
+    "        else:\n",
+    "            new_seq.append(seq[i])\n",
+    "            new_labels.append(labels[i])\n",
+    "    return new_seq, new_labels\n",
+    "\n",
+    "def prepare_sequences(seqs, labels):\n",
+    "    clear_tokens = [keep_only_alnum(i) if check_isalnum(i) else i for i in seqs]\n",
+    "    d_p_tokens, d_p_labels = drop_punct(clear_tokens, labels)\n",
+    "    return drop_duplicate_tokens(d_p_tokens, d_p_labels)\n",
+    "    \n",
+    "\n",
+    "def map_label_to_id(ids_dict, labels):\n",
+    "    \"\"\"\n",
+    "    Convert string label to corresponding id\n",
+    "\n",
+    "    :param ids_dict: {\"age\": 0, \"event\": 1.....}\n",
+    "    :type ids_dict: dict\n",
+    "    :param labels: List of entities [\"age\", \"event\", \"O\"....]\n",
+    "    :type labels: list\n",
+    "    \"\"\"\n",
+    "    return [ids_dict[i] for i in labels]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5b735210",
+   "metadata": {},
+   "source": [
+    "### Preparing files in folders"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "23ad44bb",
+   "metadata": {},
+   "source": [
+    "#### The data have been taken from https://github.com/dialogue-evaluation/RuNNE"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1c2748fa",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "folders = [\"train\", \"test\", \"dev\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ab65dc18",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for folder in folders:\n",
+    "    base_path = f\"RuNNE/data/{folder}\"\n",
+    "    temp_folder = os.listdir(base_path)\n",
+    "    \n",
+    "    ## getting list filenames of annotation\n",
+    "    files_with_ann = [i for i in temp_folder if \".ann\" in i]\n",
+    "\n",
+    "    all_sequences = []\n",
+    "    all_labels = []\n",
+    "    \n",
+    "    for f_ann in tqdm(files_with_ann):\n",
+    "        \n",
+    "        ## getting filename for text by replaced of extension\n",
+    "        txt_file = f_ann.replace(\".ann\", \".txt\")\n",
+    "\n",
+    "        ann = read_file(base_path +\"/\"+ f_ann, readlines=True)\n",
+    "        txt = read_file(base_path +\"/\"+ txt_file)\n",
+    "        \n",
+    "        ## check len, because in dev folder there are empty files\n",
+    "        if len(ann) == 0:\n",
+    "            continue\n",
+    "        labels = grouped_and_sort_labeled_data(ann)\n",
+    "        \n",
+    "        ## splitting text on tokens and labeling each of them\n",
+    "        split_text, ner_label = split_text_on_labeled_tokens(txt, labels)\n",
+    "        seq_split_indexes = [i for i, v in enumerate(split_text) if v == \".\"]\n",
+    "        \n",
+    "        ## adding prepared data from each file to general list\n",
+    "        prev = 0\n",
+    "        for i in seq_split_indexes:\n",
+    "            \n",
+    "            short_text = split_text[prev: i]\n",
+    "            short_label = ner_label[prev: i]\n",
+    "            \n",
+    "            clear_tokens, clear_label = prepare_sequences(short_text, short_label)\n",
+    "            \n",
+    "            all_sequences.append(clear_tokens)\n",
+    "            all_labels.append(clear_label)\n",
+    "            ## we don't take into account the dots in text  \n",
+    "            prev = i+1\n",
+    "    \n",
+    "    ## save data to file for each part of splitted dataset\n",
+    "    df_folder = pd.DataFrame({\"sequences\": all_sequences, \"labels\": all_labels})\n",
+    "    with open(f'{folder}_data.pickle', 'wb') as f:\n",
+    "        pickle.dump(df_folder, f)\n",
+    "    print(f\"For folder <{folder}> prepared <{df_folder.shape[0]}> sequences\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cc61030b",
+   "metadata": {},
+   "source": [
+    "### Creating DatasetDict fro prepared data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8c24ab41",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "## load 3 dataframe and init them into transformer dataset\n",
+    "dsd = DatasetDict()\n",
+    "for folder in folders:\n",
+    "    with open(f'{folder}_data.pickle', 'rb') as f:\n",
+    "        data = pickle.load(f)\n",
+    "    dsd[folder] = Dataset.from_pandas(data)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "04e76e90",
+   "metadata": {},
+   "source": [
+    "### Creating dictionary for labels ids "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ce021634",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "## get unique entyties\n",
+    "for_df = []\n",
+    "for folder in folders:\n",
+    "    with open(f'{folder}_data.pickle', 'rb') as f:\n",
+    "        for_df.append(pickle.load(f))\n",
+    "lbls = pd.concat(for_df)[\"labels\"].values\n",
+    "\n",
+    "dd = dict()\n",
+    "ids = 0\n",
+    "for ll in lbls:\n",
+    "    for lbl in ll:\n",
+    "        if lbl not in dd:\n",
+    "            dd[lbl] = ids\n",
+    "            ids += 1\n",
+    "\n",
+    "            \n",
+    "# # count each entity\n",
+    "# countss = dict()\n",
+    "# for ll in lbls:\n",
+    "#     for lbl in ll:\n",
+    "#         if lbl not in countss:\n",
+    "#             countss[lbl] = 1\n",
+    "#         else:\n",
+    "#             countss[lbl] += 1\n",
+    "\n",
+    "# del countss[\"O\"]\n",
+    "# sorted_counts = {k: v for k, v in sorted(countss.items(), key=lambda item: item[0].split(\"-\")[1])}\n",
+    "\n",
+    "# for k, v in sorted_counts.items():\n",
+    "#     print(\"- \"+k+f\": {v}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "58000df7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "## sort mapper\n",
+    "\n",
+    "ll = [i for i in dd.keys() if i != \"O\"]            \n",
+    "ll_sort = (sorted(ll, key=lambda x: x.split(\"-\")[1]))\n",
+    "new_dd = {k: v for v, k in enumerate([\"O\"] + ll_sort)}\n",
+    "            \n",
+    "            \n",
+    "reverse_dd = {v: k for k, v in new_dd.items()}\n",
+    "with open('id_to_label_map.pickle', 'wb') as f:\n",
+    "        pickle.dump(reverse_dd, f)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b30a7098",
+   "metadata": {},
+   "source": [
+    "### Creating new column with numerical labels"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "51fd6b38",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dsd_with_ids = dsd.map(\n",
+    "    lambda x: {\"ids\": [map_label_to_id(new_dd, i) for i in x[\"labels\"]]}, batched=True, remove_columns = \"labels\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b7ecf94f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dsd_with_ids.push_to_hub(\"\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5eb5f3fa",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "hf_env",
+   "language": "python",
+   "name": "hf_env"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}