utils.py

# coding=utf-8
import numpy as np
import pandas as pd
import os
import seaborn as sns
from typing import Tuple
from torch.utils.data import Dataset, DataLoader
from transformers import BertTokenizerFast, BertTokenizer, BertForTokenClassification
import torch
import torch.nn.functional as F
import seaborn as sns
import matplotlib.pyplot as plt
from tqdm import tqdm
import json
from collections import Counter
import torch.nn as nn
from sklearn.preprocessing import LabelEncoder
import pickle
from LAC import LAC


def build_bsc_config(

    atten_type="local-g",

    max_pred_len=60,

    batch_size=256,

    n_epochs=1000,

    n_folds=5,

):
    return {
        "model_pretrained": "bert-base-chinese",
        "lr": 1e-3,
        "max_grad_norm": 10,
        "n_epochs": n_epochs,
        "n_folds": n_folds,
        "dataset": "BSC",
        "atten_type": atten_type,
        "batch_size": batch_size,
        "max_sn_len": 27,
        "max_sp_len": 40,
        "norm_type": "z-score",
        "earlystop_patience": 20,
        "max_pred_len": max_pred_len,
    }


def build_celer_config(

    atten_type="local-g",

    max_pred_len=60,

    batch_size=256,

    n_epochs=1000,

    n_folds=5,

):
    return {
        "model_pretrained": "bert-base-cased",
        "lr": 1e-3,
        "max_grad_norm": 10,
        "n_epochs": n_epochs,
        "n_folds": n_folds,
        "dataset": "celer",
        "atten_type": atten_type,
        "batch_size": batch_size,
        "max_sn_len": 24,
        "max_sn_token": 35,
        "max_sp_len": 52,
        "max_sp_token": 395,
        "norm_type": "z-score",
        "earlystop_patience": 20,
        "max_pred_len": max_pred_len,
    }


def build_label_encoder(cf):
    le = LabelEncoder()
    le.fit(np.append(np.arange(-cf["max_sn_len"] + 3, cf["max_sn_len"] - 1), cf["max_sn_len"] - 1))
    return le


# Raw text to tokenised inputs for both BSC and CELER
def text_to_bsc_inputs(sn_str, tokenizer, cf, device="cpu"):
    lac = LAC(mode="seg")
    tokens = tokenizer.encode_plus(
        sn_str,
        add_special_tokens=True,
        max_length=cf["max_sn_len"],
        padding="max_length",
    )

    sn_input_ids = torch.tensor([tokens["input_ids"]], device=device)
    sn_mask = torch.tensor([tokens["attention_mask"]], dtype=torch.float32, device=device)

    sn_word_len = compute_BSC_word_length_for_input(sn_str, lac)
    sn_word_len = pad_seq_with_nan([sn_word_len], max_len=cf["max_sn_len"], dtype=np.float32)

    # Load precomputed BSC statistics for feature normalization.
    path = os.path.join(os.path.dirname(__file__), "Data", "feature_norm_BSC.pickle")
    with open(path, "rb") as file_to_read:
        loaded_dictionary = pickle.load(file_to_read)
    sn_word_len_mean = loaded_dictionary["sn_word_len_mean"].numpy()
    sn_word_len_std = loaded_dictionary["sn_word_len_std"].numpy()

    sn_word_len = (sn_word_len - sn_word_len_mean) / sn_word_len_std
    sn_word_len = np.nan_to_num(sn_word_len)
    sn_word_len = torch.tensor(sn_word_len, dtype=torch.float32, device=device)

    return sn_input_ids, sn_mask, sn_word_len


def text_to_celer_inputs(sn_str, tokenizer, cf, device="cpu"):
    text = sn_str.split()

    tokens = tokenizer(
        [tokenizer.cls_token, *text, tokenizer.sep_token],
        add_special_tokens=False,
        max_length=cf["max_sn_token"],
        padding="max_length",
        is_split_into_words=True,
    )

    sn_input_ids = torch.tensor([tokens["input_ids"]], device=device)
    sn_mask = torch.tensor([tokens["attention_mask"]], dtype=torch.float32, device=device)

    word_ids_sn = tokens.word_ids()
    word_ids_sn = [val if val is not None else np.nan for val in word_ids_sn]
    word_ids_sn = torch.tensor([word_ids_sn], dtype=torch.float32, device=device)

    word_lengths = np.asarray([len(t) for t in text], dtype=np.float32)
    sn_word_len = compute_word_length_celer(word_lengths)
    sn_word_len = pad_seq_with_nan([sn_word_len], max_len=cf["max_sn_len"], dtype=np.float32)

    # Load precomputed CELER statistics for feature normalization.
    path = os.path.join(os.path.dirname(__file__), "Data", "feature_norm_celer.pickle")
    with open(path, "rb") as file_to_read:
        loaded_dictionary = pickle.load(file_to_read)
    sn_word_len_mean = float(loaded_dictionary["sn_word_len_mean"])
    sn_word_len_std = float(loaded_dictionary["sn_word_len_std"])

    sn_word_len = (sn_word_len - sn_word_len_mean) / sn_word_len_std
    sn_word_len = np.nan_to_num(sn_word_len)
    sn_word_len = torch.tensor(sn_word_len, dtype=torch.float32, device=device)

    return sn_input_ids, sn_mask, word_ids_sn, sn_word_len


def load_bsc() -> Tuple[pd.DataFrame, ...]:
    """

    :return: word info dataframe, part-of-speech info, eye movements

    """
    bsc_path = "./Data/beijing-sentence-corpus/"
    info_path = os.path.join(bsc_path, "BSC.Word.Info.v2.xlsx")
    bsc_emd_path = os.path.join(bsc_path, "BSC.EMD/BSC.EMD.txt")
    word_info_df = pd.read_excel(info_path, "word")
    pos_info_df = pd.read_excel(info_path, header=None)
    eyemovement_df = pd.read_csv(bsc_emd_path, delimiter="\t")
    return word_info_df, pos_info_df, eyemovement_df


def load_corpus(corpus, task=None):
    if corpus == "BSC":
        # load word data, POS data, EM data
        word_info_df, pos_info_df, eyemovement_df = load_bsc()
        return word_info_df, pos_info_df, eyemovement_df
    elif corpus == "celer":
        eyemovement_df = pd.read_csv("./Data/celer/data_v2.0/sent_fix.tsv", delimiter="\t")
        eyemovement_df["CURRENT_FIX_INTEREST_AREA_LABEL"] = (
            eyemovement_df.CURRENT_FIX_INTEREST_AREA_LABEL.replace("\t(.*)", "", regex=True)
        )
        word_info_df = pd.read_csv("./Data/celer/data_v2.0/sent_ia.tsv", delimiter="\t")
        word_info_df["IA_LABEL"] = word_info_df.IA_LABEL.replace("\t(.*)", "", regex=True)
        return word_info_df, None, eyemovement_df


def compute_BSC_word_length(sn_df):
    word_len = sn_df.LEN.values
    wl_list = []
    for wl in word_len:
        wl_list.extend([wl] * wl)
    arr = np.asarray(wl_list, dtype=np.float32)
    # length of a punctuation is 0, plus an epsilon to avoid division output inf
    arr[arr == 0] = 1 / (0 + 0.5)
    arr[arr != 0] = 1 / (arr[arr != 0])
    return arr


def compute_BSC_word_length_for_input(sentence, lac):
    word_string = lac.run(sentence)
    # print(word_string)
    word_len = [len(i) for i in word_string]
    wl_list = []
    for wl in word_len:
        wl_list.extend([wl] * wl)
    arr = np.asarray(wl_list, dtype=np.float32)
    # length of a punctuation is 0, plus an epsilon to avoid division output inf
    arr[arr == 0] = 1 / (0 + 0.5)
    arr[arr != 0] = 1 / (arr[arr != 0])
    return arr


def pad_seq(seqs, max_len, pad_value, dtype=np.compat.long):
    padded = np.full((len(seqs), max_len), fill_value=pad_value, dtype=dtype)
    for i, seq in enumerate(seqs):
        padded[i, 0] = 0
        padded[i, 1 : (len(seq) + 1)] = seq
        if pad_value != 0:
            padded[i, len(seq) + 1] = pad_value - 1

    return padded


def pad_seq_with_nan(seqs, max_len, dtype=np.compat.long):
    padded = np.full((len(seqs), max_len), fill_value=np.nan, dtype=dtype)
    for i, seq in enumerate(seqs):
        padded[i, 1 : (len(seq) + 1)] = seq
    return padded


def _process_BSC_corpus(sn_list, reader_list, word_info_df, eyemovement_df, tokenizer, cf):
    """

    SN_token_embedding   <CLS>, bla, bla, <SEP>

    SP_token_embedding   <CLS>, bla, bla, <SEP>

    SP_ordinal_pos 0, bla, bla, max_sp_len

    SP_fix_dur     0, bla, bla, 0

    SN_len         original sentence length without start and end tokens

    """
    SN_input_ids, SN_attention_mask, SN_WORD_len = [], [], []
    SP_input_ids, SP_attention_mask = [], []
    SP_ordinal_pos, SP_landing_pos, SP_fix_dur = [], [], []
    sub_id_list = []
    for sn_id in sn_list:
        # print('sub_id:', sub_id)
        # process sentence sequence
        sn_df = eyemovement_df[eyemovement_df.sn == sn_id]
        sn = word_info_df[word_info_df.SN == sn_id]
        sn_str = "".join(sn.WORD.values)
        sn_word_len = compute_BSC_word_length(sn)

        # tokenization and padding
        tokenizer.padding_side = "right"
        tokens = tokenizer.encode_plus(
            sn_str,
            add_special_tokens=True,
            truncation=True,
            max_length=cf["max_sn_len"],
            padding="max_length",
            return_attention_mask=True,
        )
        encoded_sn = tokens["input_ids"]
        mask_sn = tokens["attention_mask"]

        # process fixation sequence
        for sub_id in reader_list:
            sub_df = sn_df[sn_df.id == sub_id]
            if len(sub_df) == 0:
                # no scanpath data found for the subject
                continue

            # last fixation go back to the first character with fl = 0 -- seems to be outlier point? remove
            if sub_df.iloc[-1].wn == 1 and sub_df.iloc[-1].fl == 0:
                sub_df = sub_df.iloc[:-1]

            sp_word_pos, sp_fix_loc, sp_fix_dur = (
                sub_df.wn.values,
                sub_df.fl.values,
                sub_df.dur.values,
            )
            sp_landing_pos_char = np.modf(sp_fix_loc)[0]
            SP_landing_pos.append(sp_landing_pos_char)

            # Convert word-based ordinal positions to token(character)-based ordinal positions
            # When the fixated word index is less than 0, set it to 0
            sp_fix_loc = np.where(sp_fix_loc < 0, 0, sp_fix_loc)
            sp_ordinal_pos = [
                np.sum(sn[sn.NW < value].LEN) + np.ceil(sp_fix_loc[count] + 1e-10)
                for count, value in enumerate(sp_word_pos)
            ]
            SP_ordinal_pos.append(sp_ordinal_pos)
            SP_fix_dur.append(sp_fix_dur)

            # tokenization and padding for scanpath, i.e. fixated word sequence
            sp_token = [sn_str[int(i - 1)] for i in sp_ordinal_pos]
            sp_token_str = "[CLS]" + "".join(sp_token) + "[SEP]"
            sp_tokens = tokenizer.encode_plus(
                sp_token_str,
                add_special_tokens=False,
                truncation=True,
                max_length=cf["max_sp_len"],
                padding="max_length",
                return_attention_mask=True,
            )
            encoded_sp = sp_tokens["input_ids"]
            mask_sp = sp_tokens["attention_mask"]
            SP_input_ids.append(encoded_sp)
            SP_attention_mask.append(mask_sp)

            # sentence information
            SN_input_ids.append(encoded_sn)
            SN_attention_mask.append(mask_sn)
            SN_WORD_len.append(sn_word_len)
            sub_id_list.append(sub_id)

    # padding for batch computation
    SP_ordinal_pos = pad_seq(SP_ordinal_pos, max_len=(cf["max_sp_len"]), pad_value=cf["max_sn_len"])
    SP_fix_dur = pad_seq(SP_fix_dur, max_len=(cf["max_sp_len"]), pad_value=0)
    SP_landing_pos = pad_seq(SP_landing_pos, cf["max_sp_len"], pad_value=0, dtype=np.float32)
    SN_WORD_len = pad_seq_with_nan(SN_WORD_len, cf["max_sn_len"], dtype=np.float32)

    # assign type
    SN_input_ids = np.asarray(SN_input_ids, dtype=np.int64)
    SN_attention_mask = np.asarray(SN_attention_mask, dtype=np.float32)
    SP_input_ids = np.asarray(SP_input_ids, dtype=np.int64)
    SP_attention_mask = np.asarray(SP_attention_mask, dtype=np.float32)
    sub_id_list = np.asarray(sub_id_list, dtype=np.int64)

    data = {
        "SN_input_ids": SN_input_ids,
        "SN_attention_mask": SN_attention_mask,
        "SN_WORD_len": SN_WORD_len,
        "SP_input_ids": SP_input_ids,
        "SP_attention_mask": SP_attention_mask,
        "SP_ordinal_pos": np.array(SP_ordinal_pos),
        "SP_landing_pos": np.array(SP_landing_pos),
        "SP_fix_dur": np.array(SP_fix_dur),
        "sub_id": sub_id_list,
    }

    return data


class BSCdataset(Dataset):
    """Return BSC dataset."""

    def __init__(self, word_info_df, eyemovement_df, cf, reader_list, sn_list, tokenizer):
        self.data = _process_BSC_corpus(
            sn_list, reader_list, word_info_df, eyemovement_df, tokenizer, cf
        )

    def __len__(self):
        return len(self.data["SN_input_ids"])

    def __getitem__(self, idx):
        sample = {}
        sample["sn_input_ids"] = self.data["SN_input_ids"][idx, :]
        sample["sn_attention_mask"] = self.data["SN_attention_mask"][idx, :]
        sample["sn_word_len"] = self.data["SN_WORD_len"][idx, :]

        sample["sp_input_ids"] = self.data["SP_input_ids"][idx, :]
        sample["sp_attention_mask"] = self.data["SP_attention_mask"][idx, :]

        sample["sp_pos"] = self.data["SP_ordinal_pos"][idx, :]
        sample["sp_fix_dur"] = self.data["SP_fix_dur"][idx, :]
        sample["sp_landing_pos"] = self.data["SP_landing_pos"][idx, :]

        sample["sub_id"] = self.data["sub_id"][idx]

        return sample


def calculate_mean_std(dataloader, feat_key, padding_value=0, scale=1):
    # calculate mean
    total_sum = 0
    total_num = 0
    for batchh in dataloader:
        batchh.keys()
        feat = batchh[feat_key] / scale
        feat = torch.nan_to_num(feat)
        total_num += len(feat.view(-1).nonzero())
        total_sum += feat.sum()
    feat_mean = total_sum / total_num
    # calculate std
    sum_of_squared_error = 0
    for batchh in dataloader:
        batchh.keys()
        feat = batchh[feat_key] / scale
        feat = torch.nan_to_num(feat)
        mask = ~torch.eq(feat, padding_value)
        sum_of_squared_error += (((feat - feat_mean).pow(2)) * mask).sum()
    feat_std = torch.sqrt(sum_of_squared_error / total_num)
    return feat_mean, feat_std


def load_label(sp_pos, cf, labelencoder, device):
    # prepare label and mask
    pad_mask = torch.eq(sp_pos[:, 1:], cf["max_sn_len"])
    end_mask = torch.eq(sp_pos[:, 1:], cf["max_sn_len"] - 1)
    mask = pad_mask + end_mask
    sac_amp = sp_pos[:, 1:] - sp_pos[:, :-1]
    label = sp_pos[:, 1:] * mask + sac_amp * ~mask
    label = (
        torch.where(label > cf["max_sn_len"] - 1, cf["max_sn_len"] - 1, label)
        .to("cpu")
        .detach()
        .numpy()
    )
    label = labelencoder.transform(label.reshape(-1)).reshape(label.shape[0], label.shape[1])
    label = torch.from_numpy(label).long().to(device)
    pad_mask = pad_mask.to(device)
    return pad_mask, label


def likelihood(pred, label, mask):
    if torch.is_tensor(label):
        label = label.detach().to("cpu").numpy()
    if torch.is_tensor(mask):
        mask = mask.detach().to("cpu").numpy()
    # test
    # res = F.nll_loss(torch.tensor(pred), torch.tensor(label))
    label = one_hot_encode(label, pred.shape[1])
    res = np.sum(np.multiply(pred, label), axis=1)
    res = np.sum(res * ~mask) / np.sum(~mask)
    return res


def eval_log_llh(dnn_out, label, pad_mask):
    res = []
    dnn_out = np.log2(dnn_out + 1e-10)
    # For each scanpath calculate the likelihood and then find the average
    for sp_indx in range(dnn_out.shape[0]):
        out = likelihood(dnn_out[sp_indx, :, :], label[sp_indx, :], pad_mask[sp_indx, :])
        res.append(out)

    return res


def prepare_scanpath(sp_dnn, sn_len, sp_human, cf):
    max_sp_len = sp_dnn.shape[1]
    sp_human = sp_human.detach().to("cpu").numpy()

    # stop_indx = [np.where(sp_dnn[i,:]==(sn_len[i]+1))[0][0] for i in range(sp_dnn.shape[0])]
    # Find the number "sn_len+1" -> the end point
    stop_indx = []
    for i in range(sp_dnn.shape[0]):
        stop = np.where(sp_dnn[i, :] == (sn_len[i] + 1))[0]
        if (
            len(stop) == 0
        ):  # no end point can be find -> exceeds the maximum length of the generated scanpath
            stop_indx.append(max_sp_len - 1)
        else:
            stop_indx.append(stop[0])

    # Truncating data after the end point
    sp_dnn_cut = [sp_dnn[i][: stop_indx[i] + 1] for i in range(sp_dnn.shape[0])]
    # replace the last teminal number to cf["max_sn_len"]-1, keep the same as the human scanpath label
    for i in range(len(sp_dnn_cut)):
        sp_dnn_cut[i][-1] = cf["max_sn_len"] - 1

    # process the human scanpath data, truncating data after the end point
    stop_indx = [
        np.where(sp_human[i, :] == cf["max_sn_len"] - 1)[0][0] for i in range(sp_human.shape[0])
    ]
    sp_human_cut = [sp_human[i][: stop_indx[i] + 1] for i in range(sp_human.shape[0])]
    return sp_dnn_cut, sp_human_cut


def celer_load_native_speaker():
    sub_metadata_path = "./Data/celer/metadata.tsv"
    sub_infor = pd.read_csv(sub_metadata_path, delimiter="\t")
    native_sub_list = sub_infor[sub_infor.L1 == "English"].List.values
    return native_sub_list.tolist()


def compute_word_length_celer(arr):
    # length of a punctuation is 0, plus an epsilon to avoid division output inf
    arr = arr.astype("float64")
    arr[arr == 0] = 1 / (0 + 0.5)
    arr[arr != 0] = 1 / (arr[arr != 0])
    return arr


def _process_celer(sn_list, reader_list, word_info_df, eyemovement_df, tokenizer, cf):
    """

    SN_token_embedding   <CLS>, bla, bla, <SEP>

    SP_token_embedding       <CLS>, bla, bla, <SEP>

    SP_ordinal_pos 0, bla, bla, max_sp_len

    SP_fix_dur     0, bla, bla, 0

    """
    SN_input_ids, SN_attention_mask, SN_WORD_len, WORD_ids_sn = [], [], [], []
    SP_input_ids, SP_attention_mask, WORD_ids_sp = [], [], []
    SP_ordinal_pos, SP_landing_pos, SP_fix_dur = [], [], []
    sub_id_list = []
    for sn_id in tqdm(sn_list):
        # process sentence sequence
        sn_df = eyemovement_df[eyemovement_df.sentenceid == sn_id]
        # notice: Each sentence is recorded multiple times in file |word_info_df|.
        sn = word_info_df[word_info_df.sentenceid == sn_id]
        sn = sn[sn["list"] == sn.list.values.tolist()[0]]
        # compute word length for each word
        sn_word_len = compute_word_length_celer(sn.WORD_LEN.values)

        sn_str = sn.sentence.iloc[-1]
        # nessacery sanity check, when split sentence to words, the length of sentence should match the sentence length recorded in celer dataset
        if sn_id in [
            "1987/w7_019/w7_019.295-3",
            "1987/w7_036/w7_036.147-43",
            "1987/w7_091/w7_091.360-6",
        ]:
            # extra inverted commas at the end of the sentence
            sn_str = sn_str[:-3] + sn_str[-1:]
        if sn_id == "1987/w7_085/w7_085.200-18":
            sn_str = sn_str[:43] + sn_str[44:]
        sn_len = len(sn_str.split())

        # tokenization and padding
        tokenizer.padding_side = "right"
        sn_str = "[CLS]" + " " + sn_str + " " + "[SEP]"
        # pre-tokenized input
        tokens = tokenizer.encode_plus(
            sn_str.split(),
            add_special_tokens=False,
            truncation=False,
            max_length=cf["max_sn_token"],
            padding="max_length",
            return_attention_mask=True,
            is_split_into_words=True,
        )
        encoded_sn = tokens["input_ids"]
        mask_sn = tokens["attention_mask"]
        # use offset mapping to determine if two tokens are in the same word.
        # index start from 0, CLS -> 0 and SEP -> last index
        word_ids_sn = tokens.word_ids()
        word_ids_sn = [val if val is not None else np.nan for val in word_ids_sn]

        # process fixation sequence
        for sub_id in reader_list:
            sub_df = sn_df[sn_df.list == sub_id]
            # remove fixations on non-words
            sub_df = sub_df.loc[sub_df.CURRENT_FIX_INTEREST_AREA_LABEL != "."]
            if len(sub_df) == 0:
                # no scanpath data found for the subject
                continue

            # prepare decoder input and output
            sp_word_pos, sp_fix_loc, sp_fix_dur = (
                sub_df.CURRENT_FIX_INTEREST_AREA_ID.values,
                sub_df.CURRENT_FIX_NEAREST_INTEREST_AREA_DISTANCE.values,
                sub_df.CURRENT_FIX_DURATION.values,
            )

            # dataset is noisy -> sanity check
            # 1) check if recorded fixation duration are within reasonable limits
            # Less than 50ms attempt to merge with neighbouring fixation if fixate is on the same word, otherwise delete
            outlier_indx = np.where(sp_fix_dur < 50)[0]
            if outlier_indx.size > 0:
                for out_idx in range(len(outlier_indx)):
                    outlier_i = outlier_indx[out_idx]
                    merge_flag = False

                    # outliers are commonly found in the fixation of the last record and the first record, and are removed directly
                    if outlier_i == len(sp_fix_dur) - 1 or outlier_i == 0:
                        merge_flag = True

                    else:
                        if outlier_i - 1 >= 0 and merge_flag == False:
                            # try to merge with the left fixation
                            if (
                                sub_df.iloc[outlier_i].CURRENT_FIX_INTEREST_AREA_LABEL
                                == sub_df.iloc[outlier_i - 1].CURRENT_FIX_INTEREST_AREA_LABEL
                            ):
                                sp_fix_dur[outlier_i - 1] = (
                                    sp_fix_dur[outlier_i - 1] + sp_fix_dur[outlier_i]
                                )
                                merge_flag = True

                        if outlier_i + 1 < len(sp_fix_dur) and merge_flag == False:
                            # try to merge with the right fixation
                            if (
                                sub_df.iloc[outlier_i].CURRENT_FIX_INTEREST_AREA_LABEL
                                == sub_df.iloc[outlier_i + 1].CURRENT_FIX_INTEREST_AREA_LABEL
                            ):
                                sp_fix_dur[outlier_i + 1] = (
                                    sp_fix_dur[outlier_i + 1] + sp_fix_dur[outlier_i]
                                )
                                merge_flag = True

                    sp_word_pos = np.delete(sp_word_pos, outlier_i)
                    sp_fix_loc = np.delete(sp_fix_loc, outlier_i)
                    sp_fix_dur = np.delete(sp_fix_dur, outlier_i)
                    sub_df.drop(sub_df.index[outlier_i], axis=0, inplace=True)
                    outlier_indx = outlier_indx - 1

            # 2) scanpath too long, remove outliers, speed up the inference
            if len(sp_word_pos) > 50:  # 72/10684
                continue
            # 3)scanpath too short for a normal length sentence
            if len(sp_word_pos) <= 1 and sn_len > 10:
                continue

            # 4) check landing position feature
            # assign missing value to 'nan'
            sp_fix_loc = np.where(sp_fix_loc == ".", np.nan, sp_fix_loc)
            # convert string of number of float type
            sp_fix_loc = [float(i) for i in sp_fix_loc]

            # Outliers in calculated landing positions due to lack of valid AOI data, assign to 'nan'
            if np.nanmax(sp_fix_loc) > 35:
                missing_idx = np.where(np.array(sp_fix_loc) > 5)[0]
                for miss in missing_idx:
                    if sub_df.iloc[miss].CURRENT_FIX_INTEREST_AREA_LEFT in [
                        "NONE",
                        "BEFORE",
                        "AFTER",
                        "BOTH",
                    ]:
                        sp_fix_loc[miss] = np.nan
                    else:
                        print(
                            "Landing position calculation error. Unknown cause, needs to be checked"
                        )

            sp_ordinal_pos = sp_word_pos.astype(int)
            SP_ordinal_pos.append(sp_ordinal_pos)
            SP_fix_dur.append(sp_fix_dur)
            SP_landing_pos.append(sp_fix_loc)

            sp_token = [sn_str.split()[int(i)] for i in sp_ordinal_pos]
            sp_token_str = "[CLS]" + " " + " ".join(sp_token) + " " + "[SEP]"

            # tokenization and padding for scanpath, i.e. fixated word sequence
            sp_tokens = tokenizer.encode_plus(
                sp_token_str.split(),
                add_special_tokens=False,
                truncation=False,
                max_length=cf["max_sp_token"],
                padding="max_length",
                return_attention_mask=True,
                is_split_into_words=True,
            )
            encoded_sp = sp_tokens["input_ids"]
            mask_sp = sp_tokens["attention_mask"]
            # index start from 0, CLS -> 0 and SEP -> last index
            word_ids_sp = sp_tokens.word_ids()
            word_ids_sp = [val if val is not None else np.nan for val in word_ids_sp]
            SP_input_ids.append(encoded_sp)
            SP_attention_mask.append(mask_sp)
            WORD_ids_sp.append(word_ids_sp)

            # sentence information
            SN_input_ids.append(encoded_sn)
            SN_attention_mask.append(mask_sn)
            SN_WORD_len.append(sn_word_len)
            WORD_ids_sn.append(word_ids_sn)
            sub_id_list.append(int(sub_id))

    # padding for batch computation
    SP_ordinal_pos = pad_seq(SP_ordinal_pos, max_len=(cf["max_sp_len"]), pad_value=cf["max_sn_len"])
    SP_fix_dur = pad_seq(SP_fix_dur, max_len=(cf["max_sp_len"]), pad_value=0)
    SP_landing_pos = pad_seq(SP_landing_pos, cf["max_sp_len"], pad_value=0, dtype=np.float32)
    SN_WORD_len = pad_seq_with_nan(SN_WORD_len, cf["max_sn_len"], dtype=np.float32)

    # assign type
    SN_input_ids = np.asarray(SN_input_ids, dtype=np.int64)
    SN_attention_mask = np.asarray(SN_attention_mask, dtype=np.float32)
    SP_input_ids = np.asarray(SP_input_ids, dtype=np.int64)
    SP_attention_mask = np.asarray(SP_attention_mask, dtype=np.float32)
    sub_id_list = np.asarray(sub_id_list, dtype=np.int64)
    WORD_ids_sn = np.asarray(WORD_ids_sn)
    WORD_ids_sp = np.asarray(WORD_ids_sp)

    data = {
        "SN_input_ids": SN_input_ids,
        "SN_attention_mask": SN_attention_mask,
        "SN_WORD_len": SN_WORD_len,
        "WORD_ids_sn": WORD_ids_sn,
        "SP_input_ids": SP_input_ids,
        "SP_attention_mask": SP_attention_mask,
        "WORD_ids_sp": WORD_ids_sp,
        "SP_ordinal_pos": np.array(SP_ordinal_pos),
        "SP_landing_pos": np.array(SP_landing_pos),
        "SP_fix_dur": np.array(SP_fix_dur),
        "sub_id": sub_id_list,
    }

    return data


class celerdataset(Dataset):
    """Return celer dataset."""

    def __init__(self, word_info_df, eyemovement_df, cf, reader_list, sn_list, tokenizer):

        self.data = _process_celer(
            sn_list, reader_list, word_info_df, eyemovement_df, tokenizer, cf
        )

    def __len__(self):
        return len(self.data["SN_input_ids"])

    def __getitem__(self, idx):
        sample = {}
        sample["sn_input_ids"] = self.data["SN_input_ids"][idx, :]
        sample["sn_attention_mask"] = self.data["SN_attention_mask"][idx, :]
        sample["sn_word_len"] = self.data["SN_WORD_len"][idx, :]
        sample["word_ids_sn"] = self.data["WORD_ids_sn"][idx, :]

        sample["sp_input_ids"] = self.data["SP_input_ids"][idx, :]
        sample["sp_attention_mask"] = self.data["SP_attention_mask"][idx, :]
        sample["word_ids_sp"] = self.data["WORD_ids_sp"][idx, :]

        sample["sp_pos"] = self.data["SP_ordinal_pos"][idx, :]
        sample["sp_fix_dur"] = self.data["SP_fix_dur"][idx, :]
        sample["sp_landing_pos"] = self.data["SP_landing_pos"][idx, :]

        sample["sub_id"] = self.data["sub_id"][idx]

        return sample


def one_hot_encode(arr, dim):
    # one hot encode
    onehot_encoded = np.zeros((arr.shape[0], dim))
    for idx, value in enumerate(arr):
        onehot_encoded[idx, value] = 1

    return onehot_encoded


def gradient_clipping(dnn_model, clip=10):
    torch.nn.utils.clip_grad_norm_(dnn_model.parameters(), clip)