pelican-nlp 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

pelican_nlp/Nils_backup/fluency/coherence.py

@@ -0,0 +1,653 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Compute semantic and phonetic coherence metrics for VELAS fluency tasks.
+
+Algorithm Overview:
+------------------
+The script implements two main coherence metrics:
+
+1. Semantic Coherence:
+   - Uses FastText word embeddings to convert words to 300d vectors
+   - Calculates cosine similarity between word pairs
+   - Analyzes in sliding windows (e.g., 2-word, 8-word)
+   - For each window:
+     a) Creates similarity matrix of all word pairs
+     b) Computes mean and std of similarities
+     c) Aggregates across windows
+
+2. Phonetic Coherence:
+   - Converts words to IPA (International Phonetic Alphabet)
+   - Computes feature-based edit distance between phonetic transcriptions
+   - Uses same window approach as semantic coherence
+   - Normalizes distances by word length
+
+Window Analysis:
+---------------
+- Window size n (e.g., n=2 or n=8)
+- For each position i in text:
+  1. Take words[i:i+n]
+  2. Compute all pairwise similarities
+  3. Calculate window statistics
+  4. Move to next position
+- Final metrics:
+  * Mean of window means (average coherence)
+  * Std of window means (coherence variability)
+  * Mean of window stds (within-window variability)
+  * Std of window stds (variability of within-window variability)
+"""
+import os
+import re
+import time
+import logging
+from typing import List, Tuple, Dict, Union, Optional, Any
+from pathlib import Path
+from collections import Counter
+from itertools import combinations
+from concurrent.futures import ProcessPoolExecutor
+
+import numpy as np
+import pandas as pd
+import scipy
+import fasttext
+import fasttext.util
+import epitran
+import panphon
+from utils import ensure_output_dir
+from config import COHERENCE_CONFIG, RESULTS_DIR
+
+# Set up logging
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+    handlers=[
+        logging.StreamHandler(),
+        logging.FileHandler(str(RESULTS_DIR / 'coherence.log'))
+    ]
+)
+logger = logging.getLogger(__name__)
+
+# Type aliases
+Vector = np.ndarray
+Matrix = np.ndarray
+TokenList = List[str]
+VectorList = List[Vector]
+
+def preprocess(
+    in_text: str,
+    lower: bool = COHERENCE_CONFIG["preprocessing"]["lower"],
+    free_text: bool = COHERENCE_CONFIG["preprocessing"]["free_text"]
+) -> TokenList:
+    """
+    Preprocess text by tokenizing and optionally lowercasing.
+    
+    Args:
+        in_text: Input text to process
+        lower: Whether to convert to lowercase
+        free_text: If True, split on whitespace; if False, split on semicolons/commas
+    
+    Returns:
+        List of preprocessed tokens
+    """
+    # Strip leading/trailing whitespace
+    in_text = in_text.strip()
+
+    if free_text:
+        # Remove punctuation and split on whitespace
+        in_text = re.sub(r"[^\w\s]", "", in_text)
+        words = in_text.split()
+    else:
+        # Split structured text on delimiters
+        words = re.split(";|,", in_text)
+
+    # Process tokens
+    if lower:
+        processed_words = [word.lower().strip() for word in words if word.strip()]
+    else:
+        processed_words = [word.strip() for word in words if word.strip()]
+
+    return processed_words
+
+def get_vector(
+    model: Any,
+    mode: str,
+    tokens: TokenList,
+    error_messages: bool = COHERENCE_CONFIG["error_messages"]
+) -> List[Union[Vector, str]]:
+    """
+    Get vector representations for tokens.
+    
+    Args:
+        model: Either FastText model (semantic) or Epitran model (phonetic)
+        mode: Either "semantic" or "phonetic"
+        tokens: List of words to vectorize
+        error_messages: Whether to print error messages
+    
+    Returns:
+        List of vectors (semantic) or IPA transcriptions (phonetic)
+    """
+    if mode == "semantic":
+        try:
+            return [model.get_word_vector(token) for token in tokens]
+        except KeyError as e:
+            if error_messages:
+                print(f"Vector lookup error: {e}")
+            return [np.nan]
+    elif mode == "phonetic":
+        try:
+            return [model.transliterate(token) for token in tokens]
+        except KeyError as e:
+            if error_messages:
+                print(f"Phonetic transcription error: {e}")
+            return [np.nan]
+    else:
+        raise ValueError(f"Unknown mode: {mode}")
+
+def get_semantic_similarity(vec1: Vector, vec2: Vector) -> float:
+    """
+    Compute cosine similarity between two vectors.
+    
+    Args:
+        vec1: First vector
+        vec2: Second vector
+    
+    Returns:
+        Cosine similarity (1 - cosine distance)
+    """
+    try:
+        return 1 - scipy.spatial.distance.cosine(vec1, vec2)
+    except ValueError:
+        return np.nan
+
+def get_phonetic_similarity(vec1: str, vec2: str, dist: Any) -> float:
+    """
+    Compute normalized phonetic similarity using feature edit distance.
+    
+    Args:
+        vec1: First IPA transcription
+        vec2: Second IPA transcription
+        dist: Panphon distance calculator
+    
+    Returns:
+        Normalized similarity score (1 - normalized edit distance)
+    """
+    try:
+        return 1 - dist.feature_edit_distance(vec1, vec2) / max(len(vec1), len(vec2))
+    except ValueError:
+        return np.nan
+
+def wordseq(
+    tokens: TokenList,
+    vectors: Union[VectorList, List[str]],
+    mode: str,
+    dist: Optional[Any] = None,
+    word_sim: bool = False
+) -> Union[float, Tuple[float, List[Union[str, float]]]]:
+    """
+    Calculate mean similarity between consecutive words.
+    
+    Args:
+        tokens: List of original words
+        vectors: List of vector representations
+        mode: Either "semantic" or "phonetic"
+        dist: Panphon distance calculator (required for phonetic mode)
+        word_sim: If True, return word-by-word similarities
+    
+    Returns:
+        If word_sim=False: Mean similarity
+        If word_sim=True: Tuple of (mean_similarity, list of alternating words and similarities)
+    """
+    similarities = np.array([])
+    
+    for position, vec in enumerate(vectors):
+        if position == 0:
+            vec1 = vec
+            continue
+            
+        vec2 = vec
+        # Calculate similarity based on mode
+        if mode == "semantic":
+            similarity = get_semantic_similarity(vec1, vec2)
+        elif mode == "phonetic":
+            similarity = get_phonetic_similarity(vec1, vec2, dist)
+        vec1 = vec2
+
+        similarities = np.append(similarities, similarity)
+
+    mean_sim = similarities[~np.isnan(similarities)].mean()
+
+    if word_sim:
+        word_sims = [i for sublist in list(zip(tokens, np.append(similarities, np.nan))) for i in sublist][:-1]
+        return mean_sim, word_sims
+
+    return mean_sim
+
+def wordmatrix(
+    tokens: TokenList,
+    vectors: Union[VectorList, List[str]],
+    mode: str,
+    dist: Optional[Any] = None,
+    dataframe: bool = False
+) -> Union[Matrix, pd.DataFrame]:
+    """
+    Compute similarity matrix for all word pairs.
+    
+    Args:
+        tokens: List of words
+        vectors: List of vector representations
+        mode: Either "semantic" or "phonetic"
+        dist: Panphon distance calculator (required for phonetic mode)
+        dataframe: If True, return pandas DataFrame; if False, return numpy array
+    
+    Returns:
+        Similarity matrix as either numpy array or pandas DataFrame
+    """
+    vectors = np.array(vectors)
+    if mode == "semantic":
+        # Compute cosine similarity matrix
+        similarity_matrix = 1 - scipy.spatial.distance.cdist(vectors, vectors, 'cosine')
+        # Zero out upper triangle
+        upper_triangle_indices = np.triu_indices_from(similarity_matrix)
+        similarity_matrix[upper_triangle_indices] = np.nan
+    elif mode == "phonetic":
+        # Compute pairwise phonetic similarities
+        distances = [get_phonetic_similarity(i, j, dist) for (i, j) in combinations(vectors, 2)]
+        similarity_matrix = scipy.spatial.distance.squareform(distances)
+        upper_triangle_indices = np.triu_indices_from(similarity_matrix)
+        similarity_matrix[upper_triangle_indices] = np.nan
+
+    if dataframe:
+        return pd.DataFrame(similarity_matrix, index=tokens, columns=tokens)
+
+    # Return lower triangle as list of lists
+    return [list(row[:i+1]) for i, row in enumerate(similarity_matrix)]
+
+def calculate_segment_avg(
+    tokens: TokenList,
+    vectors: Union[VectorList, List[str]],
+    mode: str,
+    start_idx: int,
+    window_size: int,
+    dist: Optional[Any] = None
+) -> Tuple[float, float]:
+    """
+    Calculate average similarity for a segment of tokens.
+    
+    Args:
+        tokens: List of words
+        vectors: List of vector representations
+        mode: Either "semantic" or "phonetic"
+        start_idx: Starting index of segment
+        window_size: Size of window
+        dist: Panphon distance calculator (required for phonetic mode)
+    
+    Returns:
+        Tuple of (mean_similarity, std_similarity)
+    """
+    segment_tokens = tokens[start_idx:start_idx + window_size]
+    segment_vectors = vectors[start_idx:start_idx + window_size]
+    
+    # Get similarity matrix for segment
+    segment_df = wordmatrix(segment_tokens, segment_vectors, mode, dist=dist, dataframe=True)
+    segment_values = segment_df.stack()
+    
+    return segment_values.mean(), segment_values.std()
+
+def coherence(
+    tokens: TokenList,
+    vectors: Union[VectorList, List[str]],
+    mode: str,
+    window_size: int,
+    dist: Optional[Any] = None
+) -> Tuple[float, float, float, float]:
+    """
+    Compute coherence metrics for a sequence of words.
+    
+    Args:
+        tokens: List of words
+        vectors: List of vector representations
+        mode: Either "semantic" or "phonetic"
+        window_size: Size of sliding window (0 for whole text)
+        dist: Panphon distance calculator (required for phonetic mode)
+    
+    Returns:
+        Tuple of (mean_of_means, std_of_means, mean_of_stds, std_of_stds)
+    """
+    # Handle empty or single-word sequences
+    if len(tokens) < 2:
+        return np.nan, np.nan, np.nan, np.nan
+    
+    # Handle whole-text analysis
+    elif window_size == 0:
+        tokens_df = wordmatrix(tokens, vectors, mode, dist=dist, dataframe=True)
+        matrix_values = tokens_df.stack()
+        return matrix_values.mean(), np.nan, matrix_values.std(), np.nan
+    
+    # Handle sliding window analysis
+    else:
+        window_means = []
+        window_stds = []
+        
+        for i in range(len(tokens) - window_size + 1):
+            window_tokens = tokens[i:i + window_size]
+            window_vectors = vectors[i:i + window_size]
+            
+            # Get similarity matrix for window
+            window_df = wordmatrix(window_tokens, window_vectors, mode, dist=dist, dataframe=True)
+            window_values = window_df.stack()
+            
+            # Calculate window statistics
+            window_means.append(window_values.mean())
+            window_stds.append(window_values.std())
+        
+        # Calculate aggregate statistics
+        mean_mean = np.mean(window_means)
+        mean_std = np.std(window_means)
+        std_mean = np.mean(window_stds)
+        std_std = np.std(window_stds)
+        
+        return mean_mean, mean_std, std_mean, std_std
+
+def split_coherence(
+    row: pd.Series,
+    window: int,
+    mode: str,
+    dist: Optional[Any] = None
+) -> pd.Series:
+    """
+    Compute coherence metrics for a single row with given window size.
+    
+    Args:
+        row: DataFrame row containing tokens and vectors
+        window: Window size for coherence calculation
+        mode: Either "semantic" or "phonetic"
+        dist: Panphon distance calculator (required for phonetic mode)
+    
+    Returns:
+        Series with coherence metrics for this window size
+    """
+    # Both modes use 'tokens' column
+    tokens = row['tokens']
+    vectors = row["phonetic_vectors" if mode == "phonetic" else "embeddings"]
+    
+    mean_mean, mean_std, std_mean, std_std = coherence(
+        tokens, vectors, mode, window_size=window, dist=dist
+    )
+    
+    return pd.Series({
+        f"{mode}_coherence_{window}_mean_of_window_means": mean_mean,
+        f"{mode}_coherence_{window}_std_of_window_means": mean_std,
+        f"{mode}_coherence_{window}_mean_of_window_stds": std_mean,
+        f"{mode}_coherence_{window}_std_of_window_stds": std_std
+    })
+
+def process_window(
+    data_df: pd.DataFrame,
+    window: int,
+    mode: str,
+    dist: Optional[Any] = None
+) -> pd.DataFrame:
+    """
+    Process entire DataFrame for a given window size.
+    
+    Args:
+        data_df: DataFrame containing tokens and vectors
+        window: Window size for coherence calculation
+        mode: Either "semantic" or "phonetic"
+        dist: Panphon distance calculator (required for phonetic mode)
+    
+    Returns:
+        DataFrame with coherence metrics for this window size
+    """
+    logger.info(f"Processing {mode} coherence with window size: {window}")
+    return data_df.apply(lambda row: split_coherence(row, window, mode, dist), axis=1)
+
+def apply_coherence(
+    data_df: pd.DataFrame,
+    windows: List[int],
+    mode: str,
+    dist: Optional[Any] = None,
+    parallelize: bool = False
+) -> pd.DataFrame:
+    """
+    Apply coherence calculation across multiple window sizes.
+    
+    Args:
+        data_df: DataFrame containing tokens and embedding vectors
+        windows: List of window sizes to process
+        mode: Either "semantic" or "phonetic"
+        dist: Panphon distance calculator (required for phonetic mode)
+        parallelize: Whether to use parallel processing
+    
+    Returns:
+        DataFrame with coherence metrics for all window sizes
+    """
+    if parallelize:
+        with ProcessPoolExecutor() as executor:
+            futures = [
+                executor.submit(
+                    process_window,
+                    data_df.copy(),
+                    window,
+                    mode,
+                    dist
+                )
+                for window in windows
+            ]
+            results = [future.result() for future in futures]
+    else:
+        results = [
+            process_window(data_df.copy(), window, mode, dist)
+            for window in windows #window_sizes not windows
+        ]
+
+    # Combine results into main DataFrame
+    for result in results:
+        for col in result.columns:
+            data_df[col] = result[col]
+
+    return data_df
+
+def ipa_to_features(ipa_tokens: List[str]) -> List[List[float]]:
+    """
+    Convert IPA tokens into phonetic feature vectors.
+    
+    Args:
+        ipa_tokens: List of IPA transcriptions
+    
+    Returns:
+        List of feature vectors for each token
+    """
+    return [fasttext.word_to_vector_list(ipa) for ipa in ipa_tokens]
+
+def load_models() -> Tuple[Any, Any, Any]:
+    """Load FastText, Epitran, and Panphon models."""
+    logger.info("Loading models...")
+    
+    # Load FastText model
+    logger.info("Loading FastText model...")
+    ft_model = fasttext.load_model(COHERENCE_CONFIG["model"]["fasttext_path"])
+    
+    # Load Epitran model
+    logger.info("Loading Epitran model...")
+    epi = epitran.Epitran(COHERENCE_CONFIG["model"]["language_code"])
+    
+    # Load Panphon distance calculator
+    logger.info("Loading Panphon model...")
+    dist = panphon.distance.Distance()
+    
+    return ft_model, epi, dist
+
+def load_transcripts() -> pd.DataFrame:
+    """Load and preprocess transcripts."""
+    logger.info("Loading transcripts...")
+    
+    # Get list of transcript files
+    transcript_files = [f for f in os.listdir(COHERENCE_CONFIG["paths"]["data_dir"]) if f.endswith('.txt')]
+    logger.info(f"Found {len(transcript_files)} transcript files")
+    
+    # Load each transcript
+    data = []
+
+
+    # Load each transcript
+    data = []
+    for filename in transcript_files:
+        filepath = os.path.join(COHERENCE_CONFIG["paths"]["data_dir"], filename)
+        
+        try:
+            # Read file with UTF-8, ignoring errors or replacing unknown chars
+            with open(filepath, 'r', encoding='utf-8') as f:
+                content = f.read()
+                tokens = preprocess(content)
+                data.append({
+                    'file_name': filename,
+                    'transcript': content,
+                    'tokens': tokens
+                })
+        except UnicodeDecodeError:
+            print(f"Warning: UnicodeDecodeError in file {filename}. Trying alternative encoding...")
+            
+            # Try alternative encoding (ISO-8859-1 or cp1252)
+            try:
+                with open(filepath, 'r', encoding='ISO-8859-1') as f:
+                    content = f.read()
+                    tokens = preprocess(content)
+                    data.append({
+                        'file_name': filename,
+                        'transcript': content,
+                        'tokens': tokens
+                    })
+            except Exception as e:
+                print(f"Failed to read {filename} with alternative encoding: {e}")
+                continue  # Skip the file
+
+    return pd.DataFrame(data)
+
+def process_transcripts(
+    data_df: pd.DataFrame,
+    ft_model: Any,
+    epi: Any,
+    dist: Any,
+    config: Dict
+) -> pd.DataFrame:
+    """
+    Process transcripts to compute coherence metrics.
+    
+    Args:
+        data_df: DataFrame with raw transcripts
+        ft_model: FastText model
+        epi: Epitran model
+        dist: Panphon distance calculator
+        config: Configuration dictionary
+    
+    Returns:
+        DataFrame with computed metrics
+    """
+    logger.info("Processing transcripts...")
+    
+    # Tokenization
+    logger.info("Tokenizing transcripts...")
+    data_df["tokens"] = data_df["transcript"].apply(
+        lambda x: preprocess(x, config["preprocessing"]["lower"], config["preprocessing"]["free_text"])
+    )
+    
+    # Process each mode
+    for mode in config["modes"]:
+        if mode == "semantic":
+            # Generate embeddings
+            logger.info("Generating FastText embeddings...")
+            data_df["embeddings"] = data_df["tokens"].apply(
+                lambda x: get_vector(ft_model, "semantic", x)
+            )
+            
+            # Calculate word sequence similarities
+            logger.info("Computing word sequence similarities...")
+            data_df["wordseq_ft"] = data_df.apply(
+                lambda row: wordseq(row["tokens"], row["embeddings"], "semantic"),
+                axis=1
+            )
+            
+            # Apply coherence calculations
+            logger.info("Computing coherence metrics...")
+            data_df = apply_coherence(data_df, config["windows"], "semantic")
+            
+        elif mode == "phonetic":
+            # Generate phonetic vectors
+            logger.info("Generating phonetic vectors...")
+            data_df["phonetic_vectors"] = data_df["tokens"].apply(
+                lambda x: get_vector(epi, "phonetic", x)
+            )
+            
+            # Calculate word sequence similarities
+            data_df["wordseq_phon"] = data_df.apply(
+                lambda row: wordseq(row["tokens"], row["phonetic_vectors"], "phonetic", dist),
+                axis=1
+            )
+            
+            # Apply coherence calculations
+            data_df = apply_coherence(data_df, config["windows"], "phonetic", dist=dist)
+    
+    # Calculate additional metrics
+    logger.info("Computing additional metrics...")
+    data_df["number_tokens"] = data_df["tokens"].apply(len)
+    data_df["multiword_count"] = data_df["tokens"].apply(
+        lambda x: len([i for i in x if len(i.split()) > 1])
+    )
+    
+    return data_df
+
+def save_results(data_df: pd.DataFrame) -> None:
+    """Save processed results to CSV."""
+    # Extract study_id and sub_task from filename
+    data_df["study_id"] = data_df["file_name"].apply(lambda x: x.split("_")[0])  # Get first part (0029)
+    data_df["sub_task"] = data_df["file_name"].apply(lambda x: x.split("_")[-1].replace(".txt", ""))
+    
+    # Determine output path
+    out_file = os.path.join(
+        COHERENCE_CONFIG["paths"]["results_dir"],
+        f'coherence_results{"_lower" if COHERENCE_CONFIG["preprocessing"]["lower"] else "_upper"}.csv'
+    )
+    
+    # Ensure output directory exists
+    ensure_output_dir(out_file)
+    
+    # Save results, dropping intermediate columns if they exist
+    columns_to_drop = [
+        col for col in [
+            "transcript", "tokens",
+            "embeddings", "phonetic_vectors", "file_name"
+        ] if col in data_df.columns
+    ]
+    
+    # Reorder columns to put study_id and sub_task first
+    final_df = data_df.drop(columns=columns_to_drop)
+    cols = ["study_id", "sub_task"] + [col for col in final_df.columns if col not in ["study_id", "sub_task"]]
+    final_df = final_df[cols]
+    
+    final_df.to_csv(out_file, index=None)
+    logger.info(f"Results saved to: {out_file}")
+
+def main():
+    """Main execution function."""
+    try:
+        logger.info("Starting coherence analysis...")
+        
+        # Load models
+        ft_model, epi, dist = load_models()
+        
+        # Load and process transcripts
+        data_df = load_transcripts()
+        data_df = process_transcripts(data_df, ft_model, epi, dist, COHERENCE_CONFIG)
+        
+        # Save results
+        save_results(data_df)
+        
+        logger.info("Coherence analysis completed successfully!")
+        
+    except Exception as e:
+        logger.error(f"Error during execution: {str(e)}", exc_info=True)
+        raise
+
+if __name__ == "__main__":
+    main()