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| """ | |
| CardD (Card Draw Test) dataset processor. | |
| Processes ESP card drawing test data with two schema versions: | |
| - Old format (pre 2006-06-22): 14-15 columns, combined Markov bits | |
| - New format (post 2006-06-22): 15-16 columns, separate Markov bits, optional image_filename | |
| """ | |
| from pathlib import Path | |
| from typing import List, Dict, Any, Optional | |
| from datetime import datetime | |
| import pandas as pd | |
| import re | |
| from ..core.base_classes import BaseProcessor | |
| from ..core.config import Config | |
| from ..core.exceptions import ProcessorError | |
| from ..cleaners.encoding_cleaner import EncodingCleaner | |
| from ..cleaners.delimiter_cleaner import DelimiterCleaner | |
| from ..cleaners.temporal_parser import TemporalParser | |
| class CardDProcessor(BaseProcessor): | |
| """ | |
| Processes CardD (Card Draw Test) data. | |
| Schema versions: | |
| - v1 (pre 2006-06-22): Markov bits combined in single 32-bit word | |
| - v2 (post 2006-06-22): Markov bits in separate words | |
| """ | |
| # File discovery patterns | |
| FILE_PATTERNS = ['cardD*.dat'] | |
| # Schema change date | |
| SCHEMA_CHANGE_DATE = datetime(2006, 6, 22) | |
| # Column definitions | |
| COLUMNS_OLD = [ | |
| 'user_id', 'target_bit', 'cards_done', 'cards_hit', | |
| 'markov_stages', 'markov_output', 'markov_prob', | |
| 'markov_bits_combined', # Single word with both chains | |
| 'card_number', 'is_hit', 'run_hits', 'trial_number', | |
| 'timestamp', 'target_image', 'extra' | |
| ] | |
| COLUMNS_NEW = [ | |
| 'user_id', 'target_bit', 'cards_done', 'cards_hit', | |
| 'markov_stages', 'markov_output', 'markov_prob', | |
| 'markov_bits_main', 'markov_bits_aux', # Separate words | |
| 'card_number', 'is_hit', 'run_hits', 'trial_number', | |
| 'timestamp', 'image_filename', 'target_image', 'extra' | |
| ] | |
| COLUMNS_UNIFIED = [ | |
| 'user_id', 'target_bit', 'cards_done', 'cards_hit', | |
| 'markov_stages', 'markov_output', 'markov_prob', | |
| 'markov_bits_main', 'markov_bits_aux', | |
| 'card_number', 'is_hit', 'run_hits', 'trial_number', | |
| 'timestamp', 'image_filename', 'target_image', | |
| 'file_date', 'schema_version', 'source_file', 'source_row_number' | |
| ] | |
| def __init__(self, config: Config): | |
| """ | |
| Initialize CardD processor. | |
| Args: | |
| config: Configuration object | |
| """ | |
| super().__init__(config, 'cardd') | |
| # Initialize cleaners | |
| self.encoding_cleaner = EncodingCleaner(config, self.errata_logger) | |
| self.delimiter_cleaner = DelimiterCleaner(config, self.errata_logger) | |
| self.temporal_parser = TemporalParser(config, self.errata_logger) | |
| # Statistics | |
| self.stats = { | |
| 'files_processed': 0, | |
| 'files_failed': 0, | |
| 'rows_total': 0, | |
| 'rows_valid': 0, | |
| 'rows_invalid': 0, | |
| 'schema_v1_files': 0, | |
| 'schema_v2_files': 0 | |
| } | |
| def extract_file_date(self, file_path: Path) -> Optional[datetime]: | |
| """ | |
| Extract date from filename (cardDYYMMDD.dat). | |
| Args: | |
| file_path: Path to file | |
| Returns: | |
| datetime object or None | |
| """ | |
| match = re.search(r'cardD(\d{6})\.dat', file_path.name) | |
| if not match: | |
| return None | |
| date_str = match.group(1) | |
| return self.temporal_parser.extract_date_from_filename(file_path.name) | |
| def detect_schema_version(self, file_path: Path, df: pd.DataFrame) -> tuple: | |
| """ | |
| Detect schema version based on file date and column count distribution. | |
| Checks first, middle, and last rows to detect mixed schemas. | |
| Args: | |
| file_path: Path to file | |
| df: DataFrame with raw data (no headers) | |
| Returns: | |
| Tuple of (primary_version, is_mixed) | |
| - primary_version: 'v1' or 'v2' | |
| - is_mixed: True if file contains both schemas | |
| """ | |
| file_date = self.extract_file_date(file_path) | |
| # Make schema change date timezone-aware for comparison | |
| schema_change_aware = self.temporal_parser.timezone.localize(self.SCHEMA_CHANGE_DATE) | |
| # Check column count distribution across sample rows | |
| sample_indices = [0, len(df) // 2, len(df) - 1] if len(df) > 2 else [0] | |
| column_counts = [] | |
| for idx in sample_indices: | |
| if idx < len(df): | |
| # Count non-null columns in this row | |
| col_count = df.iloc[idx].notna().sum() | |
| column_counts.append(col_count) | |
| unique_counts = set(column_counts) | |
| is_mixed = len(unique_counts) > 1 | |
| # Determine primary version | |
| max_col_count = max(column_counts) | |
| if file_date and file_date >= schema_change_aware: | |
| primary_version = 'v2' | |
| elif max_col_count >= 15: # v2 has >= 15 columns (separate Mbits0 and Mbits1) | |
| primary_version = 'v2' | |
| else: | |
| primary_version = 'v1' | |
| return primary_version, is_mixed | |
| def unpack_markov_bits_old(self, combined: int, n_stages: int) -> tuple: | |
| """ | |
| Unpack combined Markov bits (old format). | |
| In old format, both main and aux chains stored in one 32-bit word: | |
| - Main chain: lower n_stages bits | |
| - Aux chain: next n_stages bits | |
| Args: | |
| combined: Combined 32-bit value | |
| n_stages: Number of Markov stages | |
| Returns: | |
| Tuple of (main_bits, aux_bits) | |
| """ | |
| mask = (1 << n_stages) - 1 | |
| main_bits = combined & mask | |
| aux_bits = (combined >> n_stages) & mask | |
| return main_bits, aux_bits | |
| def _process_mixed_schema_file(self, df: pd.DataFrame, file_path: Path) -> Optional[pd.DataFrame]: | |
| """ | |
| Process a file with mixed schema versions (row-by-row). | |
| Args: | |
| df: Raw DataFrame with no headers | |
| file_path: Source file path | |
| Returns: | |
| Processed DataFrame or None | |
| """ | |
| processed_rows = [] | |
| file_date = self.extract_file_date(file_path) | |
| for idx, row in df.iterrows(): | |
| try: | |
| # Count non-null columns to detect schema | |
| col_count = row.notna().sum() | |
| # Determine schema for this row | |
| if col_count >= 15: | |
| # v2 schema (new format with separate Markov bits) | |
| schema = 'v2' | |
| columns = self.COLUMNS_NEW[:col_count] | |
| elif col_count >= 14: | |
| # v1 schema (old format with combined Markov bits) | |
| schema = 'v1' | |
| columns = self.COLUMNS_OLD[:col_count] | |
| else: | |
| # Insufficient columns, skip row | |
| continue | |
| # Create dict for this row | |
| row_dict = {} | |
| for i, col_name in enumerate(columns): | |
| if i < len(row): | |
| row_dict[col_name] = row.iloc[i] | |
| # Handle old format: unpack combined Markov bits | |
| if schema == 'v1' and 'markov_bits_combined' in row_dict: | |
| try: | |
| n_stages = int(row_dict.get('markov_stages', 0)) | |
| combined = int(row_dict['markov_bits_combined']) | |
| main_bits, aux_bits = self.unpack_markov_bits_old(combined, n_stages) | |
| row_dict['markov_bits_main'] = main_bits | |
| row_dict['markov_bits_aux'] = aux_bits | |
| del row_dict['markov_bits_combined'] | |
| except (ValueError, TypeError): | |
| # Skip row if unpacking fails | |
| continue | |
| # Add metadata | |
| row_dict['file_date'] = file_date | |
| row_dict['schema_version'] = schema | |
| # Add audit columns (source file and row numbers) | |
| row_dict['source_file'] = file_path.name | |
| row_dict['source_row_number'] = idx + 1 | |
| # Remove 'extra' column if present | |
| if 'extra' in row_dict: | |
| del row_dict['extra'] | |
| processed_rows.append(row_dict) | |
| except Exception as e: | |
| import traceback | |
| self.errata_logger.log_error( | |
| 'row_processing_failed', | |
| f'Row {idx}: {type(e).__name__}: {e}', | |
| file_path=str(file_path), | |
| scope='row', | |
| line_number=idx, | |
| context={'traceback': traceback.format_exc()}, | |
| ) | |
| continue | |
| if not processed_rows: | |
| return None | |
| # Create DataFrame from processed rows | |
| result_df = pd.DataFrame(processed_rows) | |
| # Validate and clean | |
| result_df = self.validate_dataframe(result_df, file_path) | |
| # Ensure all unified columns exist AFTER validation | |
| for col in self.COLUMNS_UNIFIED: | |
| if col not in result_df.columns: | |
| result_df[col] = None | |
| # Reorder to unified schema | |
| result_df = result_df[self.COLUMNS_UNIFIED] | |
| return result_df | |
| def process_file(self, file_path: Path, pre_cleaned_text: Optional[str] = None) -> Optional[pd.DataFrame]: | |
| """ | |
| Process a single CardD file. | |
| Args: | |
| file_path: Path to file | |
| pre_cleaned_text: Pre-cleaned text from parallel batch cleaning. | |
| If None, cleans the file inline (backward compat). | |
| Returns: | |
| DataFrame or None if processing fails | |
| """ | |
| try: | |
| # Use pre-cleaned text if available, otherwise clean inline | |
| if pre_cleaned_text is not None: | |
| text = pre_cleaned_text | |
| else: | |
| text = self.encoding_cleaner.clean(file_path) | |
| text = self.delimiter_cleaner.clean(text, file_path=str(file_path)) | |
| # Pre-validate lines so bad rows are logged before being removed | |
| text = self.pre_validate_csv_lines(text, file_path=str(file_path)) | |
| from io import BytesIO | |
| df = pd.read_csv(BytesIO(text.encode('utf-8')), header=None, on_bad_lines='skip', engine='pyarrow') | |
| if df.empty: | |
| self.errata_logger.log_error( | |
| 'empty_file', | |
| 'File is empty or has no valid rows - entire file omitted', | |
| file_path=str(file_path), | |
| scope='file' | |
| ) | |
| return None | |
| # Detect schema version and check for mixed schemas | |
| schema_version, is_mixed = self.detect_schema_version(file_path, df) | |
| if is_mixed: | |
| self.errata_logger.log_error( | |
| 'mixed_schema_detected', | |
| f'File contains mixed schema versions (v1 and v2)', | |
| file_path=str(file_path), | |
| scope='row' | |
| ) | |
| # Process row-by-row for mixed schema files | |
| return self._process_mixed_schema_file(df, file_path) | |
| # Single schema processing (original logic) | |
| column_count = len(df.columns) | |
| # Assign column names | |
| if schema_version == 'v1': | |
| if column_count >= 14: | |
| df.columns = self.COLUMNS_OLD[:column_count] | |
| self.stats['schema_v1_files'] += 1 | |
| else: | |
| self.errata_logger.log_error( | |
| 'insufficient_columns', | |
| f'Too few columns: {column_count} - entire file omitted', | |
| file_path=str(file_path), | |
| scope='file' | |
| ) | |
| return None | |
| else: # v2 | |
| if column_count >= 15: | |
| df.columns = self.COLUMNS_NEW[:column_count] | |
| self.stats['schema_v2_files'] += 1 | |
| else: | |
| self.errata_logger.log_error( | |
| 'insufficient_columns', | |
| f'Too few columns: {column_count} - entire file omitted', | |
| file_path=str(file_path), | |
| scope='file' | |
| ) | |
| return None | |
| # Unpack Markov bits for old format | |
| if schema_version == 'v1' and 'markov_bits_combined' in df.columns: | |
| df[['markov_bits_main', 'markov_bits_aux']] = df.apply( | |
| lambda row: pd.Series( | |
| self.unpack_markov_bits_old( | |
| row['markov_bits_combined'], | |
| row['markov_stages'] | |
| ) | |
| ), | |
| axis=1 | |
| ) | |
| df = df.drop(columns=['markov_bits_combined']) | |
| # Add metadata | |
| file_date = self.extract_file_date(file_path) | |
| df['file_date'] = file_date | |
| df['schema_version'] = schema_version | |
| # Add audit columns (source file and row numbers) | |
| df['source_file'] = file_path.name | |
| df['source_row_number'] = range(1, len(df) + 1) | |
| # Remove 'extra' column if present (not needed in unified schema) | |
| if 'extra' in df.columns: | |
| df = df.drop(columns=['extra']) | |
| # Validate and clean | |
| df = self.validate_dataframe(df, file_path) | |
| # Ensure all unified columns exist AFTER validation | |
| for col in self.COLUMNS_UNIFIED: | |
| if col not in df.columns: | |
| df[col] = None | |
| # Reorder to unified schema | |
| df = df[self.COLUMNS_UNIFIED] | |
| self.stats['files_processed'] += 1 | |
| self.stats['rows_valid'] += len(df) | |
| return df | |
| except Exception as e: | |
| import traceback | |
| self.errata_logger.log_error( | |
| 'file_processing_failed', | |
| f'{type(e).__name__}: {e} - entire file omitted', | |
| file_path=str(file_path), | |
| scope='file', | |
| context={'traceback': traceback.format_exc()}, | |
| ) | |
| return None | |
| def validate_dataframe(self, df: pd.DataFrame, file_path: Path) -> pd.DataFrame: | |
| """ | |
| Validate and clean DataFrame. | |
| Args: | |
| df: Input DataFrame | |
| file_path: Source file path | |
| Returns: | |
| Cleaned DataFrame | |
| """ | |
| initial_count = len(df) | |
| valid_mask = pd.Series([True] * len(df), index=df.index) | |
| # Validate user_id length | |
| long_users = df['user_id'].str.len() > 64 | |
| if long_users.any(): | |
| valid_mask &= ~long_users | |
| self.errata_logger.log_error( | |
| 'user_id_too_long', | |
| f'{long_users.sum()} rows with user_id > 64 chars', | |
| file_path=str(file_path), | |
| scope='row' | |
| ) | |
| # Validate card_number range (0-4) | |
| if 'card_number' in df.columns: | |
| df['card_number'] = self.to_numeric_logged(df['card_number'], 'card_number', str(file_path)) | |
| invalid_card = (df['card_number'] < 0) | (df['card_number'] > 4) | |
| if invalid_card.any(): | |
| valid_mask &= ~invalid_card | |
| self.errata_logger.log_error( | |
| 'card_number_out_of_range', | |
| f'{invalid_card.sum()} rows with card_number not in 0-4', | |
| file_path=str(file_path), | |
| scope='row' | |
| ) | |
| # Validate trial_number (must be >= 1, no upper limit since trperrun is configurable) | |
| if 'trial_number' in df.columns: | |
| df['trial_number'] = self.to_numeric_logged(df['trial_number'], 'trial_number', str(file_path)) | |
| invalid_trial = (df['trial_number'] < 1) | |
| if invalid_trial.any(): | |
| valid_mask &= ~invalid_trial | |
| self.errata_logger.log_error( | |
| 'trial_number_invalid', | |
| f'{invalid_trial.sum()} rows with trial_number < 1', | |
| file_path=str(file_path), | |
| scope='row' | |
| ) | |
| # Validate cards_done/cards_hit | |
| for col in ['cards_done', 'cards_hit']: | |
| if col in df.columns: | |
| df[col] = self.to_numeric_logged(df[col], col, str(file_path)) | |
| invalid = (df[col] < 0) | (df[col] > 5) | |
| if invalid.any(): | |
| valid_mask &= ~invalid | |
| # Parse timestamps | |
| if 'timestamp' in df.columns: | |
| df['timestamp'] = self.temporal_parser.parse_dates_vectorized( | |
| df['timestamp'], file_path=str(file_path) | |
| ) | |
| # Convert numeric columns | |
| numeric_cols = [ | |
| 'target_bit', 'cards_done', 'cards_hit', 'markov_stages', | |
| 'markov_output', 'markov_prob', 'markov_bits_main', 'markov_bits_aux', | |
| 'card_number', 'is_hit', 'run_hits', 'trial_number' | |
| ] | |
| for col in numeric_cols: | |
| if col in df.columns: | |
| df[col] = self.to_numeric_logged(df[col], col, str(file_path)) | |
| # Filter to valid rows | |
| df_valid = df[valid_mask].copy() | |
| invalid_count = initial_count - len(df_valid) | |
| if invalid_count > 0: | |
| self.errata_logger.log_file_summary( | |
| str(file_path), | |
| 'partial', | |
| initial_count, | |
| len(df_valid), | |
| invalid_count | |
| ) | |
| return df_valid | |
| def get_stats(self) -> Dict[str, Any]: | |
| """Get processing statistics.""" | |
| return self.stats.copy() |