# Helper functions to reduce RAM utilization # Please install dependencies before: # pip install -r requirements.txt # Import necessary libraries import os import pickle import tarfile import pandas as pd import numpy as np from tqdm import tqdm from tqdm import trange from pathlib import Path from sklearn.model_selection import train_test_split def delete_temporary_files(): if Path('tmp_dataset_X.pkl').exists(): os.remove('tmp_dataset_X.pkl') if Path('tmp_dataset_y.pkl').exists(): os.remove('tmp_dataset_y.pkl') if Path('tmp_dataset_X.npy').exists(): os.remove('tmp_dataset_X.npy') if Path('tmp_dataset_y.npy').exists(): os.remove('tmp_dataset_y.npy') if Path('tmp_X_train.pkl').exists(): os.remove('tmp_X_train.npy') if Path('tmp_y_train.pkl').exists(): os.remove('tmp_y_train.npy') if Path('tmp_X_test.npy').exists(): os.remove('tmp_X_test.npy') if Path('tmp_y_test.npy').exists(): os.remove('tmp_y_test.npy') def load_dataset(file_path='dataset.tar.bz2'): """ Decompress and load already prepared dataset. Parameters: file_path (str): Path to the compressed version of the prepared dataset (default dataset.tar.bz2) Returns: X_train (np.memmap): Memory-mapped NumPy array of the X training data X_test (np.memmap): Memory-mapped NumPy array of the X test data y_train (np.memmap): Memory-mapped NumPy array of the y training data y_test (np.memmap): Memory-mapped NumPy array of the y test data """ # Return the pepared dataset if it already exists if Path('X_train.npy').exists() and Path('y_train.npy').exists() and Path('X_test.npy').exists() and Path('y_test.npy').exists(): X_train = np.load('X_train.npy', mmap_mode='r') y_train = np.load('y_train.npy', mmap_mode='r') X_test = np.load('X_test.npy', mmap_mode='r') y_test = np.load('y_test.npy', mmap_mode='r') return X_train, X_test, y_train, y_test # Decompress memory mapped files if Path(file_path).exists(): with tarfile.open(file_path) as dataset: dataset.extractall(path='.') # Load the dataset dataset_X = np.load('dataset_X.npy', mmap_mode='r') dataset_y = np.load('dataset_y.npy', mmap_mode='r') # Create a train test split with memory mapped files X_train, X_test, y_train, y_test = train_test_split_memmapped(dataset_X, dataset_y) return X_train, X_test, y_train, y_test else: print('ERROR: file not found') def convert_and_load_dataset(file_path='dataset.csv.bz2'): """ Converts a CSV dataset into a NumPy memory-mapped dataset and load it. This function transforms a given CSV dataset into a memory-mapped NumPy array. Memory-mapping helps to reduce RAM usage by loading the dataset in smaller chunks. However, it requires additional disk space during the conversion process. Parameters: file_path (str): Path to the CSV dataset file (default dataset.csv.bz2) Returns: X_train (np.memmap): Memory-mapped NumPy array of the X training data X_test (np.memmap): Memory-mapped NumPy array of the X test data y_train (np.memmap): Memory-mapped NumPy array of the y training data y_test (np.memmap): Memory-mapped NumPy array of the y test data """ # Return the pepared dataset if it already exists if Path('X_train.npy').exists() and Path('y_train.npy').exists() and Path('X_test.npy').exists() and Path('y_test.npy').exists(): return load_dataset() # Load and prepare dataset delete_temporary_files() with open('tmp_dataset_X.pkl', 'ab') as tmp_dataset_X, open('tmp_dataset_y.pkl', 'ab') as tmp_dataset_y: shape = None num_of_chunks = 0 # Load the dataset from a local file path # Replace with Huggingface dataset call if applicable for real_data_chunk in tqdm(pd.read_csv(file_path, compression='bz2', chunksize=4096), desc='Read and Prepare Dataset'): # Select relevant columns (replace these with actual column names from your dataset) # Here we assume that the dataset contains sensor readings like gyroscope and accelerometer data relevant_columns = ['gyro_x', 'gyro_y', 'gyro_z', 'acc_x', 'acc_y', 'acc_z', 'upright'] sensordata_chunk = real_data_chunk[relevant_columns] # Split the data into features (X) and labels (y) # 'fall_label' is assumed to be the column indicating whether a fall occurred X_chunk = np.array(sensordata_chunk.drop(columns=['upright'])) # Replace 'fall_label' with the actual label column y_chunk = np.array(sensordata_chunk['upright']) if shape is None: # Preview the dataset print('\n' + str(real_data_chunk.head())) if shape is None: shape = np.array(X_chunk.shape) else: shape[0] += X_chunk.shape[0] pickle.dump(X_chunk, tmp_dataset_X) pickle.dump(y_chunk, tmp_dataset_y) num_of_chunks += 1 # Convert dataset into a memory-mapped array stored in a binary file on disk. X_idx = 0 y_idx = 0 dataset_X = np.memmap('tmp_dataset_X.npy', mode='w+', dtype=np.float32, shape=(shape[0], shape[1], 1)) dataset_y = np.memmap('tmp_dataset_y.npy', mode='w+', dtype=np.float32, shape=(shape[0], 1)) with open('tmp_dataset_X.pkl', 'rb') as tmp_dataset_X, open('tmp_dataset_y.pkl', 'rb') as tmp_dataset_y: for _ in trange(0, num_of_chunks, 1, desc='Convert Dataset'): X_chunk = pickle.load(tmp_dataset_X) y_chunk = pickle.load(tmp_dataset_y) # Reshape data for LSTM input (assuming time-series data) # Adjust the reshaping based on your dataset structure for X_data in X_chunk: dataset_X[X_idx] = np.expand_dims(X_data, axis=-1) X_idx += 1 for y_data in y_chunk: dataset_y[y_idx] = np.expand_dims(y_data, axis=-1) y_idx += 1 # Delete temporary files os.remove('tmp_dataset_X.pkl') os.remove('tmp_dataset_y.pkl') # Save the memory-mapped arrays with open('dataset_X.npy', 'wb') as dataset_x_file, open('dataset_y.npy', 'wb') as dataset_y_file: np.save(dataset_x_file, dataset_X, allow_pickle=False, fix_imports=True) np.save(dataset_y_file, dataset_y, allow_pickle=False, fix_imports=True) # Delete temporary files dataset_X._mmap.close() dataset_y._mmap.close() os.remove('tmp_dataset_X.npy') os.remove('tmp_dataset_y.npy') # Reload memory-mapped arrays dataset_X = np.load('dataset_X.npy', mmap_mode='r') dataset_y = np.load('dataset_y.npy', mmap_mode='r') # Create a train test split with memory mapped files X_train, X_test, y_train, y_test = train_test_split_memmapped(dataset_X, dataset_y) return X_train, X_test, y_train, y_test def train_test_split_memmapped(dataset_X, dataset_y, test_size=0.2, random_state=42): """ Create memory-mapped files for train and test datasets. Parameters: dataset_X (np.memmap): X part of the complete dataset dataset_y (np.memmap): y part of the complete dataset test_size (float): Propotion of the dataset used for the test split (default 0.2) random_state (int): Random state used for repeatability (default 42) Returns: X_train (np.memmap): Memory-mapped NumPy array of the X training data X_test (np.memmap): Memory-mapped NumPy array of the X test data y_train (np.memmap): Memory-mapped NumPy array of the y training data y_test (np.memmap): Memory-mapped NumPy array of the y test data """ delete_temporary_files() # Split data into training and test sets idxs = np.arange(dataset_X.shape[0]) train_idx, test_idx = train_test_split(idxs, test_size=test_size, random_state=random_state) # Create memory-mapped files for train and test sets X_train = np.memmap('tmp_X_train.npy', dtype=dataset_X.dtype, mode='w+', shape=(len(train_idx), dataset_X.shape[1], 1)) y_train = np.memmap('tmp_y_train.npy', dtype=dataset_y.dtype, mode='w+', shape=(len(train_idx), dataset_y.shape[1])) X_test = np.memmap('tmp_X_test.npy', dtype=dataset_X.dtype, mode='w+', shape=(len(test_idx), dataset_X.shape[1], 1)) y_test = np.memmap('tmp_y_test.npy', dtype=dataset_y.dtype, mode='w+', shape=(len(test_idx), dataset_y.shape[1])) # Assign values to the train and test memmap arrays X_train[:] = dataset_X[train_idx] y_train[:] = dataset_y[train_idx] X_test[:] = dataset_X[test_idx] y_test[:] = dataset_y[test_idx] # Save the memory-mapped arrays with open('X_train.npy', 'wb') as X_train_file, open('y_train.npy', 'wb') as y_train_file, open('X_test.npy', 'wb') as X_test_file, open('y_test.npy', 'wb') as y_test_file: np.save(X_train_file, X_train, allow_pickle=False, fix_imports=True) np.save(y_train_file, y_train, allow_pickle=False, fix_imports=True) np.save(X_test_file, X_test, allow_pickle=False, fix_imports=True) np.save(y_test_file, y_test, allow_pickle=False, fix_imports=True) X_train._mmap.close() y_train._mmap.close() X_test._mmap.close() y_test._mmap.close() # Delete temporary files os.remove('tmp_X_train.npy') os.remove('tmp_y_train.npy') os.remove('tmp_X_test.npy') os.remove('tmp_y_test.npy') X_train = np.load('X_train.npy', mmap_mode='r') y_train = np.load('y_train.npy', mmap_mode='r') X_test = np.load('X_test.npy', mmap_mode='r') y_test = np.load('y_test.npy', mmap_mode='r') return X_train, X_test, y_train, y_test