import astropy.table import numpy as np import pandas as pd def load(path, x_cols=('psfMag_u', 'psfMag_g', 'psfMag_r', 'psfMag_i', 'psfMag_z'), y_col='redshift', class_col='class', class_val='Galaxy'): # Cast x_cols to list so Pandas doesn't complain… x_cols_l = list(x_cols) if '.h5' in path or '.hdf' in path: # We have an HDF5 file data = pd.read_hdf(path) return data, x_cols_l, y_col elif '.fits' in path: x_cols_l = ['umag', 'gmag', 'rmag', 'imag', 'zmag'] y_col = 'z' dat = astropy.table.Table.read(path, format='fits') data = dat.to_pandas() data = data[x_cols_l + [y_col]] return data, x_cols_l, y_col else: # We have a CSV file data_iter = pd.read_csv( path, iterator=True, chunksize=100000, usecols=x_cols_l + [y_col, class_col]) # Filter out anything that is not a galaxy without loading the # whole file into memory. data = pd.concat(chunk[chunk[class_col] == class_val] for chunk in data_iter) return data[x_cols_l + [y_col]], x_cols_l, y_col def split(data, train_n, test_n): data, x_cols, y_col = data X_data = data[x_cols].as_matrix() y_data = data[y_col].as_matrix() assert X_data.shape[0] == y_data.shape[0] == data.shape[0] assert X_data.shape[1] == data.shape[1] - 1 assert len(y_data.shape) == 1 # Shuffle data indices = list(range(data.shape[0])) np.random.seed(seed=12) np.random.shuffle(indices) X_data = X_data[indices] y_data = y_data[indices] train_X = X_data[:train_n] test_X = X_data[train_n:train_n+test_n] train_y = y_data[:train_n] test_y = y_data[train_n:train_n+test_n] assert train_X.shape == (train_n, len(x_cols)) assert train_y.shape == (train_n,) assert test_X.shape == (test_n, len(x_cols)) assert test_y.shape == (test_n,) return (train_X, train_y), (test_X, test_y) def save_as_hdf5(path, data): data.to_hdf(path, '👀') if __name__ == '__main__': # TODO: Use argparse if this gets any longer... import sys if len(sys.argv) == 3 and sys.argv[2] == '--test': # Tiny test data = load(sys.argv[1]) data = split(data, 2, 1) print(data) elif len(sys.argv) == 4 and sys.argv[2] == '--to-hdf5': data, _, _ = load(sys.argv[1]) save_as_hdf5(sys.argv[3], data) elif len(sys.argv) == 3 and sys.argv[2] == '--time': from time import time start_time = time() data = load(sys.argv[1]) total_time = time() - start_time print('Took {}s'.format(total_time)) else: print('No options specified.')