Source code for resqpy.olio.ab_toolbox

"""Small utility functions related to use of pure binary files."""

# Nexus is a registered trademark of the Halliburton Company

import logging

log = logging.getLogger(__name__)

import numpy as np
from typing import Tuple, Optional

ab_dtype_dict = {'.db': np.float64, '.fb': np.float32, '.lb': np.int64, '.ib': np.int32, '.bb': np.int8}

[docs]def load_array_from_ab_file(file_name, shape, return_64_bit = False): """Loads a pure binary file into a numpy array, optionally converting to 64 bit.""" count = 1 for axis in range(len(shape)): count *= shape[axis] dtype = ab_dtype_dict[file_name[-3:]] with open(file_name, 'rb') as fp: a = np.fromfile(fp, dtype = dtype, count = count).reshape(tuple(shape)) try: # expected to return null c = if len(c): log.warning('binary file contains more data than expected: ' + file_name) except Exception: pass return a
[docs]def cp_binary_filename(file_name, nexus_ordering = True): """Returns a version of the file name with extension adjusted to indicate reseq order and pure binary.""" if file_name[-9:] == '.reseq.db': root_name = file_name[:-9] elif file_name[-3:] == '.db': root_name = file_name[:-3] else: root_name = file_name if nexus_ordering: return root_name + '.db' else: return root_name + '.reseq.db'
[docs]def binary_file_extension_and_np_type_for_data_type(data_type: str) -> Optional[Tuple[str, object]]: """Returns a file extension suitable for a pure binary array (ab) file of given data type.""" binary_file_ext_and_type = { 'real': ('.db', np.dtype('f8')), 'float': ('.db', np.dtype('f8')), 'int': ( '.lb', np.dtype('i8'), ), 'integer': ('.lb', np.dtype('i8')), 'bool': ('.bb', np.dtype('?')), 'boolean': ('.bb', np.dtype('?')) } try: return binary_file_ext_and_type.get(data_type) except KeyError: log.error(f'Unknown data_type [{data_type}] passed to binary_file_extension_and_np_type_for_data_type') raise