Source code for

import os
from ast import literal_eval
from pathlib import Path

import numpy as np

[docs]def read_info(filename: os.PathLike) -> dict: """Read volume metadata. Parameters ---------- filename : PathLike Path to the file. Returns ------- dct : dict Dictionary with the metadata. """ dct = {} with open(filename, 'r') as f: for line in f: line = line.strip() if not line: continue if line.startswith('!'): continue key, val = line.split('=') key = key.strip() val = val.strip() try: val = literal_eval(val) except ValueError: pass dct[key] = val return dct
[docs]def load_vol(filename: os.PathLike, dtype=np.float32, mmap_mode: str = None, shape: tuple = None) -> np.ndarray: """Load data from `.vol` file. The image shape is deduced from the `` file. If this file is not present, the shape can be specified using the `shape` keyword. Parameters ---------- filename : os.PathLike Path to the file. dtype : dtype, optional Numpy dtype of the data. mmap_mode : None, optional If not None, open the file using memory mapping. For more info on the modes, see: :func:`numpy.memmap` shape : tuple, optional Tuple of three ints specifying the shape of the data (order: z, y, x). Returns ------- result : numpy.ndarray Data stored in the file. """ filename = Path(filename) if not filename.exists(): raise IOError(f'No such file: {filename}') try: filename_info = filename.with_suffix(filename.suffix + '.info') if not shape: info = read_info(filename_info) shape = info['NUM_Z'], info['NUM_Y'], info['NUM_X'] except FileNotFoundError: raise ValueError( f'Info file not found: {}, specify ' 'the volume shape using the `shape` parameter.') from None result: np.ndarray if mmap_mode: result = np.memmap(filename, dtype=dtype, shape=shape, mode=mmap_mode) # type: ignore else: result = np.fromfile(filename, dtype=dtype) result = result.reshape(shape) return result