MRC format#

The .mrc format is widely used for tomographic data. The implementation of this plugin is based on this specification and has partial support for FEI’s custom header.

Note

When reading 4D-STEM data saved by the Velox software, the data are read as a stack of diffraction patterns, but the navigation_shape argument can be used to specify the shape of the navigation space.

Note

For .mrc files, the file_reader takes the mmap_mode keyword argument to load the file using a different mode (default is copy-on-write) . However, note that lazy loading does not support in-place writing (i.e lazy loading and the r+ mode are incompatible).

See also the format documentation by the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM).

This plugin does not support writing .mrc files, which can however be done using the mrcz plugin. No additional feature of the mrcz format should be used in order to write a .mrc compliant file. In particular, the compressor argument should not be passed (Default is None):

import numpy as np
from rsciio import mrcz

data = np.random.randint(100, size=(10, 100, 100)).astype('int16')
s = hs.signals.Signal2D(data)
s_dict = s.as_dictionary()

mrcz.file_writer('test.mrc', s_dict)

Alternatively, use hyperspy.signal.BaseSignal.save(), which will pick the mrcz plugin automatically:

import hyperspy.api as hs
import numpy as np

data = np.random.randint(100, size=(10, 100, 100)).astype('int16')
s = hs.signals.Signal2D(data)
s.save("data.mrc")

API functions#

rsciio.mrc.file_reader(filename, lazy=False, mmap_mode=None, navigation_shape=None, endianess='<', **kwds)#

File reader for the MRC format for tomographic data.

Parameters:

  • filename (str, pathlib.Path) – Filename of the file to read or corresponding pathlib.Path.

  • lazy (bool, Default=False) – Whether to open the file lazily or not.

  • endianess (str, Default="<") – "<" or ">", depending on how the bits are written to the file.

  • navigation_shape (tuple, None) – Specify the shape of the navigation space.

  • mmap_mode ({None, "r+", "r", "w+", "c"}, Default=None) – Argument passed to numpy.memmap(). If None (default), the value is "r" when lazy=True, otherwise it is "c".

Returns:

List of dictionaries containing the following fields:

  • ’data’ – multidimensional numpy array

  • ’axes’ – list of dictionaries describing the axes containing the fields ‘name’, ‘units’, ‘index_in_array’, and either ‘size’, ‘offset’, and ‘scale’ or a numpy array ‘axis’ containing the full axes vector

  • ’metadata’ – dictionary containing the parsed metadata

  • ’original_metadata’ – dictionary containing the full metadata tree from the input file

Return type:

list of dicts