1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
|
# Copyright (c) 2016, Science and Technology Facilities Council
# This software is distributed under a BSD licence. See LICENSE.txt.
"""
mrcfile
=======
A pure Python implementation of the MRC2014 file format.
For a full introduction and documentation, see http://mrcfile.readthedocs.io/
Functions
---------
* :func:`new`: Create a new MRC file.
* :func:`open`: Open an MRC file.
* :func:`open_async`: Open an MRC file asynchronously.
* :func:`mmap`: Open a memory-mapped MRC file (fast for large files).
* :func:`new_mmap`: Create a new empty memory-mapped MRC file (fast for large files).
* :func:`validate`: Validate an MRC file
Basic usage
-----------
Examples assume that this package has been imported as ``mrcfile`` and numpy
has been imported as ``np``.
To open an MRC file and read a slice of data:
>>> with mrcfile.open('tests/test_data/EMD-3197.map') as mrc:
... mrc.data[10,10]
...
array([ 2.58179283, 3.1406002 , 3.64495397, 3.63812137, 3.61837363,
4.0115056 , 3.66981959, 2.07317996, 0.1251585 , -0.87975615,
0.12517013, 2.07319379, 3.66982722, 4.0115037 , 3.61837196,
3.6381247 , 3.64495087, 3.14059472, 2.58178973, 1.92690361], dtype=float32)
To create a new file with a 2D data array, and change some values:
>>> with mrcfile.new('tmp.mrc') as mrc:
... mrc.set_data(np.zeros((5, 5), dtype=np.int8))
... mrc.data[1:4,1:4] = 10
... mrc.data
...
array([[ 0, 0, 0, 0, 0],
[ 0, 10, 10, 10, 0],
[ 0, 10, 10, 10, 0],
[ 0, 10, 10, 10, 0],
[ 0, 0, 0, 0, 0]], dtype=int8)
Background
----------
The MRC2014 format was described in the Journal of Structural Biology:
http://dx.doi.org/10.1016/j.jsb.2015.04.002
The format specification is available on the CCP-EM website:
http://www.ccpem.ac.uk/mrc_format/mrc2014.php
"""
# Import Python 3 features for future-proofing
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from .load_functions import new, open, read, write, open_async, mmap, new_mmap
from .validator import validate
from .version import __version__
|
