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
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
|
Change log for mrcfile
======================
Version 1.5.4 (2025-01-21)
--------------------------
* Fix rare bug in mmap alignment with certain extended header sizes
* Add test and documentation code to source distribution
* Add support for Python 3.13 and numpy 2.1 & 2.2
Version 1.5.3 (2024-07-24)
--------------------------
* Fix opening of large files in numpy 2.0 (in general this time, not just for
mmap)
* Raise errors if data or extended header arrays are too large for their
dimensions to be stored in the header
* Validate header statistics only if they are set
Version 1.5.2 (2024-07-18)
--------------------------
* Fix opening of very large files with mmap in numpy 2.0 (thanks to Hanjin
Liu)
Version 1.5.1 (2024-07-11)
--------------------------
* Add support for numpy 2.0
Version 1.5.0 (2024-01-10)
--------------------------
* Add new 'indexed_extended_header' attribute to access the indexed part of
the extended header if it exists (thanks to David Waterman). Note that this
introduces a change in behaviour: code that used the 'extended_header'
attribute directly to access items in FEI1- and FEI2-type extended headers
will need to be updated to use 'indexed_extended_header' instead.
* Add support for numpy 1.24, 1.25 and 1.26 and Python 3.12
Version 1.4.3 (2022-09-22)
--------------------------
* Add helper functions for working with header labels.
* Update header statistics calculation to use float32 instead of float64. This
is about twice as fast and uses less memory, but does make the calculations
slightly less accurate and will overflow (to 'inf') if the data array
contains very large values (larger than approximately 1e19).
Version 1.4.2 (2022-07-14)
--------------------------
* Add support for passing file names as pathlib Path objects.
Version 1.4.1 (2022-07-12)
--------------------------
* Add file names to mrcfile-header output
* Improvements to validation functions (mrcfile-validate command and the
mrcfile.validate() function):
* Add a message with the file name of each file processed, to enable valid
and invalid files to be identified.
* Add a message confirming that valid files are valid.
* Ensure that all files are processed when validating multiple files, even
if some are invalid or raise exceptions on opening.
* Add support for numpy 1.23 and Python 3.10 and 3.11
Version 1.4.0 (2022-07-02)
--------------------------
* Change default MRC format version from 20140 to 20141 and update validation
to allow files with both format numbers as valid.
* Add mrcfile.read() and mrcfile.write() functions for quick one-off accesses
to the MRC data array without needing to keep an MrcFile object open (thanks
to Alister Burt).
* Allow the extended header to be set when creating a file with
mrcfile.new_mmap() (thanks to James Parkhurst).
* Add file size checks to avoid allocating huge amounts of memory when opening
corrupt or non-MRC files in permissive mode.
* Update numpy and Python version compatibility to drop support for Python
3.4 and 3.5 and numpy < 1.16, and add support for numpy 1.21 and 1.22.
* Fix bug intepreting FEI extended headers on big-endian hardware.
* Documentation updates.
Version 1.3.0 (2021-02-18)
--------------------------
* Add support for the new proposed data mode 12 (numpy float16). Note that
this causes a change in behaviour: previously float16 arrays would be
widened to float32 and saved in mode 2; now they will be kept in float16 and
saved in mode 12, which could be incompatible with other software.
* Issue Python warnings if NaN or infinite values are found when a new data
array is passed to set_data() (or if update_header_stats() is called).
* Update numpy version compatibility to include numpy 1.20
* Minor updates to documentation
Version 1.2.0 (2020-11-30)
--------------------------
* mrcfile is now available through conda-forge (thanks to Billy Poon)
* Add support for FEI2-format extended headers (thanks to Michael Saur)
* Add nstart property for convenient access to the header nxstart, nystart and
nzstart fields in the same style as the existing voxel_size property
* Read files without the final ' ' space in the map ID field (for example, as
written by MotionCor2) without errors
* Add help text for mrcfile-header and mrcfile-validate command line programs
* Fix bug in stats calculations when an empty array is passed to set_data()
* Update Python and numpy version compatibility. Now works with Python 2.7
and 3.4 - 3.9, and numpy 1.12 - 1.19
* Minor updates to documentation
Version 1.1.2 (2019-01-23)
--------------------------
* Fix incompatibility with numpy 1.16 by reading files into mutable bytearrays
instead of immutable bytes objects. Note this will cause slower reading of
bzip2-compressed files on Python 2 because Python 2's bz2 module does not
support reading directly into a bytearray and therefore the data must be
copied.
* Check that the file is large enough when reading the extended header.
(Previously, the size was only checked for reading the data array.)
Version 1.1.1 (2019-01-17)
--------------------------
* Add automated tests for numpy 1.15 and Python 3.7
* Set maximum numpy version to 1.15 to avoid known incompatibility with 1.16
Version 1.1.0 (2018-11-21)
--------------------------
* Add open_async() function for background file loading
* Add new_mmap() function for fast creation of large files
* Speed up mrcfile-header command line tool by reading headers only, not data
* Allow opening of files with incorrect machine stamps in permissive mode
* Fix bug in validation of exttyp field in Python 3 (thanks to Holger Kohr)
* Fix bug in opening files with misleading exttyp information
* Update documentation to point to Python 3.6 instead of 2.7, and fix all
cross-references
* Other documentation improvements
Version 1.0.4 (2018-01-22)
--------------------------
* Add command-line tools ('mrcfile-validate' and 'mrcfile-header') for easy MRC
file validation and header viewing
Version 1.0.3 (2018-01-19)
--------------------------
* Fix bugs due to changed behaviour in numpy 1.14
* Add automated tests for numpy 1.13 and 1.14
Version 1.0.2 (2018-01-18)
--------------------------
* Add support for FEI-format extended headers
* Documentation improvements
Version 1.0.1 (2017-10-09)
--------------------------
* Add automated tests for Python 3.4 and 3.6
* Documentation improvements
Version 1.0.0 (2017-05-22)
--------------------------
Initial stable release
Main features:
* Clean, simple API for access to MRC files
* Easy to install and use
* Validation of files according to the MRC2014 format
* Seamless support for gzip and bzip2 files
* Memory-mapped file option for fast random access to very large files
* Runs in Python 2 & 3, on Linux, Mac OS X and Windows
Automatically tested on Linux and Mac OS X for Python versions 2.7 and 3.5
and numpy versions 1.11 and 1.12
|
