Skip to content

Releases: ccpem/mrcfile

v1.5.0

10 Jan 15:35
Compare
Choose a tag to compare
  • 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

v1.4.3

22 Sep 15:49
Compare
Choose a tag to compare
  • 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).

v1.4.2

14 Jul 12:45
Compare
Choose a tag to compare
  • Add support for passing file names as pathlib Path objects.

v1.4.1

13 Jul 10:31
Compare
Choose a tag to compare
  • 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

v1.4.0

02 Jul 20:11
Compare
Choose a tag to compare
  • 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.

v1.3.0

18 Feb 18:38
32cbe61
Compare
Choose a tag to compare
  • 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

v1.2.0

30 Nov 13:25
Compare
Choose a tag to compare
  • 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

v1.1.2

23 Jan 16:48
Compare
Choose a tag to compare
  • 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.)

v1.1.1

17 Jan 16:29
Compare
Choose a tag to compare
  • 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

v1.1.0

21 Nov 18:44
Compare
Choose a tag to compare
  • 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