mrcfile - v1.5.4

• 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

- Python
Published by colinpalmer about 1 year ago

mrcfile - v1.5.3

• 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
• Improve tests

- Python
Published by colinpalmer over 1 year ago

mrcfile - v1.5.2

• Fix opening of very large files with mmap (thanks to Hanjin Liu)

- Python
Published by colinpalmer over 1 year ago

mrcfile - v1.5.1

• Add support for numpy 2.0

- Python
Published by colinpalmer over 1 year ago

mrcfile - v1.5.0

• 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

- Python
Published by colinpalmer about 2 years ago

mrcfile - v1.4.3

• 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).

- Python
Published by colinpalmer over 3 years ago

mrcfile - v1.4.2

• Add support for passing file names as pathlib Path objects.

- Python
Published by colinpalmer over 3 years ago

mrcfile - v1.4.1

• 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

- Python
Published by colinpalmer over 3 years ago

mrcfile - v1.4.0

• 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.

- Python
Published by colinpalmer over 3 years ago

mrcfile - v1.3.0

• 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 setdata() (or if updateheader_stats() is called).
• Update numpy version compatibility to include numpy 1.20
• Minor updates to documentation

- Python
Published by colinpalmer about 5 years ago

mrcfile - v1.2.0

• 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

- Python
Published by colinpalmer over 5 years ago

mrcfile - v1.1.2

• 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.)

- Python
Published by colinpalmer about 7 years ago

mrcfile - v1.1.1

• 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

- Python
Published by colinpalmer about 7 years ago

mrcfile - v1.1.0

• 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

- Python
Published by colinpalmer over 7 years ago

mrcfile -

- Python
Published by colinpalmer over 7 years ago

mrcfile - Minor update

Changes in this release: - Small updates to documentation - Add automated testing with Python 3.4 and 3.6

- Python
Published by colinpalmer over 8 years ago

mrcfile - First stable release

- Python
Published by colinpalmer almost 9 years ago