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RELEASE_NOTES.rst

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0.5.6

  • TODO

0.5.6

  • In 0.5.5 a for-loop was omitted which lead to every frame being the zeroth frame in the stack. For this reason, upgrading from 0.5.5 is _strongly_ recommended.

0.5.5

  • Meta-data with keys that match those used in the header could accidently overwrite critical values, such as 'dimensions'. Any keys in the JSON meta-dictionary that overlap with the standard values are now ignored.
  • Integration tests are now performed for Python 3.8.

0.5.4

  • Added support for serialization of Python Enum objects in JSON serialization of meta-data.

0.5.3

  • Ricardo Righetto added the means to append frames to a stack.
  • Support for Python 3.4 was dropped as it is past end-of-life by Python.org.

0.5.2

  • Improved on serialization of non-standard (i.e. NumPy) types in JSON-ized meta-data by making use of the default callable in json.dumps. In particular deeply nested NumPy types should now serialize without erroring. Note that there is no support for complex numbers in JSON meta-data, as JSON itself does not support it by default.

0.5.1

  • Versions of MRCZ <= 0.4.1 were improperly writing the dimensions into the (Mx, My, Mz) volume fields. Added a check for the MRCZ version tag, and if an older file is found, it defaults to slices == 1, i.e. one 2D frame per element in the returned list. - In order to suppress the warning message, files can be read into memory and

    re-saved. A utility script for batch processing is provided in utils\update_mrcz_0.5.0.py.

0.5.0

  • Added support for lists of 3D numpy.ndarray objects. This is largely intended to support multi-channel STEM time series. Stores the number of channels per frame in the MZ value of the MRC2014 header, which must be uniform for every ndarray in the list. Any MRCZ archive that has a 'strides' key in the JSON metadata will be returned as a list of arrays. - See http://www.ccpem.ac.uk/mrc_format/mrc2014.php for header details - asList keyword arguments have been removed.
  • Fixed a bug in casting from float64/complex128 that was not actually casting.
  • Cleaned up the code to be more PEP8 compliant.

0.4.1

  • Improved docstrings in ioDM4.py.
  • Added asyncReadDM4 function, analogous to asyncReadMRC.

0.4.0

  • Fix a minor bug with casting for lists of arrays
  • Improved uncompressed write times by not using list comphrension
  • Add scaling block size for small format images (e.g. Medipix) to scale to the number of threads.
  • If the passed arrays are C_CONTIGUOUS and ALIGNED, writeMRC will use blosc.compress_ptr instead of coverting the array to a bytes object which is a significant speedup.

0.3.8

  • Auto-casts np.float64 -> np.float32 and np.complex128 -> np.complex64 but logs a warning to the user.

0.3.7

  • Updated MANIFEST.in and setup.py to make Conda-forge happy.

0.3.6

  • mrcz.ReliablePy must be imported explicitely now, as it has requirements that the base mrcz package does not. This file may be removed in the future if no users are using it.

0.3.5

  • If blosc is not installed and the user attempts to operate with compression on an ImportError is raised.
  • Documentation now using Numpy docstrings.

0.3.4

  • Add (temporarily) MRC types for uint32 and int32 to support 24-bit detectors. May break in the future, as the CCP-EM committee should make the final decision on such enumerations.
  • Added handling of NumPy scalars (i.e. np.float32(1.0)) in metadata so that JSON serialization does not generate errors. Values will be case to Python int or float as appropriate.

0.3.3

  • Removed use of star-expansion of args as it breaks Python 2.7/3.4.

0.3.2

  • Made blosc an optional dependency due to difficulties involved in building wheels for PyPi.
  • Implemented reading/writing of list of equally-shaped 2D ndarray`s instead of a single 3D `ndarray, where the list represents the Z-axis. This approach can be helpful for larger arrays that do not have to be continuous as the operating system can more easily interleave them into memory.

0.3.1

  • Added ascii identifier label 'MRCZ' + <__version__> to the labels. I.e. at byte 224 in the header will appear b'MRCZ0.3.1'

0.3.0

  • Documentation now available at http://python-mrcz.readthedocs.io/
  • Added continuous integration testing with Appveyor and TravisCI, which was previously handled by c-mrcz.
  • Added handling for dask.array.core.Array objects.
  • numpy.ndarrays inside meta dictionaries will be converted to list objects to facilitate serialization.
  • Updated license to BSD-3-clause from BSD-2-clause.
  • Various bug fixes.

0.2.1-4

  • Various bug fixes to incorporate into Hyperspy.

0.2.0

  • Added support for asynchronous reading and writing.

0.1.4a1

  • Fixed a bug with the machine-stamp not being converted to bytes properly.

0.1.4a0

  • Fixed a bug in import of mrcz from ReliablePy

0.1.3a2

  • Added ReliablePy, an interface for Relion .star and Frealign .par files.
  • Fixes to maintain cross-compatibility with c-mrcz. Main functions are readMRC and writeMRC. readMRC always returns a header now.
  • Added mrcz_test suite, which also tests c-mrcz if it's found in the path.
  • Fixed bugs related to mrcz_test.py

0.1.1a1

  • Renamed 'cLevel' to 'clevel' to maintain consistency with blosc naming convention.
  • Updated license from MIT to BSD 2-clause.

0.1.0dev0

Initial commit