Changelog

All notable changes to FISSA will be documented here.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Categories for changes are: Added, Changed, Deprecated, Removed, Fixed, Security.

Version 0.7.1

Release date: 2020-05-22. Full commit changelog.

Fixed

  • Loading oval, ellipse, brush/freehand, freeline, and polyline ImageJ ROIs on Python 3. (#135)

Added

  • Support for rotated rectangle and multipoint ROIs on Python 3. (#135)

Version 0.7.0

Release date: 2020-05-04. Full commit changelog.

Security

  • Caution: This release knowingly exposes a new security vulnerability. In numpy 1.16, the default behaviour of numpy.load changed to stop loading files saved with pickle compression by default, due to potential security problems. However, the default behaviour of numpy.save is still to save with pickling enabled. In order to preserve our user-experience and backward compatibility with existing fissa cache files, we have changed our behaviour to allow numpy to load from pickled files. (#111)

Changed

  • Officially drop support for Python 3.3 and 3.4. Add python_requires to package metadata, specifying Python 2.7 or >=3.5 is required. (#114)
  • Allow tuples and other sequences to be image and roi inputs to FISSA, not just lists. (#73)
  • Multiprocessing is no longer used when the number of cores is specified as 1. (#74)
  • Changed default axis argument to internal function fissa.roitools.shift_2d_array from None to 0. (#54)
  • Documentation updates. (#112, #115, #119, #120, #121)

Fixed

  • Allow loading from pickled numpy saved files. (#111)
  • Problems reading ints correctly from ImageJ rois on Windows; fixed for Python 3 but not Python 2. This problem does not affect Unix, which was already working correctly on both Python 2 and 3. (#90)
  • Reject unsupported axis argument to internal function fissa.roitools.shift_2d_array. (#54)
  • Don’t round number of npil segments down to 0 in fissa.roitools.split_npil when using adaptive_num=True. (#54)
  • Handling float num_slices in fissa.roitools.split_npil, for when adaptive_num=True, which was causing problems on Python 3. (#54)

Added

  • Test suite additions. (#54, #99)

Version 0.6.4

Release date: 2020-04-07. Full commit changelog.

This version fully supports Python 3.8, but unfortunately this information was not noted correctly in the PyPI metadata for the release.

Fixed

  • Fix multiprocessing pool closure on Python 3.8. (#105)

Version 0.6.3

Release date: 2020-04-03. Full commit changelog.

Fixed

  • Specify a maximum version for the panel dependency of holoviews on Python <3.6, which allows us to continue supporting Python 3.5, otherwise dependencies fail to install. (#101)
  • Save deltaf to MATLAB compatible output. (#70)
  • Wipe downstream data stored in the experiment object if upstream data changes, so data that is present is always consistent with each other. (#93)
  • Prevent slashes in paths from doubling up if the input path has a trailing slash. (#71)
  • Documentation updates. (#91, #88, #97, #89)

Version 0.6.2

Release date: 2020-03-11. Full commit changelog.

Fixed

  • Specify a maximum version for tifffile dependency on Python <3.6, which allows us to continue supporting Python 2.7 and 3.5, which otherwise fail to import dependencies correctly. (#87)
  • Documentation fixes and updates. (#64, #65, #67, #76, #77, #78, #79, #92)

Version 0.6.1

Release date: 2019-03-11. Full commit changelog.

Fixed

  • Allow deltaf.findBaselineF0 to run with fewer than 90 samples, by reducing the pad-length if necessary. (#62)
  • Basic usage notebook wasn’t supplying the correct datahandler_custom argument for the custom datahandler (it was using datahandler instead, which is incorrect; this was silently ignored previously but will now trigger an error). (#62)
  • Use ncores_preparation for perparation step, not ncores_separation. (#59)
  • Only use ncores_separation for separation step, not all cores. (#59)
  • Allow both byte strings and unicode strings to be arguments of functions which require strings. Previously, byte strings were required on Python 2.7 and unicode strings on Python 3. (#60)

Version 0.6.0

Release date: 2019-02-26. Full commit changelog.

Added

  • Python 3 compatibility. (#33)
  • Documentation generation, with Sphinx, Sphinx-autodoc, and Napoleon. (#38)

Version 0.5.3

Release date: 2019-02-18. Full commit changelog.

Fixed

  • Fix f0 detection with low sampling rates. (#27)

Version 0.5.2

Release date: 2018-03-07. Full commit changelog.

Changed

  • The default alpha value was changed from 0.2 to 0.1. (#20)

Version 0.5.1

Release date: 2018-01-10. Full commit changelog.

Added

  • Possibility to define custom datahandler script for other formats
  • Added low memory mode option to load larger tiffs frame-by-frame (#14)
  • Added option to use ICA instead of NMF (not recommended, but is a lot faster).
  • Added the option for users to define a custom data and ROI loading script. (#13)

Fixed

  • Fixed custom datahandler usage. (#14)
  • Documentation fixes. (#12)

Version 0.5.0

Release date: 2017-10-05

Initial release