Skip to content

v0.5.0

Choose a tag to compare

View all tags
@kbestak kbestak released this 13 Nov 20:03
· 4 commits to main since this release
v0.5.0
b3a6dc1
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

What's Changed

Rework of Backsub to not have Palom as a dependency reducing the environment size and making it lightweight, and reducing the output file size, while keeping the time and memory usage efficiency.

Added

  • compression parameter
  • two RAM profiles: (1) default, uses moderate RAM. (2) Uses approximately half of the default RAM at the cost of a slight loss in precision of the calculation of the downsized dimensions of the pyramidal output image. This means the dimensions of the pyramidal level will differ between profile 1 and 2. The high-resolution level is not affected by this.
  • organizes the tool in five scripts: (1) CLI, (2) ome-schema structure, (3) ome-schema writer, (4) background subtraction and writing of output image and (5) extraction of metadata from Lunaphore COMET images to create the marker table.
  • restructured README
  • tile-size parameter now defaults to 256 instead of 1024
  • support for different data types - primarily np.uint8 in addition to np.uint16
  • Added validation and warnings for invalid or missing backgrounds
  • Necessary prerequisites for PyPI release

Fixed

  • output image file-size is reduced by applying lossless compression ("LZW" by default)
  • Updated documentation, Dockerfile, and environment setup
  • Improved logging system and CLI descriptions

Removed

  • Palom and OpenCV as dependencies
  • old scripts, version history should be checked instead.
  • chunksize argument - chunking is done now only by the default dask.array behaviour

Full Changelog: v0.4.1...v0.5.0

Assets 2
Loading