Release notes

v0.5

  • API: all readers do not support the keyword arguments process_func, dtype and as_grey anymore. Please consult the documentation on Pipelines on how to convert videos. (see Pipelines) (PR 250)

v0.4

  • API: N-dimensional readers now smartly use get_frame methods; depending on the bundle_axes settings, the reader optimizes which get_frame methods is optimal to use. Readers that derive from FramesSequenceND will need to call FramesSequenceND.__init__() on initialization, and also will need to register get_frame methods using _register_get_frame(method, axes). (PR 227)
  • API: Swap elements of frame_shape in SpeStack to match frames’ shape. (PR 241)
  • API: Swap elements of frame_shape in PyAVVideoReader to match frames’ shape. (PR 251)
  • API: Reimplement the PyAVVideoReader (or: Video) into a reader that uses the frame timestamps and reader frame rate to compute the frame index. The new reader is named PyAVReaderTimed and the names PyAVVideoReader and Video refer to it. For the case when the video misses timestamps, the old implementation is available under PyAVReaderIndexed.
  • API: The video exporter (export) takes more arguments. The argument 'format' has been renamed to 'pixel_format', while 'format' now refers to the container format. (PR 257)
  • Fixed filename sorting when list is provided explicitely to ImageSequence (PR 252)
  • Fixed plot_to_frame with savefig.bbox == 'tight' (PR 248)
  • Added a reader that wraps ImageIO ImageIOReader (PR 233)
  • Added a reader that wraps MoviePy MoviePyReader (PR 233)
  • Added a reader for single images ImageReader and ImageReaderND (PR 249)
  • Added a reader that stacks readers into a multidimensional reader ReaderSequence (PR 249)
  • Added a video exporter based on MoviePy (PR 233)
  • Added BioformatsReader.metadata.fields that lists all metadata fields. (PR 230)

v0.3.4

  • API: Swap elements of frame_shape in SpeStack to match frames’ shape.

v0.3.3

  • Fix compatibility with Pillow v0.3.0 (PR 204)
  • API: plot_to_frame and plots_to_frame now take fig_size_inches and bbox_inches as keyword arguments instead of passing on all keyword arguments to imsave (PR 206)
  • Fix zipfile handling in Py3 (PR 199)
  • Fix CINE reader for Py2 (PR 219)
  • Support non-monochrome and packed-bits images in NorpixSeq (PR 218)
  • Update documentation
  • Update slicerator dependency to v0.9.7 (fixes pipeline nesting)
  • Update bioformats version to v5.1.7 (PR 224)

v0.3.2

  • Bug fixes
  • Build fixes and fewer required deps

v0.3.1

  • Fix build-related mistakes in v0.3.0.

v0.3.0

  • Refactor the slicing logic into a separate package, slicerator.
  • Extend the slicing logic to allow nested lazy slicing.
  • Add pipeline feature; deprecate process_func.
  • Support multispectral and multidimensional images.
  • Add Norpix reader.

v0.2.2

This is a simple maintenance release, introducing no functionality changes. The packaging and installation are simplified by adopting tifffile as a dependency rather than directly including the source PIMS.

Henceforth, to install PIMS on any platform, we recommend conda install -c soft-matter pims, but pip install pims is also supported.

v0.2.1

  • Use PyAV for handling video files
  • Ships with Christoph Gohlke’s tifffile
  • Added support for .cine files
  • Added prototype of universal open function which tries to guess the correct class to use to handle a given file based on the extension
  • Added ability to create an ImageSequence from a list of paths