Skip to content

skimage.io use is deprecated #465

@nkeim

Description

@nkeim

Starting with skimage 0.25, the plugin argument to e.g. imread() is deprecated and will be removed in 0.27. Using the imageio package directly is the favored replacement. A simple read operation in pims will give an error like this:

pims/image_sequence.py:85: FutureWarning: The plugin infrastructure in `skimage.io` and the parameter `plugin` are deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not use the parameter `plugin`. Instead, use `imageio` or other I/O packages directly. See also `imread`.
  return imread(filename, **kwargs)

A discussion of the change is here: https://discuss.scientific-python.org/t/long-term-plan-for-skimage-io-plugin-infrastructure/1079

This should be a straightforward change for pims, if we can get to it soon. Off the top of my head, it means

  • Checking the reader resolution order to make sure imageio is preferred over skimage
  • Adding imageio as a package requirement
  • Trying to drop skimage as a package requirement

In the future, we would drop support for skimage readers altogether (rather than check the version).

Metadata

Metadata

Assignees

No one assigned

    Labels

    maintenanceCaused by newer versions of dependencies

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions