Description

This PR proposes several improvements mainly to the io module:

• Add option to specify dataset description in phasor_to_ometiff. Requires tifffile>=2024.8.30.

• Add a note to phasor_to_ometiff that the format is experimental and not meant for long-term storage.

• Add phasor_to_simfcs_referenced function to store phasor coordinates in SimFCS R64 format. The function writes chunked and/or padded files for dimensions not supported by the R64 format.

• Add phasor_from_simfcs_referenced function to directly read phasor coordinates from SimFCS REF or R64 files.

• Remove redundant read_ref and read_r64 functions, which are replaced by phasor_from_simfcs_referenced.

• Delay import of xarray since not all functions are using xarray.

• Add private _utils.chunk_iter function to iterate over chunk indices of ndarrays.

• Move phasor._parse_harmonic function to _utils.parse_harmonic since it is used in more than one module.

• Add tests for parse_harmonic function.

• Update tutorials with new functionality.

• Add private _utils module to API documentation to make sure docstrings are rendered correctly.

Things postponed from this PR to another PR:

• Add read_imspector_tiff function to read FLUTE dataset files (Support ImSpector FLIM TIFF files #105).

• Add option to return specific harmonics from phasor_from_ometiff.

• Consider changing phasor_from_ometiff function to return numpy instead of xarray arrays. Attributes would be returned as a separate dict.

Release note

Summarize the changes in the code block below to be included in the
release notes:

Improve io module

Checklist

• The pull request title, summary, and description are concise.
• Related issues are linked in the description.
• New dependencies are explained.
• The source code and documentation can be distributed under the MIT license.
• The source code adheres to code standards.
• New classes, functions, and features are thoroughly tested.
• New, user-facing classes, functions, and features are documented.
• New features are covered in tutorials.
• No files other than source code, documentation, and project settings are added to the repository.