Bdv update library

[lguerard]

This pull request introduces several enhancements and refactorings to the src/imcflibs/imagej/bdv.py module, focusing on improving dataset definition and export workflows, as well as increasing flexibility and maintainability. The most significant updates include support for directly passing file lists to the manual dataset definition, improved options for exporting datasets to OME-TIFF, and the addition of a utility for channel-suffixed file naming.

Enhancements to dataset definition and export:

• Added support for passing a list of files (list_files) directly to the define_dataset_manual function, enabling the use of explicit file lists in "show_list" mode rather than relying solely on file patterns. The options string is now constructed accordingly. [1] [2] [3]
• Refactored the fuse_dataset_bdvp function to allow specifying the number of resolution levels, LZW compression, and the fusion method, and updated its parameter names and documentation for clarity and flexibility. The function now also waits for the export command to complete.

Utility and code quality improvements:

• Added a new utility function join_files_with_channel_suffix to generate lists of filenames with channel suffixes, facilitating workflows where each channel is stored in a separate file.
• Updated the resave_as_h5 function to use the correct processing options object and changed the ImageJ command to "Resave as HDF5 (local)" for better accuracy. [1] [2]

Imports and minor cleanups:

• Added import for AlphaFusedResampledSource to support the new fusion method default, and made minor whitespace and code cleanups. [1] [2]

[ehrenfeu]

As discussed, please remove the changes to fuse_dataset_bdvp from this PR and merge them into #106.

[codecov]

Codecov Report

❌ Patch coverage is 4.54545% with 21 lines in your changes missing coverage. Please review.
✅ Project coverage is 24%. Comparing base (745fc61) to head (a03a62e).
⚠️ Report is 51 commits behind head on devel.

Files with missing lines	Patch %	Lines
src/imcflibs/imagej/bdv.py	5%	21 Missing ⚠️

Additional details and impacted files

@@         Coverage Diff          @@
##           devel   #118   +/-   ##
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- Coverage     25%    24%   -1%     
====================================
  Files         25     25           
  Lines       1688   1733   +45     
====================================
+ Hits         421    423    +2     
- Misses      1267   1310   +43     

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[ehrenfeu]

🚨 Please do a git pull before, as I made a few changes to the PR already! 🚨

I added several comments to be addressed here before we can merge this.

[ehrenfeu]

This is expected to fail as DefinitionOptions is a class defined in this very file here.

➡️ Nicely illustrates the need for unit tests.

[ehrenfeu]

Same as above.

[ehrenfeu]

This example doesn't provide any additional information as it is just the most simple case of how to call this function.

Possible options:

• either remove the example or
• provide additional value by adding code that shows at least how to construct the two parameters used here
• if possible also have a more complex example that uses more of the function's parameters

Note: please use the right syntax for docstring examples (they need to be prefixed with ">>> ") in order to have them rendered correctly, see the numpydoc format documentation, section "Examples" for details.

[ehrenfeu]

Several requests here:

• Please move this into imcflibs.pathtools as this is not BDV related and potentially useful for other parts as well.
• Any import command should be at the module top, unless there is a very good reason.
• Please fix the docstring syntax to use single backticks instead of doubled backticks: https://pdoc.dev/docs/pdoc.html#link-to-other-identifiers