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@lguerard lguerard commented Jan 14, 2026

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]

* Add optional list_files parameter to define_dataset_manual
* Update processing options to use bdv.ProcessingOptions
* Improve logging for manual dataset definition options
* Refactor fuse_dataset_bdvp parameters for clarity
* Introduce join_files_with_channel_suffix function for file handling
@lguerard lguerard changed the base branch from master to devel January 14, 2026 08:32
@ehrenfeu ehrenfeu added blocked Blocked by another issue / PR new-major Change introduced in PR will require a new major release. labels Jan 14, 2026
@ehrenfeu ehrenfeu added this to the 1.6.0 milestone Jan 14, 2026
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As discussed, please remove the changes to fuse_dataset_bdvp from this PR and merge them into #106.

@ehrenfeu ehrenfeu added the duplicate This issue or pull request already exists label Jan 14, 2026
@ehrenfeu ehrenfeu moved this to In progress in imcflibs Jan 14, 2026
@CellKai CellKai mentioned this pull request Jan 14, 2026
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codecov bot commented Jan 14, 2026

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 (24126c7).
⚠️ Report is 27 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   +/-   ##
====================================
- Coverage     25%    24%   -1%     
====================================
  Files         25     25           
  Lines       1688   1733   +45     
====================================
+ Hits         421    423    +2     
- Misses      1267   1310   +43     

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