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Bdv update library #118
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Bdv update library #118
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* 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
ehrenfeu
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As discussed, please remove the changes to fuse_dataset_bdvp from this PR and merge them into #106.
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #118 +/- ##
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- Coverage 25% 24% -1%
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Files 25 25
Lines 1688 1733 +45
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+ Hits 421 423 +2
- Misses 1267 1310 +43 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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This pull request introduces several enhancements and refactorings to the
src/imcflibs/imagej/bdv.pymodule, 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:
list_files) directly to thedefine_dataset_manualfunction, 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]fuse_dataset_bdvpfunction 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:
join_files_with_channel_suffixto generate lists of filenames with channel suffixes, facilitating workflows where each channel is stored in a separate file.resave_as_h5function 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:
AlphaFusedResampledSourceto support the new fusion method default, and made minor whitespace and code cleanups. [1] [2]