[CellKai]

Fixes #158
Fixes #159
Related: #160

Target: devel. Branch based on devel (8482d1a).

Changes (imcflibs.imagej.bdv)

• run_command: MVR / BigStitcher commands are started by plugin class, so the legacy
  SPIM_Registration plugin can no longer take over a command (see IJ.run() can start the legacy SPIM_Registration plugin instead of BigStitcher / multiview-reconstruction #158). All MVR / BigStitcher
  wrappers use it; outside Fiji (test mocks) it falls back to IJ.run.
• Dialog keys and choices match MVR 9.0.11 / BigStitcher 3.0.8 (see the table in imcflibs.imagej.bdv wrappers do not match multiview-reconstruction 9 / BigStitcher 3 #159).
• New optional parameters, defaults keep the previous behaviour:
  • interest_points_registration: label, transformation and regularisation, groupings and merge
    distance, view / point selection, descriptor values, search radius, RANSAC options (new helper
    fmt_ransac_options), global optimisation strategy, fixed views, pre-alignment
  • optimize_and_apply_shifts: strategy, fixed groups, pre-alignment
  • detect_interest_points: label, downsampling, fixed intensity range, groupings
  • fuse_dataset: bounding box, preserve_original, non-rigid fusion, TIFF file name, N5 /
    OME-ZARR container name, compression, block sizes, compute-block factor (= shard size), pyramid
    levels, sharding, single container
  • stitching steps: backup_xml (default True)
• fuse_dataset default export is TIFF (uncompressed); HDF5 is not available in MVR 9 and
  raises a ValueError. N5 and OME-ZARR (v3, helper export_choice) always write a BDV/BigStitcher
  XML and a multi-resolution pyramid. Compression and block sizes are always passed (MVR's initial
  defaults), because MVR's dialogs keep the values of the previous call for the rest of the Fiji
  session. Other wrappers only pass what they set; whether all wrappers should always pass every
  value is open in MVR / BigStitcher dialogs reuse the previous call's values within a Fiji session #160.
• imcflibs.imagej.bdv imports without the PTBIOP update site (BIOP command imported in
  fuse_dataset_bdvp only).

Behaviour changes for existing callers: fuse_dataset() without export now writes TIFF
instead of (no longer possible) HDF5; ProcessingOptions timepoint strings changed (they did not
match the dialogs before).

Tests

• tests/bdv/test_mvr_wrappers.py (mock-based string tests, 16 new tests); 65 tests pass, ruff check and markdownlint clean. The Python 2 job was not run locally.
• Used in a registration / fusion pipeline (mesoSPIM whole-brain datasets) on Fiji latest with MVR
  9.0.11 / BigStitcher 3.0.8: offline on a synthetic BDV dataset (2 x 2 tiles, 2 channels, known
  shifts) the registration is identical to the previous MVR 7.0.7 pipeline (0.000 px) and the fused
  TIFFs are bit-identical; N5 / OME-ZARR export options verified in the written containers
  (compression, chunk and shard sizes, pyramid levels).

[codecov]

Codecov Report

❌ Patch coverage is 78.72340% with 20 lines in your changes missing coverage. Please review.
✅ Project coverage is 37%. Comparing base (8482d1a) to head (12e77ce).

Files with missing lines	Patch %	Lines
src/imcflibs/imagej/bdv.py	79%	20 Missing ⚠️

Additional details and impacted files

@@         Coverage Diff          @@
##           devel   #161   +/-   ##
====================================
+ Coverage     33%    37%   +4%     
====================================
  Files         25     25           
  Lines       1806   1878   +72     
====================================
+ Hits         591    689   +98     
+ Misses      1215   1189   -26     

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[Copilot]

🟡 Changes recommended

Detection and registration labels containing spaces are not preserved, and the class-based plugin dispatch lacks tests for option handling and cleanup on success and failure.

3 open issues

• Test class-based dispatch and cleanup paths · New
• Bracket interest-point label values containing spaces · New
• Bracket registration label values containing spaces · New

What changed in this PR

Updates imcflibs.imagej.bdv for multiview-reconstruction 9 and BigStitcher 3, addressing legacy plugin command collisions (#158) and outdated dialog options (#159).

Changes:

• Dispatches mapped commands by plugin class and defers the optional BIOP import.
• Expands registration, detection, stitching, and fusion options; defaults fusion to TIFF and supports N5/OME-ZARR exports.
• Adds mock-based wrapper tests and documents compatibility and behavior changes.

File	Description
tests/​bdv/​test_mvr_wrappers.py	Adds macro-string tests for updated wrappers and export options.
tests/​bdv/​test_definitionoptions.py	Updates expectations for the illumination dialog key.
src/​imcflibs/​imagej/​bdv.py	Implements class-based dispatch, corrected dialog options, and expanded wrapper parameters.
CHANGELOG.md	Documents new helpers, compatibility fixes, and changed defaults.

_{Review effort: Balanced}