Add AreTomo3 wrapper for tilt series alignment#407
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alisterburt merged 1 commit intowarpem:mainfrom Aug 28, 2025
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- Add ProcessingOptionsTomoAretomo3 class to WarpLib/TiltSeries/TiltSeries.cs - Add TomoAretomo3 worker method to WarpLib/WorkerWrapper.cs - Add AreTomo3 command to WarpTools/Commands/Tiltseries/AreTomo3Tiltseries.cs - Add AreTomo3 case to WarpWorker/WarpWorker.cs with proper command construction - Support automatic sample thickness estimation when AlignZ=0 - Maintain compatibility with existing Warp features (axis iteration, batch processing) - Add comprehensive parameter validation and help text This implementation follows the same architecture pattern as the existing AreTomo2 command and provides AreTomo3-specific parameters and functionality.
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Amazing work @davidetorre99 - thanks for putting time into this, I'm sure being on the latest version of AreTomo will be appreciated by many of our users 🙂 relevant context: AreTomo support was initially introduced at AreTomo v1.3.4
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release v2.0.0dev35 building here, congrats on your first PR to Warp! 🥳 |
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This PR adds AreTomo3 support to WarpTols, providing a new
ts_aretomo3command that enables tilt series alignment using AreTomo3 with full integration into the existing WarpTools workflow.New Files
WarpTools/Commands/Tiltseries/AreTomo3Tiltseries.cs- New command implementationModified Files
WarpLib/TiltSeries/TiltSeries.cs- AddedProcessingOptionsTomoAretomo3classWarpLib/WorkerWrapper.cs- AddedTomoAretomo3methodWarpWorker/WarpWorker.cs- Added AreTomo3 case with proper command constructionNotes
Acknowledgement
This PR comes directly from the encouragement and support of @alisterburt, big big thanks to him for helping and guiding this feature!