Sorry to bother you, I’m having some trouble using the tool. I selected alignment in groom and set it to ICP algorithm alignment, and then I clicked the run button. A groomed file will appear in the current folder, and the files inside all end with ‘_groomed.vtk’. When visualizing, I found that these groomed files were not aligned. How do I download the aligned .vtk data displayed on the interface?
ShapeWorks doesn’t modify the position of the meshes for a couple of reasons:
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This allows both the original and groomed shapes to be in the original coordinate space
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This minimizes resampling for segmentations
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Allows for multiple alignments when using multiple anatomies (e.g. local alignment per domain and global alignment, combined)
In the Studio GUI and in the optimization, we instead pass the transform and the original data. The viewer applies the transform only as part of a view/camera transform. The optimization uses the initial transform and may add additional transforms with procrustes.
To apply the alignment transform you can use the ShapeWorks Python API (Mesh.applyTransform)