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Centralizing and simplifying transformation system in SpatialData - #1291

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ajkswamy wants to merge 54 commits into

mainfrom

transformation_manager

Draft

Centralizing and simplifying transformation system in SpatialData#1291
ajkswamy wants to merge 54 commits into
mainfrom
transformation_manager

Commits on Oct 27, 2026
- Transformation manager foundation (#1164)
  ajkswamy
  committed
  15d8f00
- Transformation manager foundation (#1164)
  ajkswamy
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  89b8667
- Creates the graph module based on the Ngff* classes
  
  Tomaz-Vieira
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  ajkswamy
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  db849b7
- addresses some PR comments, simplifies MapAxis
  
  Tomaz-Vieira
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  ajkswamy
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  dccc3f6
- Adds ProjectAxisEdge, makes inverse return optional
  
  Tomaz-Vieira
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  ajkswamy
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  950ffd7
- Moves exceptions to exceptions.py, edge names default to None
  
  Tomaz-Vieira
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  0a2f374
- Use custom exceptions everywhere, adds Raises to docstrings
  
  Tomaz-Vieira
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  ajkswamy
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  d29a2a4
- Fix Affine.from_affine_matrix slicing]
  
  Tomaz-Vieira
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  ajkswamy
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  3618cdd
- Fix coords bug when reading from OMEZarrMultiscale. Some cleanup
  
  Tomaz-Vieira
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  4313c56
- Adds test for parsing OMEZarrMultiscale
  
  Tomaz-Vieira
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  9c2e1d3
- Adds transformations tests, fixes some slicing bugs
  
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  f94498e
- Adds basic .sel test to parsed multiscale
  
  Tomaz-Vieira
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  c0da25f
- Removes unused class
  
  Tomaz-Vieira
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  ajkswamy
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  3a94382
- Adds more slicing tests to parsed multiscales
  
  Tomaz-Vieira
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  ajkswamy
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  129fd2d
- Adds/fixes comments in try_parse_ngff06_multiscales
  
  Tomaz-Vieira
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  ajkswamy
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  e050c10
- Removes to_model methods for now
  
  Tomaz-Vieira
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  ajkswamy
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  5836cd0
- Moves AxisParsingException to exceptions.py
  
  Tomaz-Vieira
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  ajkswamy
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  de5718c
- Moves AxisParsingException back into vert.py to prevent circular imports
  
  Tomaz-Vieira
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  d58038d
- Fixes docstrings, list exceptions in "Raises"
  
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  55e1ba5
- Incorporates parse_project_axis
  
  Tomaz-Vieira
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  ajkswamy
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  d802aa8
- Fixes parsing translatiion model getting bad name
  
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  ajkswamy
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  c18df09
- Adds test for parsing *Edge transforms from ngff
  
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  c10c758
- Fixes dependencies on ome-zarr and ome-zarr-models
  
  Tomaz-Vieira
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  b6d4a66
- Cleans up transform_points for rotation and affine
  
  Tomaz-Vieira
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  ec7f22b
- Fixes renamed fields in ome-zarr-models
  
  Tomaz-Vieira
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  ajkswamy
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  05a28c7
- Use frozen dataclasses for CoordSystems and Axis. Fix MapAxisEdge
  
  Tomaz-Vieira
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  ajkswamy
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  98c1b37
- Enforces Rotation matrix is orthonormal with det==1
  
  Tomaz-Vieira
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  ajkswamy
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  834f921
- Bump xarray so we can use RangeIndex
  
  Tomaz-Vieira
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  ajkswamy
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  6ca7e21
- Removes try-from_model_or_defaul for now
  
  Tomaz-Vieira
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  ajkswamy
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  0c3ae64
- Emits warning on AffineEdge.inverse when condition is big
  
  Tomaz-Vieira
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  ajkswamy
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  1951436
- Uses matrix in exceptions
  
  Tomaz-Vieira
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  ajkswamy
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  475d15b
Commits on Nov 9, 2026
- feat(NgffAxisTypes): defined
  
  ajkswamy
  authored and
  Tomaz-Vieira
  committed
  9832d6d
- refac + fix(TransformationManager + Tests): to work with new Vert and Edge classes; split into files
  
  ajkswamy
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  Tomaz-Vieira
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  20af288
- feat(transformations): added _to_ngff_transformation_edge() for all classes
  
  ajkswamy
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  Tomaz-Vieira
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  095686f
- feat(transformations_facade): setting and removing transformations
  
  ajkswamy
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  Tomaz-Vieira
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  3f83416
- feat(sd-transformations): MapAxis._to_ngff_transformation_edge
  
  ajkswamy
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  Tomaz-Vieira
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  261a5f7
- feat: doc strings
  
  ajkswamy
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  Tomaz-Vieira
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  5f24aa7
- refac(model, transformation._graph): code reorganization in files and imports centralized from __init__s
  
  ajkswamy
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  Tomaz-Vieira
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  672b569
- feat(spatialdata.SpatialData): add transform info from spatialelement.attrs to graph
  
  ajkswamy
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  Tomaz-Vieira
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  0f08a75
- fix + reorg (transformations): fix circular import issue
  
  ajkswamy
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  Tomaz-Vieira
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  5c0f3cd
- feat(transformations): get_union_of_axes + tests
  
  ajkswamy
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  Tomaz-Vieira
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  3451462
- feat(transformations): dynamic project axis classes, no tests yet
  
  ajkswamy
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  Tomaz-Vieira
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  732b94b
- reorg (tests/transformations/graph/utils)
  
  ajkswamy
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  7f03be0
- reorg (tests/transformations/graph): consolidated conftest files
  
  ajkswamy
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  Tomaz-Vieira
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  04344cc
- feat (transformations/_graph/exceptions): passing only name instead of complete transformation object
  
  ajkswamy
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  Tomaz-Vieira
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  5bc5100
- wip (dynamic projection axes)
  
  ajkswamy
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  Tomaz-Vieira
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  5fb6860
- fix (test_dynamic_axis_edges.py): tests passing
  
  ajkswamy
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  Tomaz-Vieira
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  541b087
- fix (transformations/utils/get_union_of_axes): during union, sorting axes based on type first, name next
  
  ajkswamy
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  Tomaz-Vieira
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  26b39b2
- fix (dynamic project axis): removed unused code
  
  ajkswamy
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  Tomaz-Vieira
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  d6c435f
- fix (transformation graph): assorted minor fixes
  
  ajkswamy
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  Tomaz-Vieira
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  7bcce04
- feat (spatialdata.__init__): coordinate systems and edges added based on bags of elements
  
  ajkswamy
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  Tomaz-Vieira
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  6aabf6a
- fix + reorg (literals, get_axes_names, get_spatial_axes): avoid circular imports
  
  ajkswamy
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  Tomaz-Vieira
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  a540da3
- fix (attrs accessor registration for dask data structures) explicit function call
  
  ajkswamy
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  Tomaz-Vieira
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  743a9c3
- fix (docs): moved get_spatial_axes from model utils to tranformations utils
  
  ajkswamy
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  Tomaz-Vieira
  committed
  14578ff

Commits

Commits on Oct 27, 2026

Commits on Nov 9, 2026