Add SBEM stage-position XY alignment option

[msayr]

Motivation

• Improve coarse XY tile placement when SBEM Image stage coordinates are available because filename-based grid inference can place tiles far from their true positions. The new option uses stage x,y origins to stabilize initial tile positions before elastic alignment.

Description

• Add a --use-sbem-stage-positions prep-config flag (persisted to main_config.json) and validate it is only used with --mode sbem_image in prep_config_xy.py.
• Parse raw SBEM Image stage origins from imagelist_*.txt, expose get_stage_origin_from_name and get_stage_origins in emalign.io.sbem_image.
• Extend get_coarse_offset in emalign.align_xy.stitch_ongrid to accept tile_origins and apply them via _apply_tile_origin_offsets to convert stage-origin deltas into SOFIMA neighbor offsets.
• Wire the feature into stack alignment: align_stack_xy computes pixel-space tile_origins from stage origins when use_stage_positions is enabled and only allows this in sbem_image mode.
• Add tests: a stage-origin lookup test in tests/test_sbem_image.py and a conversion test tests/test_sbem_stage_offsets.py for _apply_tile_origin_offsets.

Testing

• Ran unit tests with PYTHONPATH=. pytest -q tests/test_sbem_image.py tests/test_sbem_stage_offsets.py and all tests passed (8 passed).
• Performed syntax/compile checks with PYTHONPATH=. python -m py_compile emalign/io/sbem_image.py emalign/align_xy/stitch_ongrid.py emalign/scripts/align_stack_xy.py emalign/align_dataset_xy.py emalign/prep_config_xy.py, which succeeded.

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[chatgpt-codex-connector]

Fix stage-offset axes for SBEM tile keys

When this option is used through sbem_image, tile_origins is keyed by parse_yx_pos_from_name, which returns (row, col) (for example the SBEM tests expect an upper-right tile at (0, 1)). This loop unpacks those keys as (x, y), so a real right neighbor at (0, 1) is treated as down and its horizontal stage delta is written into cy instead of cx, producing a transposed/incorrect coarse mesh for SBEM rows with more than one tile. Convert the SBEM keys to the internal (x, y) convention before applying stage offsets, or unpack/index them consistently as (y, x) here.

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