refactored StrataMap pre-processing code

[cornhundred]

Review and Refactor Summary — IST → StrataMap Preprocessing Script

Renamed IST → StrataMap (full rename)

• File renamed: IST_Landscape_Pre-process.py → StrataMap_Landscape_Pre-process.py
• "technology" value written into landscape_parameters.json updated
• technology= arguments passed to dega.pre functions updated
• CLI description= updated

Broke up main() into smaller functions

Previously one ~350-line function; now split into named steps:

• _process_image
• _process_cell_segmentation
• _process_gene_metadata
• _save_landscape_parameters
• _save_dummy_meta_cluster
• _process_cbg
• _process_transcripts
• Small helpers: _safe_polygon, _simple_format, _transform_polygon, _tile_grid_shape, _load_prep_stats

main() now just calls these in the original order — behavior is unchanged.

Reused existing code instead of duplicating

• make_column_names_unique_fast was defined almost identically in both this file and run_pre_processing.py.
• Hoisted it into landscape.py as make_column_names_unique, exported via dega.pre, and updated both call sites (removing the now-unused local copy and its defaultdict import in run_pre_processing.py).
• Everything else (image pyramid generation, _get_name_mapping, read_cbg_mtx, save_cbg_gene_parquets, write_pseudotranscripts_from_sbg, etc.) already reused shared dega.pre code.
• Left the StrataMap-specific logic (custom OME-TIFF handling, Expanded_5um_cell_contour_coords.csv polygon format, barcode-encoded transcript coordinates) as-is — it genuinely isn't shared with the Xenium/MERSCOPE path in boundary_tile.py/trx_tile.py, and forcing a cross-technology abstraction there would be a riskier, larger change.

Bugs/cleanup fixed while touching the file

• CLI defaults bug: --tile_size, --image_scale, --jitter had no default=, so omitting them on the command line silently passed None into main(), overriding its real defaults (500 / 1.0 / 1) and breaking tile-grid arithmetic. Added matching defaults.
• Missing required flags: --data_dir / --sample / --path_landscape_files weren't marked required=True, so omitting them produced a confusing None-path FileNotFoundError instead of a clear argparse error.
• Removed unused imports (scipy.sparse.coo_matrix, pathlib.Path).
• Removed ~40 lines of commented-out dead code for an old (non-segmented) cell-metadata path.

Verification

• py_compile passes on all touched files
• ruff check clean on the shared modules
• git mv used to preserve file history
• Existing tests/unit/test_pre suite (26 tests) still passes