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Two spec mismatches from cellmap-flow: source_voxel_size under relabel, box under resample (0.3.1) - #5
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on_mismatch="relabel" renamed the grid and source_voxel_size read the renamed grid, so it reported the requested size; the spec says the stored level's. Reads, voxel_size, translation and corner are unchanged. Reported by cellmap-flow. Version 0.3.1. Claude-Session: https://claude.ai/code/session_0141wgF8mkGbjGfBFKfKhp64
With a resample target, box was the stored data's extent while shape, voxel_size and translation were the target grid's, so read(box) could return fewer voxels than shape (7 voxels of 8 nm at 24 nm: box ended at 56 nm, shape said 3). box is now the extent of the target voxels shape counts, as the spec's [corner, corner + shape * voxel_size) says and as Grid.from_meta's box already was. resample.target_range is shared by both. Found by cellmap-flow. Claude-Session: https://claude.ai/code/session_0141wgF8mkGbjGfBFKfKhp64
davidackerman
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kilometer/kilometre/km at 1e3 m convert, abbreviate to km and are written as OME's kilometer (chunkmirage's ask). The README's placement rule gains the corner formula, a worked example, why the centre is the model and how the read rule follows from it. Claude-Session: https://claude.ai/code/session_0141wgF8mkGbjGfBFKfKhp64
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Two fixes from cellmap-flow's migration, both cases where the code disagreed with the spec, and two small additions. No voxel moves in any read.
source_voxel_sizenow reports the stored level's voxel size underon_mismatch="relabel", as spec section 2 says. It used to report the relabelled size, because relabel renames the grid and the property read the renamed grid. A funlib level at 16, 4, 4 nm opened withvoxel_size=(8, 8, 8)and relabel reported 8, 8, 8.boxof an array opened with a resample target is now the extent of the target voxelsshapecounts, as the spec's[corner, corner + shape * voxel_size)says and asGrid.from_meta(meta, voxel_size=t).boxalready was. It used to be the stored data's extent, soread(box)could return fewer voxels thanshape: 7 voxels of 8 nm read at 24 nm gave a box ending at 56 nm, withshapesaying 3. Now it ends at 72 nm.kilometer,kilometre,km, 1e3 m): they convert, abbreviate tokm, andome_multiscaleswrites them as OME'skilometerinstead of as given. chunkmirage asked for this so it can drop its own unit table.corner = translation - voxel_size / 2, a worked example (8 nm voxels, corner 0, translation 4), why the centre is the model, and how the read rule follows from it.No consumer repo reads
source_voxel_sizetoday; cellmap-flow reads resampled arrays byread_indexand is unaffected by theboxchange. Version 0.3.1, changelog entries added, and both new fix tests fail on main.https://claude.ai/code/session_0141wgF8mkGbjGfBFKfKhp64