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smartspim: prefer SmartSPIM's stitched All_Channels volume - #31
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Port of NDR-matlab b8f0e4b. ferret-lightsheet established that
All_Channels/ holds SmartSPIM AutoStitch's TeraStitcher merge of the
destriped tiles with flat-field / left-right correction and blended
overlaps -- the better-stitched, harmonized data Imaris is built from.
Format layer (new, bridged regular_port):
* readAllChannelsInfo - index <Y>_<X>_<z*10>_ch<k>.tiff, map channels
to ch<k> via <channel>_MIP_stitched, else filter-channel rank;
numeric z order; canvas size / class; voxel size from metadata.json.
* hasAllChannels - non-throwing probe, usable only if every channel
has slices.
* readAllChannelsVolume - one channel as (z, y, x), optional ZRange.
Reader epochs:
[root] stitched volume, all channels on C (ch<k> order)
[root, channel] stitched volume, one channel
[root, channel, tile] destriped Ex_* tile, unchanged
Without a usable All_Channels, the first two keep the "does not pin a
channel / tile" errors (the Ex_* tiles are not obsolete).
imagecodecs joins the dev and formats extras: real All_Channels slices
are LZW, and the new tests write LZW fixtures.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01U33UPxYJWPpcQimNu5t5Cb
NDR-matlab fixed readTileInfo reporting int16 for TIFFs that store SampleFormat = 1 (imfinfo's 'Unsigned integer' contains 'signed integer'). The Python port takes the numpy dtype straight from tifffile and never had the bug -- checked against a hand-built TIFF carrying SampleFormat = 1 -- so only the sync hash and decision_log change. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01U33UPxYJWPpcQimNu5t5Cb
NDR-matlab fixed tiffclass reading float TIFFs ('IEEE floating point')
as uint32. The Python port takes the dtype from tifffile and was never
affected -- float32 and int16 stacks round-trip -- so only the sync hash
and decision_log change.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01U33UPxYJWPpcQimNu5t5Cb
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Summary
This ports VH-Lab/NDR-matlab#142 (branch
claude/spim-all-channels). ferret-lightsheet established thatAll_Channels/contains SmartSPIM AutoStitch's stitched, flat-field-corrected and blended volume, which is what Imaris is built from. With this PR,ndr_reader_smartspimreads it first.New format functions (
ndr.format.smartspim, bridged asregular_port)readAllChannelsInfo: indexes<Y>_<X>_<z*10>_ch<k>.tiffand maps each channel to itsch<k>, taken from<channel>_MIP_stitchedor else from the filter-channel rank. Slices are sorted by numeric z. Also returns the canvas size and class, and the voxel size frommetadata.json.hasAllChannels: a non-throwing probe. It returns true only when every channel has slices.readAllChannelsVolume: reads one channel as (z, y, x), with an optionalZRange.Reader epochs
[root]ch<k>order)[root, channel][root, channel, tile]Ex_*tile (unchanged)Fallback: when
All_Channelsis missing or incomplete,[root]and[root, channel]raise the same "does not pin a channel / tile" errors as before. TheEx_*tiles remain the source of truth.Bridge syncs (MATLAB commits recorded)
smartspimreader + 3 new format functionsb8f0e4breadTileInfo3e300e5tiffstack8f870c1Other changes
imagecodecsis added to thedevandformatsextras. RealAll_Channelsslices are LZW-compressed, and tifffile needsimagecodecsto decode them; the new tests also write LZW fixtures.Testing
tests/test_smartspim_all_channels.py(new) andtests/test_smartspim_reader.py: 45 passed.black --checkandruff checkare clean.0013532: all checks green.Merge order: merge NDR-matlab#142 first, as a merge commit rather than a squash. The bridge YAML records that PR's commit hashes, and a squash would change them.
🤖 Generated with Claude Code
https://claude.ai/code/session_01U33UPxYJWPpcQimNu5t5Cb