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stevevanhooserstevevanhooser
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Merge pull request #979 from VH-Lab/claude/lightsheet-zarr-ndi-viewer-djp5vk
Lightsheet pyramids: ingest from OME-Zarr or SmartSPIM, chunk materialization, cloud round trip, and napari viewing
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‎find_napari_debug_log.sh‎

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#!/usr/bin/env zsh
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# find_napari_debug_log.sh - locate and print the napariViewLightsheet debug
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# log written by ndi.test.cloud.lightsheet_blob_cloud_roundtrip.
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#
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# The demo defaults DebugLogFile to fullfile(tempdir, 'NapariLightSheetDebugging.txt')
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# which on macOS resolves under $TMPDIR (typically /var/folders/xx/yyy/T/),
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# not /tmp. This script looks in the usual spots, picks the newest match,
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# and cats it.
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set -u
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setopt NULL_GLOB EXTENDED_GLOB
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name="NapariLightSheetDebugging.txt"
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# Places to check, ordered by likelihood on macOS.
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locations=(
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"${TMPDIR:-}/$name" # matches MATLAB's tempdir
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"/tmp/$name" # a user who set DebugLogFile explicitly
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"$HOME/$name" # or dropped it in their home
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"/private/tmp/$name" # macOS's real /tmp target
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)
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# De-duplicate, drop empties, and keep only paths that actually exist.
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typeset -a found
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for p in "${locations[@]}"; do
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[[ -n "$p" && -f "$p" ]] && found+=("$p")
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done
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# Wider net if the shortlist misses: recurse under /var/folders and $TMPDIR
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# (macOS parks per-user tempdirs there). Prune common noise; keep the
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# recent ones.
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if (( ${#found} == 0 )); then
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for root in "${TMPDIR:-}" /var/folders /private/var/folders /tmp; do
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[[ -n "$root" && -d "$root" ]] || continue
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while IFS= read -r hit; do
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[[ -n "$hit" ]] && found+=("$hit")
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done < <(find "$root" -maxdepth 6 -type f -name "$name" 2>/dev/null)
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done
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fi
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if (( ${#found} == 0 )); then
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print -u2 "No $name found. If your demo ran with a custom DebugLogFile,"
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print -u2 "point me at it: $0 /full/path/to/logfile"
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print -u2 "Or check the value of tempdir in MATLAB (>> tempdir)."
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exit 1
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fi
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# Pick the newest match if multiple.
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newest="$found[1]"
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newest_mtime=$(stat -f %m "$newest" 2>/dev/null || stat -c %Y "$newest" 2>/dev/null)
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for f in "$found[@]"; do
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m=$(stat -f %m "$f" 2>/dev/null || stat -c %Y "$f" 2>/dev/null)
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if [[ -n "$m" && "$m" -gt "$newest_mtime" ]]; then
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newest="$f"
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newest_mtime="$m"
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fi
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done
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print -u2 "=== Reading: $newest ==="
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if (( ${#found} > 1 )); then
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print -u2 "(also found: ${(j:, :)found[2,-1]})"
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fi
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print -u2 ""
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cat -- "$newest"

‎lightsheet_test_blob_ingest_and_view.m‎

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%LIGHTSHEET_TEST_BLOB_INGEST_AND_VIEW - end-to-end smoke test on the synthetic blob
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%
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% Builds a small OME-Zarr fixture on disk (a couple of MB), ingests it
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% into a fresh NDI session with the blosc-zstd fast path, and launches
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% the napari viewer on the resulting pyramid. Use this to sanity-check
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% the ingest -> document -> viewer pipeline without touching the real
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% SmartSPIM data. Runs in under a minute on a laptop.
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%
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% Edit CONFIG below if you want to keep the fixture / session between
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% runs, change the blob size, or point at a different napari launcher.
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%
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% See also: ndi.test.lightsheet.makeBlobFixture,
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% ndi.test.lightsheet.ingestBlobFixture,
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% ndi.fun.doc.lightsheet.fromOMEZarr,
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% ndi.fun.doc.lightsheet.view
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% -------------------- CONFIG -----------------------------------------
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% Leave scratch dirs empty to land under tempname (fresh every run).
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sessionDir = ''; % e.g. '~/ndi-sessions/blob-demo'
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zarrDir = ''; % e.g. '~/ndi-sessions/blob-demo/zarr'
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subjectName = 'blob@vhlab';
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% Blob size / shape. 128^3 uint16 across 2 channels ~= 16 MB raw; small
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% enough for a fast smoke test, big enough that the pyramid has real
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% levels to look at.
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shape = [128 128 128];
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numChannels = 2;
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chunkShape = [32 32 32];
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numLevels = 3;
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% Ingest options. blosc-zstd exercises the encodeChunk fast path; keep
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% clevel modest for a smoke test.
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codec = 'blosc-zstd';
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clevel = 5;
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% Napari launcher. Same wrapper the real-data script uses.
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launcher = '/usr/local/bin/napariViewLightsheet';
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% ---------------------------------------------------------------------
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fprintf('Building blob fixture and ingesting ...\n');
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[S, P, info] = ndi.test.lightsheet.ingestBlobFixture( ...
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'sessionDir', sessionDir, ...
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'zarrDir', zarrDir, ...
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'subject', subjectName, ...
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'Shape', shape, ...
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'NumChannels', numChannels, ...
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'ChunkShape', chunkShape, ...
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'NumLevels', numLevels, ...
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'codec', codec, ...
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'clevel', clevel);
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fprintf('Session: %s\n', char(S.path()));
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fprintf('Zarr: %s\n', info.zarrPath);
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fprintf('Pyramid: %s\n', P.id());
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fprintf('Launching napari viewer ...\n');
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ndi.fun.doc.lightsheet.view(S, P.id(), 'launcher', launcher);

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