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Fix loading multi-source zarrs where one source is missing a "C" dimension #364

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Merged
frasercl merged 3 commits into from
Jan 14, 2026
+10 −4
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Fix loading multi-source zarrs where one source is missing a "C" dimension #364

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a182237
fix counting `channelOffset`s for volumes without C dimension
frasercl Dec 17, 2025
ad736c6
fix "unexpected dimension" error
frasercl Dec 17, 2025
6785ebd
rename some variables for clarity
frasercl Dec 19, 2025
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14 changes: 10 additions & 4 deletions src/loaders/OmeZarrLoader.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,13 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
let channelCount = 0;
for (const s of sources) {
s.channelOffset = channelCount;
channelCount += s.omeroMetadata?.channels.length ?? s.scaleLevels[0].shape[s.axesTCZYX[1]];
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@ShrimpCryptid ShrimpCryptid Dec 18, 2025

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So just to check my understanding, this was failing before because s.axesTCZYX[1] evaluated to -1, which then caused the statement to effectively become:

channelCount += undefined ?? undefined

Is that right? and now in that failure case we instead increment by 1

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@frasercl frasercl Dec 19, 2025

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Yup! And adding undefined to channelCount is what eventually produced the NaNs in chunk request URLs.

(Vaguely interesting: the NaNs only appeared if the image missing the channel dimension came before the image with it. Configurations with the URLs the opposite way around fell victim to the completely separate bug I fixed further down this file.)

if (s.omeroMetadata !== undefined) {
channelCount += s.omeroMetadata.channels.length;
} else if (s.axesTCZYX[1] > -1) {
channelCount += s.scaleLevels[0].shape[s.axesTCZYX[1]];
} else {
channelCount += 1;
}
}
// Ensure the sizes of all sources' scale levels are matched up. See this function's docs for more.
matchSourceScaleLevels(sources);
Expand Down Expand Up @@ -452,10 +458,10 @@ class OMEZarrLoader extends ThreadableVolumeLoader {
});

// Get number of chunks per dimension in every source array
const chunkDimsTCZYX = this.sources.map((src) => {
const level = src.scaleLevels[scaleLevel];
const chunkDimsTCZYX = this.sources.map((source, sourceIndex) => {
const level = source.scaleLevels[scaleLevel];
const chunkDimsUnordered = level.shape.map((dim, idx) => Math.ceil(dim / level.chunks[idx]));
return this.orderByTCZYX(chunkDimsUnordered, 1);
return this.orderByTCZYX(chunkDimsUnordered, 1, sourceIndex);
});

// `ChunkPrefetchIterator` yields chunk coordinates in order of roughly how likely they are to be loaded next
Expand Down