Z downsampling

[AlexSurtees]

Description

Recalculate Z-index for images which are downscaled in z-index

Fixes # (issue)
Closes #16

Type of change

• 🐛 Bug fix (non-breaking change that resolves an issue)
• ✨ New feature (non-breaking change that adds functionality)
• ⚡ Optimisation (non-breaking improvement to performance or efficiency)
• 🧩 Documentation (adds or improves documentation)
• 🧱 Maintenance (refactor, dependency update, CI/CD, etc.)
• 🔥 Breaking change (fix or feature that causes existing functionality to change)

Checklist

• All tests pass (eg. npm test)
• Pre-commit hooks run successfully (eg. pre-commit run --all-files)
• Documentation updated (if required)

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[will-moore]

https://deploy-preview-36--z-downsampling.netlify.app/?source=https://s3.janelia.org/cellmap/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/em/fibsem-uint8/ is working nicely as before (great to have the netlify deploy 👍 )

Also tested a couple of other images and all looks good.
A 2nd opinion on the code changes would be nice - thx.

[dannda]

works great, thank you!

was wondering if it is any worth having originalSizeZ also as a readonly property to simplify. Adding it to the ZarrPixelSourceOptions as optional, and providing it in loadOmeMultiscales like

  const loader = data.map(
    (arr, i) =>
      new ZarrPixelSource(arr, {
        labels: axis_labels,
        tileSize,
        originalSizeZ: data[0].shape[axis_labels.indexOf("z")], // Set originalSizeZ for all ZarrPixelSource arrays so they can adjust for Z downsampling
        ...(i === 0 ? { meta: { physicalSizes } } : {}),
      }),
  );

to avoid the additional loop to set it

also ensuring the recalculation is performed only when necessary

recalculateZSelection(z: number, zIndex: number): number {
    if (this.originalSizeZ && this.originalSizeZ !== this.shape[zIndex]) {
      return Math.floor((z * this.shape[zIndex]) / this.originalSizeZ);
    }
    return z;
  }

as multiscales will have originalSizeZ but without meaning they've been downsampled (or maybe originalSizeZ should only be defined when it's actually downsampled?)

[AlexSurtees]

Thanks @dannda, I have made those changes and added some missing documentation.