Milestone 3: Time Series optimizations

[toloudis]

Time Series Zarr Optimization

• [x] https://github.com/allen-cell-animated/volume-viewer/issues/110
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/112
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/111
• [x] #163
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/113
• [ ] #165
• [ ] bonus: https://github.com/allen-cell-animated/volume-viewer/issues/115
• [ ] bonus: https://github.com/allen-cell-animated/volume-viewer/issues/102
• [ ] bonus: https://github.com/allen-cell-animated/volume-viewer/issues/121
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/123
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/126
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/134
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/133
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/132
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/131
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/152
• [ ] https://github.com/allen-cell-animated/volume-viewer/issues/155
• [x] https://github.com/allen-cell-animated/volume-viewer/issues/157

note that XY mode is "special" vs YZ and XZ modes which require transverse projections across many slices.

[frasercl]

While we're rearchitecting large sections of volume-viewer, it may be good to work in allen-cell-animated/volume-viewer#90

[toloudis]

Notes on potential task breakdown

• implement a unit testable cache module for typedarrays
• implement a unit testable request queue (unit test via mocking a server that returns arrays)
• good candidates for TweakPane: cache mem limit, number of prefetches!
• volumeloader api changes to fetch slices (rename to volumedatasource?)
• new XY mode shader, invoked via RayMarchVolumeRendering perhaps? -- first implementation which draws from a subregion of the tiled atlas -- final implementation draws a texture which contains the whole slice so it's not a subregion
• business logic when to issue the requests, how does the cache give data back to the viewer, turn it into textures etc.

[ShrimpCryptid]

Design Questions

1. What happens and who gets notified when we switch modes?

• Integration of changes across the viewer (view3D -> VolumeDrawable + Three.js Canvas -> ray march renderer + RequestQueue + cache)

2. How do we fetch single Z-slices for multi-channel data?

• Optimize for chunks containing multiple slices (no redundant requests?)
• Add something to zarr loader to fetch slices

**3. How do we prepare multi-channel data for rendering?

4. When does pre-fetching need to happen?**

5. How do we cancel a fetch operation (or operations)?

• Implementing a RequestQueue
• Unit testing (mocking, test server, let requests complete at different time intervals)
• Observer pattern -> observe completion/rejection of request
• Check if requests overlap with existing requests, drop other requests in flight

6. Who's responsible for determining when pre-fetching happens?

• ❌ First time user loads any volume data
• First time user clicks on XY mode
• Anytime user changes time while in XY mode
• ^ 2 event handlers, each issue request to RequestQueue

7. What do we do when a fetch is completed (data arrives at the client?) -> RequestQueue 8. What happens when a user is in XY mode and changes time?

• Cancel all current requests
• Request new frame data

[toloudis]

Calling this done for the sake of the next milestone!!! At this time we have stable time series loading and playback of ome-zarr datasets characteristic of AICS (~1000x1000x100, T=~500, with at least 4 pre-generated downsampled resolutions.)