feat(core): let a deployment store labelmaps as RLE instead of a frame per slice - #2885
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feat(core): let a deployment store labelmaps as RLE instead of a frame per slice#2885wayfarer3130 wants to merge 2 commits into
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No actionable comments were generated in the recent review. 🎉 ℹ️ Recent review info⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Team Run ID: 📒 Files selected for processing (5)
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Included review availability: Your plan provides up to 4 included reviews per hour; 3 remain after this review. 📝 WalkthroughWalkthroughThe change adds configurable Volume or RLE labelmap representations. Voxel managers preserve typed RLE data, expose live-buffer access, and support representation-aware writes. Adapters, conversion logic, statistics, loaders, and tests use the new behavior. ChangesRLE labelmap support
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: 🟡 Moderate · up to Opt-in RLE labelmap storage reduces resident memory but changes how labelmap data is reconstructed and replaced. Nonzero default values may still produce inconsistent reads, and a failed whole-frame replacement could leave partial labelmap contents, so this PR should wait for a fix or explicit owner acceptance of these data-integrity risks. Sequence Diagram(s)sequenceDiagram
participant Application
participant getDefaultLabelmapVoxelRepresentation
participant createAndCacheDerivedLabelmapImage
participant VoxelManager
Application->>getDefaultLabelmapVoxelRepresentation: read segmentation configuration
getDefaultLabelmapVoxelRepresentation->>createAndCacheDerivedLabelmapImage: select Volume or RLE
createAndCacheDerivedLabelmapImage->>VoxelManager: create manager with typed storage metadata
🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✨ Finishing Touches 💡 1📝 Generate docstrings 💡
🧪 Generate unit tests (beta)
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In `@packages/core/src/loaders/imageLoader.ts`:
- Around line 544-556: Update the RLE branch in createAndCacheLocalImage to
preserve nonzero scalarData by populating the RLEVoxelMap with the supplied
values before creating the image, or explicitly reject populated scalarData for
this path. Ensure image.getPixelData() reflects the supplied data when
VoxelManagerEnum.RLE is selected, and add a regression test covering populated
scalarData.
In `@packages/core/src/utilities/VoxelManager.ts`:
- Around line 518-520: Update scalar-data replacement in VoxelManager to use
map.defaultValue ?? 0 as the sparse value instead of always treating zero as
implicit, and initialize RLEVoxelMap.updateScalarData expansions with the same
value so getScalarData() and getAtIndex() agree. Add a regression test covering
a nonzero defaultValue with zero-valued input data.
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packages/adapters/src/adapters/Cornerstone3D/Segmentation/labelmapImagesFromBuffer.tspackages/adapters/test/segBufferMetadataRoundTrip.jest.jspackages/adapters/test/segImageLoaderPath.jest.jspackages/adapters/test/segLabelmap16BitRoundTrip.jest.jspackages/adapters/test/segRealDerivationRoundTrip.jest.jspackages/core/src/init.tspackages/core/src/loaders/imageLoader.tspackages/core/src/types/Cornerstone3DConfig.tspackages/core/src/utilities/RLEVoxelMap.tspackages/core/src/utilities/VoxelManager.tspackages/core/test/labelmapVoxelRepresentation.jest.jspackages/core/test/utilities/VoxelManager.jest.jspackages/polymorphic-segmentation/src/Labelmap/convertContourToLabelmap.tspackages/tools/src/utilities/segmentation/getStatistics.ts
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…e per slice
Adds `segmentation.labelmapVoxelRepresentation` to the cornerstone
configuration. It selects the in-memory representation that
`createAndCacheDerivedLabelmapImage(s)` gives a labelmap when the caller does
not ask for one, which is what covers the labelmaps created deep inside the SEG
adapter where no per-call option can be threaded through.
`'Volume'` is the default and is the existing behaviour: one byte per pixel per
slice, segmented or not. `'RLE'` stores each frame as runs, so a large
multi-segment SEG (a whole-body AI segmentation) costs a fraction of the memory
and can answer per-row questions from the runs rather than by scanning a whole
frame. The value may be the bare string so it can come straight from a host's
JSON configuration; an unrecognized value warns and falls back to `'Volume'`
rather than silently doing nothing.
It is opt-in because it changes what a host reads back out of a labelmap: an RLE
frame's `getScalarData()` is a fresh expansion rather than the live buffer, so
in-place writes to it are discarded.
Ancillary work to make an RLE labelmap behave like the frame buffer it stands in
for:
- `createRLE{Volume,Image}VoxelManager` accept `pixelDataConstructor` and
`defaultValue`, so an expanded frame has the same array type as the buffer it
replaces and an unwritten voxel reads as that array's zero instead of
undefined. Choosing a type is also what installs `_getConstructor`, without
which `getConstructor()` had no scalar data to read the type from and fell
back to Float32Array - the stack labelmap actor builds its texture from that
type. A map whose creator chose nothing keeps the expansion type and the
constructor fallback it had before the option existed.
- `VoxelManager.getScalarDataLength` and `bytePerVoxel` derive from the
dimensions and the array constructor when there is no backing array. Without
that, anything sizing a buffer from a voxel manager
(`getCompleteScalarDataArray`, and so segmentation statistics) threw for an RLE
labelmap.
- New `VoxelManager.setFromScalarData`, for callers replacing a manager's whole
contents. `getScalarData().set(...)` writes into a throwaway expansion on a
manager that is not array backed; unlike `setScalarData` this leaves the RLE
map as the source of truth.
- New `VoxelManager.getLiveScalarData`, which answers whether there is a real
backing store to read and write, as opposed to an expansion whose reads are a
snapshot and whose writes are discarded. The SEG adapter uses it to keep
touching the frame buffer directly - these are its hot loops, one access per
non-zero voxel - and to fall back to a call per voxel only for a
representation that has no buffer. The planar overlap test in particular used
to read `getPixelData()`, which on an RLE labelmap would have missed every
collision.
- An RLE labelmap image allocates a 1-element stand-in buffer (the pixel
metadata is still derived from its type) and is charged `DEFAULT_RLE_SIZE`,
matching what `addInstanceToImage` already does for an RLE image.
- `rleForEach` no longer resets `map.defaultValue` to undefined; nothing in it
reads through `get`, so the reset only undid a default the map's creator had
chosen.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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… for Addresses two review findings, both on the paths this feature added. `createAndCacheLocalImage` created the RLE map empty and never read `scalarData`, so a caller that supplied voxels lost them - `getPixelData()` expanded the empty map. Copy them in, but only for a buffer that covers the frame: `createAndCacheDerivedImage` deliberately passes a 1-element stand-in for an RLE image, and scanning a full frame for it would cost the per-slice work the encoding exists to avoid. `defaultValue` was honoured by `get` but not by anything that expands or replaces a frame. `updateScalarData` and `getPixelData` zero-filled, so `getScalarData()` disagreed with `getAtIndex()` on every unwritten voxel, and `setFromScalarData` dropped literal zeros rather than the default - on a map defaulting to 5, supplied 0s read back as 5. All three now use `defaultValue ?? 0`, which leaves every current caller (none sets a non-zero default) on the zero behaviour it already had. Tests: 7 cases across the two files. Verified that the five covering the fixed behaviour fail against the previous commit; the two guarding the stand-in buffer and the zero-default path pass either way, which is the point of them. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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@jbocce - this change just allows using the RLE labelmap representation as an opt-in option for cs3d rendering. I've tested it with OHIF and although it needs a couple of small OHIF tweaks to avoid two places where direct buffer access is used, it does speed up large labelmaps. I don't think there is anything int he PR that is particularly concerning - we have been using RLE maps for a while now for various things, just not defaulting to them for new labelmaps. |
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Context
A large multi-segment SEG — a whole-body AI segmentation, say — costs one byte
per pixel per slice in the current labelmap representation, whether or not a
slice contains anything. A labelmap frame is mostly background: a few contiguous
runs of segment values per row. RLE holds the same content in a fraction of the
memory, and lets a per-row question ("is segment N on this slice?") be answered
from the runs instead of by scanning a whole frame.
Cornerstone already has the RLE voxel manager, and
createAndCacheDerivedImage'svoxelRepresentationoption already selects it.What was missing was a way to reach it: the labelmaps in question are created
deep inside the SEG adapter, where no per-call option can be threaded through
from the host. This adds the configuration that covers those, plus the work
needed to make an RLE labelmap behave like the frame buffer it stands in for.
Changes & Results
The configuration. New
segmentation.labelmapVoxelRepresentationin thecornerstone configuration, read by
createAndCacheDerivedLabelmapImage(s)when the caller does not passvoxelRepresentationitself:'Volume'is the default and is exactly the existing behaviour.straight from a host's JSON/deployment configuration.
'rle', the likely typo) warns and falls back to'Volume', rather than being a flag that looks set and silently does nothing.voxelRepresentationstill wins.It is deliberately opt-in, because it changes what a host reads back out of a
labelmap: an RLE frame's
getScalarData()is a fresh expansion rather than thelive buffer, so in-place writes to it are discarded.
Ancillary work, so that an RLE labelmap stands in for a typed array
correctly:
createRLE{Volume,Image}VoxelManagertakepixelDataConstructoranddefaultValue. An expanded frame then comes back as the same array type asthe buffer it replaces, and an unwritten voxel reads as that array's zero
rather than
undefined. Choosing a type is also what installs_getConstructor; without itgetConstructor()had no scalar data to readthe type from and fell back to
Float32Array, which the stack labelmap actorwould then build its texture as. A map whose creator chose nothing — the
editing history managers,
addInstanceToImage— keeps the expansion type andthe constructor fallback it had before the option existed, so no existing RLE
user is moved onto a type it never asked for.
VoxelManager.getScalarDataLengthandbytePerVoxelfall back to derivingfrom the dimensions and the array constructor when there is no backing array.
Without this, anything sizing a buffer from a voxel manager —
getCompleteScalarDataArray, and so segmentation statistics — threw for anRLE labelmap.
VoxelManager.setFromScalarData, for a caller replacing a manager's wholecontents.
getScalarData().set(...)writes into a throwaway expansion on amanager that is not array backed; unlike
setScalarDatathis leaves the RLEmap as the source of truth for later reads and edits.
convertContourToStackLabelmapnow uses it.VoxelManager.getLiveScalarData, which answers whether there is a realbacking store to read and write, as opposed to an expansion whose reads are a
snapshot and whose writes are discarded.
are its hot loops, one access per non-zero voxel — and to fall back to a call
per voxel only for a representation that has no buffer. The planar overlap
test in particular read
getPixelData(), which on an RLE labelmap would havemissed every collision. The group fill is now also bounded by the frame as
well as the group, so an over-long group cannot write past the labelmap.
full frame would be the exact per-slice cost the encoding exists to avoid,
and the pixel/bit-depth metadata is still derived from its type — and is
charged
DEFAULT_RLE_SIZEin the cache, matching whataddInstanceToImagealready does for an RLE image.
rleForEachno longer resetsmap.defaultValuetoundefined. Nothing in itreads through
get, so the reset only undid a default the map's creator hadchosen.
Backward compatibility. With the flag unset,
Volumeis passed explicitlywhere
undefinedused to be, and every consumer branches on=== VoxelManagerEnum.RLE, so the representation and every allocation areunchanged. The adapter still reads and writes the frame buffer directly, and an
RLE manager created without a chosen pixel type expands to
Uint8ClampedArrayand reports the same constructor as before, so no existing RLE user changes
either. Existing hosts need no changes.
Related work
The motivating case is segment navigation in a downstream viewer. Clicking a
segment label to jump to that segment has to either wait on the async statistics
worker for a centroid — which has not settled yet on a large SEG, so the jump
silently does nothing — or find the segment's slices from the labelmap itself.
The labelmap search is the reliable option, since the pixel data is there the
moment the SEG loads.
That search does not require this PR: it works against a full frame buffer by
scanning it. But scanning every pixel of every frame is what it costs today,
whereas an RLE frame answers "is segment N on this slice?" from a handful of runs
per row. On a large multi-segment SEG that is roughly an order of magnitude
faster, which is the difference between navigation that feels instant and
navigation the reader waits on. So the two are related but independent: this PR
is what makes that navigation fast at scale, not what makes it work.
Known limitations (RLE mode only)
sizeInBytesis the fixedDEFAULT_RLE_SIZEwhile the runs grow as voxels are written, so the cachelimit is not a true bound in RLE mode. This matches the pre-existing
addInstanceToImagebehaviour rather than introducing it.updateVTKImageDataWithCornerstoneImageand
vtkStreamingOpenGLTexturecallvoxelManager.getScalarData(), whichre-expands the frame each time. The trade is resident memory for transient
allocation: only the slices being rendered expand, instead of every slice
staying resident.
getScalarData(true)exists to cache an expansion but hasno caller yet — wiring it into the labelmap sync is the obvious follow-up if
brush-edit churn on the active slice measures badly.
Testing
Unit tests, all green (
npx jest packages/core packages/adapters packages/tools— 100 suites, 1398 passing):
packages/core/test/labelmapVoxelRepresentation.jest.js(new) — the configresolution: unset, absent section, enum member, bare string, and the
warn-and-fall-back on an unrecognized value.
packages/core/test/utilities/VoxelManager.jest.js— an RLE manager builtwith a pixel type and default value, and one built without, which is pinned to
the expansion type and constructor fallback it had before;
getLiveScalarDataacross an array-backed manager, an RLE manager, and an RLE manager holding a
cached expansion; scalar-data length and voxel size derived with no backing
array; and
getCompleteScalarDataArrayover RLE-backed slices, which is thesegmentation-statistics path.
packages/adapters/test/seg*RoundTrip.jest.js— the SEG round trips, withgetAtIndexadded to the voxel-manager mocks for the read-through path.Manually, with a multi-segment SEG:
before-baseline for memory.
segmentation: { labelmapVoxelRepresentation: 'RLE' }in thecornerstone init and load the same SEG. It should render identically; segment
statistics, brush edits, undo/redo, and contour-to-labelmap conversion should
all still work, at markedly lower resident memory.
'rle'and confirm the console warning and the fall back tothe full-frame representation.
Checklist
PR
semantic-release format and guidelines.
Code
etc.)
Public Documentation Updates
additions or removals.
Tested Environment
suites above plus
tsc --noEmiton core and tools. The manual steps inTesting are what still needs a browser run."
Summary by CodeRabbit
New Features
Bug Fixes