Feat/scaling

.github/workflows/build.yml

@@ -1,4 +1,4 @@
 name: Build
 
 on:
   push:
@@ -16,7 +16,7 @@
         default: false
 
 jobs:
   client:
     strategy:
       matrix:
         os:
@@ -25,23 +25,23 @@
           - "macos-latest"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
         with:
           # Need full history to determine version number.
           fetch-depth: 0
       - uses: actions/setup-node@v4
         with:
           node-version: 22.x
           cache: "npm"
           cache-dependency-path: |
             package-lock.json
       # uv required for javascript tests
       - uses: astral-sh/setup-uv@v5
         with:
           enable-cache: false
       # go needed for fake_gcs_server used by the javascript tests
       - name: Setup go
         uses: actions/setup-go@v5
         with:
           go-version: "stable"
       - run: npm ci
@@ -71,23 +71,23 @@
       - name: Run JavaScript benchmarks
         run: npm run benchmark
       - name: Upload NPM package as artifact
         uses: actions/upload-artifact@v4
         with:
           name: npm-package
           path: dist/package
         if: ${{ runner.os == 'Linux' }}
       - name: Upload client as artifact
         uses: actions/upload-artifact@v4
         with:
           name: client
           path: dist/client
         if: ${{ runner.os == 'Linux' }}
   example-project-test:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: Install pnpm
         uses: pnpm/action-setup@v4
         with:
           version: 10
       - uses: actions/setup-node@v4
@@ -118,11 +118,11 @@
   # On ubuntu-latest, this also runs browser-based tests.  On Mac OS and
   # Windows, this only runs tests that do not require a browser, since a working
   # headless WebGL2 implementation is not available on Github actions.
   python-tests:
     strategy:
       matrix:
         python-version:
-          - "3.9"
+          - "3.10"
           - "3.12"
         os:
           - "ubuntu-latest"
@@ -161,7 +161,7 @@
       - name: Test in editable form
         run: uvx nox -s test_editable
 
   python-build-package:
     strategy:
       matrix:
         include:
@@ -171,9 +171,6 @@
           - os: "windows-latest"
             cibw_build: "*"
             wheel_identifier: "windows"
-          - os: "macos-14"
-            cibw_build: "*_x86_64"
-            wheel_identifier: "macos_x86_64"
           - os: "macos-14"
             cibw_build: "*_arm64"
             wheel_identifier: "macos_arm64"
@@ -223,7 +220,7 @@
             dist/*.whl
             dist/*.tar.gz
 
   docs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -247,7 +244,7 @@
           path: |
             dist/docs
 
   publish-package:
     # Only publish package on push to tag or default branch.
     if: ${{ github.event_name == 'push' && (startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/master') }}
     runs-on: ubuntu-latest
@@ -277,14 +274,14 @@
       #     user: __token__
       #     password: ${{ secrets.pypi_test_token }}
       - name: Publish to PyPI (main server)
         uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806 # 2020-09-25
         with:
           user: __token__
           password: ${{ secrets.pypi_token }}
         if: ${{ startsWith(github.ref, 'refs/tags/v') }}
       - name: Publish to NPM registry
         if: ${{ startsWith(github.ref, 'refs/tags/v') }}
         run: npm publish
         working-directory: npm-package
         env:
           NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
@@ -315,7 +312,7 @@
           channelId: live
           target: docs
 
   ngauth:
     strategy:
       matrix:
         os:
@@ -330,7 +327,7 @@
           cache-dependency-path: ngauth_server/go.sum
       - run: go build .
         working-directory: ngauth_server
   wasm:
     # Ensures that .wasm files are reproducible.
     strategy:
       matrix:

HOW-TO-USE.md

@@ -0,0 +1,14 @@
+The following should already be included as the Shader
+
+```
+#uicontrol invlerp normalized(clamp=true)
+void main() {
+  float v = normalized(getDataValue(0));
+  vec4 rgba = vec4(lut[int(v*255.)].r, lut[int(v*255.)].g, lut[int(v*255.)].b, 1.0);
+  emitRGBA(rgba);
+}
+```
+
+when loading this URL.
+
+http://localhost:8080/#!%7B%22dimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B8e-9%2C%22m%22%5D%7D%2C%22position%22:%5B3156.4873046875%2C3793.629638671875%2C3543.705810546875%5D%2C%22crossSectionScale%22:3.762185354999915%2C%22projectionOrientation%22:%5B0.31435418128967285%2C0.8142172694206238%2C0.4843378961086273%2C-0.06040274351835251%5D%2C%22projectionScale%22:4593.980956070107%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22precomputed://gs://neuroglancer-public-data/flyem_fib-25/image%22%2C%22tab%22:%22rendering%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28clamp=true%29%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20v%20=%20normalized%28getDataValue%280%29%29%3B%5Cn%20%20vec4%20rgba%20=%20vec4%28lut%5Bint%28v%2A255.%29%5D.r%2C%20lut%5Bint%28v%2A255.%29%5D.g%2C%20lut%5Bint%28v%2A255.%29%5D.b%2C%201.0%29%3B%5Cn%20%20emitRGBA%28rgba%29%3B%5Cn%7D%22%2C%22name%22:%22image%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth%22%2C%22tab%22:%22source%22%2C%22segments%22:%5B%2221894%22%2C%2222060%22%2C%22158571%22%2C%2224436%22%2C%222515%22%5D%2C%22name%22:%22ground-truth%22%7D%5D%2C%22showSlices%22:false%2C%22selectedLayer%22:%7B%22size%22:390%2C%22visible%22:true%2C%22layer%22:%22image%22%7D%2C%22layout%22:%224panel%22%7D

build_tools/build-package.ts

@@ -27,6 +27,7 @@ function buildDeclarationFiles(
     ...options,
     declaration: true,
     emitDeclarationOnly: true,
+    noEmit: false,
   };
   const program = ts.createProgram(fileNames, options);
   program.emit();

python/neuroglancer/viewer_state.py

@@ -1416,7 +1416,7 @@ def navigation_link_type(x):
     x = str(x)
     x = x.lower()
     if x not in ["linked", "unlinked", "relative"]:
-        raise ValueError("Invalid navigation link type: %r" % x)
+        raise ValueError(f"Invalid navigation link type: {x!r}")
     return x
 
 

src/annotation/annotation_layer_state.ts

@@ -182,6 +182,13 @@ export class AnnotationDisplayState extends RefCounted {
     this.ignoreNullSegmentFilter,
   );
   hoverState = new AnnotationHoverState(undefined);
+  selectedAnnotation = new WatchableValue<string | undefined>(undefined);
+  hoverPinned = false;
+  // Not happy with this pattern but fine for the time being; internally neuroglancer
+  // has a built in hover/pick for annotations; we could use a different variable
+  // but for simplicity Ichnaea externally reuses selectedAnnotation, and this variable
+  // acts as a gate to prevent other parts of neuroglancer from mutating on top of it
+  controlledSelection = false;
 }
 
 export class AnnotationLayerState extends RefCounted {

src/annotation/bounding_box.ts

@@ -340,7 +340,7 @@ emitLine(uModelViewProjection * vec4(endpointA, 1.0),
 ${this.setPartIndex(builder, "uint(aBoxCornerOffset2.w)")};
 `);
       builder.setFragmentMain(`
-emitAnnotation(vec4(vColor.rgb, getLineAlpha() * vClipCoefficient));
+emitAnnotation(vec4(vColor.rgb, vColor.a * getLineAlpha() * vClipCoefficient));
 `);
     },
   );

src/annotation/frontend_source.ts

@@ -833,6 +833,36 @@ export class MultiscaleAnnotationSource
             tempUpper[i] = c + r;
           }
           break;
+        case AnnotationType.ORIENTED_BOUNDING_BOX: {
+          matrix.transformPoint(
+            tempLower,
+            source.multiscaleToChunkTransform,
+            rank + 1,
+            annotation.center,
+            rank,
+          );
+          matrix.transformVector(
+            tempUpper,
+            source.multiscaleToChunkTransform,
+            rank + 1,
+            annotation.extents,
+            rank,
+          );
+          // Conservative bound independent of orientation: the box fits within a
+          // sphere of radius 0.5 * |extents| about its center.
+          let radiusSq = 0;
+          for (let i = 0; i < rank; ++i) {
+            const h = tempUpper[i] * 0.5;
+            radiusSq += h * h;
+          }
+          const radius = Math.sqrt(radiusSq);
+          for (let i = 0; i < rank; ++i) {
+            const c = tempLower[i];
+            tempLower[i] = c - radius;
+            tempUpper[i] = c + radius;
+          }
+          break;
+        }
       }
       let totalChunks = 1;
       for (let i = 0; i < rank; ++i) {