Merge pull request #12 from lincbrain/ak-merge

merge upstream changes from neuroglancer main

.github/workflows/build.yml

@@ -101,7 +101,7 @@ jobs:
       # - name: Setup tmate session
       #   uses: mxschmitt/action-tmate@v3
       - name: Install Python packaging/test tools
-        run: pip install --upgrade pip tox nox wheel numpy -r python/requirements-test.txt
+        run: pip install tox nox wheel numpy -r python/requirements-test.txt
       - uses: ./.github/actions/setup-firefox
       - run: nox -s lint format mypy
       - name: Check for dirty working directory
@@ -296,5 +296,6 @@ jobs:
       - run: ./src/mesh/draco/build.sh
       - run: ./src/sliceview/compresso/build.sh
       - run: ./src/sliceview/png/build.sh
+      - run: ./src/sliceview/jxl/build.sh
       # Check that there are no differences.
       - run: git diff --exit-code

package.json

@@ -83,7 +83,7 @@
     "ikonate": "github:mikolajdobrucki/ikonate#a86b4107c6ec717e7877f880a930d1ccf0b59d89",
     "lodash-es": "^4.17.21",
     "nifti-reader-js": "^0.6.8",
-    "numcodecs": "^0.3.1",
+    "numcodecs": "^0.3.2",
     "pako": "^2.1.0"
   },
   "overrides": {

python/neuroglancer/json_wrappers.py

@@ -450,7 +450,7 @@ class _Map(Map):
 
 
 def typed_set(wrapped_type: Callable[[Any], T]):
-    def wrapper(x, _readonly=False) -> Callable[[Any], Union[set[T], frozenset[T]]]:
+    def wrapper(x, _readonly=False) -> Union[set[T], frozenset[T]]:
         set_type = frozenset if _readonly else set
         kwargs: dict[str, Any] = dict()
         if hasattr(wrapped_type, "supports_readonly"):

src/async_computation/decode_jpeg.ts

@@ -25,21 +25,22 @@ registerAsyncComputation(
     data: Uint8Array,
     width: number | undefined,
     height: number | undefined,
+    area: number | undefined,
     numComponents: number | undefined,
     convertToGrayscale: boolean,
   ) => {
     const parser = new JpegDecoder();
     parser.parse(data);
     // Just check that the total number pixels matches the expected value.
     if (
-      width !== undefined &&
-      height !== undefined &&
-      parser.width * parser.height !== width * height
+      (width !== undefined && width !== parser.width) ||
+      (height !== undefined && height !== parser.height) ||
+      (area !== undefined && parser.width * parser.height !== area)
     ) {
       throw new Error(
         "JPEG data does not have the expected dimensions: " +
           `width=${parser.width}, height=${parser.height}, ` +
-          `expected width=${width}, expected height=${height}`,
+          `expected width=${width}, expected height=${height}, expected area=${area}`,
       );
     }
     width = parser.width;

src/async_computation/decode_jpeg_request.ts

@@ -16,13 +16,14 @@
 import type { DecodedImage } from "#src/async_computation/decode_png_request.js";
 import { asyncComputation } from "#src/async_computation/index.js";
 
-export const decodeJpeg =
-  asyncComputation<
-    (
-      data: Uint8Array,
-      width: number | undefined,
-      height: number | undefined,
-      numComponents: number | undefined,
-      convertToGrayscale: boolean,
-    ) => DecodedImage
-  >("decodeJpeg");
+export const decodeJpeg = asyncComputation<
+  (
+    data: Uint8Array,
+    width: number | undefined,
+    height: number | undefined,
+    // Expected width * height
+    area: number | undefined,
+    numComponents: number | undefined,
+    convertToGrayscale: boolean,
+  ) => DecodedImage
+>("decodeJpeg");

src/async_computation/decode_jxl.ts

@@ -0,0 +1,37 @@
+/**
+ * @license
+ * Copyright 2024 William Silversmith
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { decodeJxl } from "#src/async_computation/decode_jxl_request.js";
+import { registerAsyncComputation } from "#src/async_computation/handler.js";
+import { decompressJxl } from "#src/sliceview/jxl/index.js";
+
+registerAsyncComputation(
+  decodeJxl,
+  async (
+    data: Uint8Array,
+    area: number | undefined,
+    numComponents: number | undefined,
+    bytesPerPixel: number,
+  ) => {
+    const result = await decompressJxl(
+      data,
+      area,
+      numComponents,
+      bytesPerPixel,
+    );
+    return { value: result, transfer: [result.uint8Array.buffer] };
+  },
+);

src/async_computation/decode_jxl_request.ts

@@ -0,0 +1,27 @@
+/**
+ * @license
+ * Copyright 2024 William Silversmith
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import type { DecodedImage } from "#src/async_computation/decode_png_request.js";
+import { asyncComputation } from "#src/async_computation/index.js";
+
+export const decodeJxl =
+  asyncComputation<
+    (
+      data: Uint8Array,
+      area: number | undefined,
+      numComponents: number | undefined,
+      bytesPerPixel: number,
+    ) => DecodedImage
+  >("decodeJxl");

src/async_computation/decode_png.ts

@@ -24,6 +24,8 @@ registerAsyncComputation(
     data: Uint8Array,
     width: number | undefined,
     height: number | undefined,
+    // Expected width * height
+    area: number | undefined,
     numComponents: number | undefined,
     bytesPerPixel: number,
     convertToGrayscale: boolean,
@@ -32,6 +34,7 @@ registerAsyncComputation(
       data,
       width,
       height,
+      area,
       numComponents,
       bytesPerPixel,
       convertToGrayscale,

src/async_computation/decode_png_request.ts

@@ -22,14 +22,15 @@ export interface DecodedImage {
   uint8Array: Uint8Array;
 }
 
-export const decodePng =
-  asyncComputation<
-    (
-      data: Uint8Array,
-      width: number | undefined,
-      height: number | undefined,
-      numComponents: number | undefined,
-      bytesPerPixel: number,
-      convertToGrayscale: boolean,
-    ) => DecodedImage
-  >("decodePng");
+export const decodePng = asyncComputation<
+  (
+    data: Uint8Array,
+    width: number | undefined,
+    height: number | undefined,
+    // Expected width * height
+    area: number | undefined,
+    numComponents: number | undefined,
+    bytesPerPixel: number,
+    convertToGrayscale: boolean,
+  ) => DecodedImage
+>("decodePng");

src/datasource/deepzoom/backend.ts

@@ -111,6 +111,7 @@ export class DeepzoomImageTileSource extends WithParameters(
             new Uint8Array(responseBuffer),
             undefined,
             undefined,
+            undefined,
             3,
             1,
             false,
@@ -133,6 +134,7 @@ export class DeepzoomImageTileSource extends WithParameters(
             new Uint8Array(responseBuffer),
             undefined,
             undefined,
+            undefined,
             3,
             false,
           );

src/datasource/precomputed/async_computation.ts

@@ -1,4 +1,5 @@
 import "#src/async_computation/decode_jpeg.js";
+import "#src/async_computation/decode_jxl.js";
 import "#src/async_computation/decode_gzip.js";
 import "#src/async_computation/decode_compresso.js";
 import "#src/async_computation/decode_png.js";

src/datasource/precomputed/backend.ts

@@ -74,6 +74,7 @@ import { decodeCompressedSegmentationChunk } from "#src/sliceview/backend_chunk_
 import { decodeCompressoChunk } from "#src/sliceview/backend_chunk_decoders/compresso.js";
 import type { ChunkDecoder } from "#src/sliceview/backend_chunk_decoders/index.js";
 import { decodeJpegChunk } from "#src/sliceview/backend_chunk_decoders/jpeg.js";
+import { decodeJxlChunk } from "#src/sliceview/backend_chunk_decoders/jxl.js";
 import { decodePngChunk } from "#src/sliceview/backend_chunk_decoders/png.js";
 import { decodeRawChunk } from "#src/sliceview/backend_chunk_decoders/raw.js";
 import type { VolumeChunk } from "#src/sliceview/volume/backend.js";
@@ -380,6 +381,7 @@ chunkDecoders.set(
 );
 chunkDecoders.set(VolumeChunkEncoding.COMPRESSO, decodeCompressoChunk);
 chunkDecoders.set(VolumeChunkEncoding.PNG, decodePngChunk);
+chunkDecoders.set(VolumeChunkEncoding.JXL, decodeJxlChunk);
 
 @registerSharedObject()
 export class PrecomputedVolumeChunkSource extends WithParameters(

src/datasource/precomputed/base.ts

@@ -27,6 +27,7 @@ export enum VolumeChunkEncoding {
   COMPRESSED_SEGMENTATION = 2,
   COMPRESSO = 3,
   PNG = 4,
+  JXL = 5,
 }
 
 export class VolumeChunkSourceParameters {

src/datasource/render/backend.ts

@@ -46,8 +46,9 @@ chunkDecoders.set(
       cancellationToken,
       [response],
       new Uint8Array(response),
-      chunkDataSize[0],
-      chunkDataSize[1] * chunkDataSize[2],
+      undefined,
+      undefined,
+      chunkDataSize[0] * chunkDataSize[1] * chunkDataSize[2],
       3,
       true,
     );

src/display_context.ts

@@ -403,6 +403,7 @@ export class DisplayContext extends RefCounted implements FrameNumberCounter {
   rootRect: DOMRect | undefined;
   resizeGeneration = 0;
   boundsGeneration = -1;
+  force3DHistogramForAutoRange = false;
   private framerateMonitor = new FramerateMonitor();
 
   private continuousCameraMotionInProgress = false;
@@ -587,7 +588,7 @@ export class DisplayContext extends RefCounted implements FrameNumberCounter {
     this.updateStarted.dispatch();
     const gl = this.gl;
     const ext = this.framerateMonitor.getTimingExtension(gl);
-    const query = this.framerateMonitor.startFrameTimeQuery(gl, ext);
+    this.framerateMonitor.startFrameTimeQuery(gl, ext, this.frameNumber);
     this.ensureBoundsUpdated();
     this.gl.clearColor(0.0, 0.0, 0.0, 0.0);
     gl.clear(gl.COLOR_BUFFER_BIT | gl.DEPTH_BUFFER_BIT);
@@ -611,7 +612,7 @@ export class DisplayContext extends RefCounted implements FrameNumberCounter {
     gl.clear(gl.COLOR_BUFFER_BIT);
     this.gl.colorMask(true, true, true, true);
     this.updateFinished.dispatch();
-    this.framerateMonitor.endFrameTimeQuery(gl, ext, query);
+    this.framerateMonitor.endLastTimeQuery(gl, ext);
     this.framerateMonitor.grabAnyFinishedQueryResults(gl);
   }
 

src/perspective_view/panel.ts

@@ -999,6 +999,7 @@ export class PerspectivePanel extends RenderedDataPanel {
       sliceViewsPresent: this.sliceViews.size > 0,
       isContinuousCameraMotionInProgress:
         this.isContinuousCameraMotionInProgress,
+      force3DHistogramForAutoRange: this.context.force3DHistogramForAutoRange,
     };
 
     mat4.copy(

src/perspective_view/render_layer.ts

@@ -66,6 +66,12 @@ export interface PerspectiveViewRenderContext
    */
   isContinuousCameraMotionInProgress: boolean;
 
+  /**
+   * Usually, the histogram in 3D is disabled during camera movement
+   * This flag is used to force 3D histogram rendering during camera movement
+   */
+  force3DHistogramForAutoRange: boolean;
+
   /**
    * Specifices how to bind the max projection buffer
    */

src/sliceview/backend_chunk_decoders/jpeg.ts

@@ -31,8 +31,9 @@ export async function decodeJpegChunk(
     cancellationToken,
     [response],
     new Uint8Array(response),
-    chunkDataSize[0],
-    chunkDataSize[1] * chunkDataSize[2],
+    undefined,
+    undefined,
+    chunkDataSize[0] * chunkDataSize[1] * chunkDataSize[2],
     chunkDataSize[3] || 1,
     false,
   );

src/sliceview/backend_chunk_decoders/jxl.ts

@@ -0,0 +1,39 @@
+/**
+ * @license
+ * Copyright 2016 Google Inc.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { decodeJxl } from "#src/async_computation/decode_jxl_request.js";
+import { requestAsyncComputation } from "#src/async_computation/request.js";
+import { postProcessRawData } from "#src/sliceview/backend_chunk_decoders/postprocess.js";
+import type { VolumeChunk } from "#src/sliceview/volume/backend.js";
+import type { CancellationToken } from "#src/util/cancellation.js";
+
+export async function decodeJxlChunk(
+  chunk: VolumeChunk,
+  cancellationToken: CancellationToken,
+  response: ArrayBuffer,
+) {
+  const chunkDataSize = chunk.chunkDataSize!;
+  const { uint8Array: decoded } = await requestAsyncComputation(
+    decodeJxl,
+    cancellationToken,
+    [response],
+    new Uint8Array(response),
+    chunkDataSize[0] * chunkDataSize[1] * chunkDataSize[2],
+    chunkDataSize[3] || 1,
+    1, // bytesPerPixel
+  );
+  await postProcessRawData(chunk, cancellationToken, decoded);
+}

src/sliceview/backend_chunk_decoders/png.ts

@@ -33,8 +33,9 @@ export async function decodePngChunk(
     cancellationToken,
     [response],
     /*buffer=*/ new Uint8Array(response),
-    /*width=*/ chunkDataSize[0],
-    /*height=*/ chunkDataSize[1] * chunkDataSize[2],
+    /*width=*/ undefined,
+    /*height=*/ undefined,
+    /*area=*/ chunkDataSize[0] * chunkDataSize[1] * chunkDataSize[2],
     /*numComponents=*/ chunkDataSize[3] || 1,
     /*bytesPerPixel=*/ DATA_TYPE_BYTES[dataType],
     /*convertToGrayscale=*/ false,