@janelia-flyem/neuroglancer - npm Package Compare versions

Comparing version 2.33.1 to 2.34.0

dist/module/main_module.js

@@ -12,2 +12,4 @@ import { bindDefaultCopyHandler, bindDefaultPasteHandler } from './neuroglancer/ui/default_clipboard_handling';
 import './neuroglancer/datasource/precomputed/register_default';
+import './neuroglancer/datasource/n5/register_default';
+import './neuroglancer/datasource/zarr/register_default';
 import './neuroglancer/segmentation_user_layer';
@@ -14,0 +16,0 @@ import './neuroglancer/image_user_layer';

dist/module/neuroglancer/datasource/dvid/api.js

@@ -46,13 +46,19 @@ import _Object$assign from 'babel-runtime/core-js/object/assign';
 }
+export function appendQueryString(url, name, value) {
+    return `${url}${url.includes('?') ? '&' : '?'}${name}=${value}`;
+}
 export function appendQueryStringForDvid(url, user) {
+    let newUrl = appendQueryString(url, 'app', 'Neuroglancer');
+    /*
     if (url.includes('?')) {
-        url += '&';
+      url += '&';
     } else {
-        url += '?';
+      url += '?';
     }
     url += 'app=Neuroglancer';
+    */
     if (user) {
-        url += `&u=${user}`;
+        newUrl += `&u=${user}`;
     }
-    return url;
+    return newUrl;
 }
@@ -59,0 +65,0 @@ export function responseText(response) {

dist/module/neuroglancer/datasource/dvid/backend.js

@@ -39,3 +39,3 @@ import _Object$assign from "babel-runtime/core-js/object/assign";
 import { WithSharedCredentialsProviderCounterpart } from "../../credentials_provider/shared_counterpart";
-import { DVIDInstance, makeRequestWithCredentials, appendQueryStringForDvid, fetchMeshDataFromService } from "./api";
+import { DVIDInstance, makeRequestWithCredentials, appendQueryStringForDvid, fetchMeshDataFromService, appendQueryString } from "./api";
 import { DVIDAnnotationFacade } from "./utils";
@@ -54,2 +54,5 @@ import { verifyObject, verifyObjectProperty, verifyString, parseIntVec } from "../../util/json";
 
+        if (parameters.supervoxels) {
+            return _Promise.reject();
+        }
         let bodyid = `${chunk.objectId}`;
@@ -76,6 +79,10 @@ const url = `${parameters.baseUrl}/api/node/${parameters['nodeKey']}` + `/${parameters['dataInstanceKey']}/key/` + bodyid + '_swc';
     download(chunk) {
-        // DVID does not currently store meshes chunked, the main
-        // use-case is for low-resolution 3D views.
-        // for now, fragmentId is the body id
-        chunk.fragmentIds = [`${chunk.objectId}`];
+        if (this.parameters.supervoxels) {
+            chunk.fragmentIds = [];
+        } else {
+            // DVID does not currently store meshes chunked, the main
+            // use-case is for low-resolution 3D views.
+            // for now, fragmentId is the body id
+            chunk.fragmentIds = [`${chunk.objectId}`];
+        }
         return _Promise.resolve(undefined);
@@ -290,2 +297,5 @@ }
             path = this.getPath(chunkPosition, chunkDataSize);
+            if (params.supervoxels) {
+                path = appendQueryString(path, 'supervoxels', 'true');
+            }
         }
@@ -292,0 +302,0 @@ const decoder = this.getDecoder(params);

dist/module/neuroglancer/datasource/dvid/frontend.js

@@ -153,9 +153,3 @@ import _Promise from 'babel-runtime/core-js/promise';
             }
-            let volParameters = {
-                'baseUrl': parameters.baseUrl,
-                'nodeKey': parameters.nodeKey,
-                'dataInstanceKey': dataInstanceKey,
-                'dataScale': level.toString(),
-                'encoding': encoding
-            };
+            let volParameters = _Object$assign(_Object$assign({}, parameters), { dataInstanceKey, dataScale: level.toString(), encoding });
             const chunkToMultiscaleTransform = mat4.create();
@@ -427,2 +421,5 @@ for (let i = 0; i < 3; ++i) {
     }
+    get supervoxels() {
+        return this.sourceParameters.supervoxels || false;
+    }
     getSegmentPosition(id) {
@@ -433,3 +430,3 @@ const dvidService = this.sourceParameters.dvidService;
             // dvid=${dvidConfig.protocol}://${dvidConfig.host}&uuid=${dvidConfig.uuid}&${(user ? `&u=${user}` : '')}
-            return fetch(`${dvidService}/locate-body?dvid=${this.baseUrl}&uuid=${this.nodeKey}&body=${id.toString()}`, {
+            return fetch(`${dvidService}/locate-body?dvid=${this.baseUrl}&uuid=${this.nodeKey}&body=${id.toString()}${this.supervoxels ? '&supervoxels=true' : ''}`, {
                 method: 'GET'
@@ -442,7 +439,3 @@ }).then(response => response.json()).then(location => new Float32Array(location));
     getSources(volumeSourceOptions) {
-        return this.info.getSources(this.chunkManager, {
-            'baseUrl': this.baseUrl,
-            'nodeKey': this.nodeKey,
-            'dataInstanceKey': this.dataInstanceKey
-        }, volumeSourceOptions, this.credentialsProvider);
+        return this.info.getSources(this.chunkManager, this.sourceParameters, volumeSourceOptions, this.credentialsProvider);
     }
@@ -483,2 +476,3 @@ }
         }
+        sourceParameters.supervoxels = parameters.supervoxels === 'true';
     }
@@ -677,13 +671,11 @@ sourceParameters.authServer = getDefaultAuthServer(sourceParameters.baseUrl);
 export function getDataSource(options) {
-    const sourceParameters = parseSourceUrl(options.providerUrl);
-    const baseUrl = sourceParameters.baseUrl,
-          nodeKey = sourceParameters.nodeKey,
-          dataInstanceKey = sourceParameters.dataInstanceKey;
-
     return options.chunkManager.memoize.getUncounted({
         type: 'dvid:MultiscaleVolumeChunkSource',
-        baseUrl,
-        nodeKey: nodeKey,
-        dataInstanceKey
+        sourceUrl: options.providerUrl
     }, async () => {
+        const sourceParameters = parseSourceUrl(options.providerUrl);
+        const baseUrl = sourceParameters.baseUrl,
+              nodeKey = sourceParameters.nodeKey,
+              dataInstanceKey = sourceParameters.dataInstanceKey;
+
         const credentialsProvider = options.credentialsManager.getCredentialsProvider(credentialsKey, { dvidServer: sourceParameters.baseUrl, authServer: sourceParameters.authServer });
@@ -690,0 +682,0 @@ const serverInfo = await getServerInfo(options.chunkManager, baseUrl, credentialsProvider);

dist/module/neuroglancer/segmentation_display_state/frontend.js

@@ -81,4 +81,4 @@ import _WeakMap from 'babel-runtime/core-js/weak-map';
         } else if (typeof value === 'number') {
-            newLow = newBaseLow = value;
-            newHigh = newBaseHigh = 0;
+            newLow = newBaseLow = value >>> 0;
+            newHigh = newBaseHigh = value < 0 ? 0xffffffff : 0;
             hasSelectedSegment = true;
@@ -144,3 +144,3 @@ } else if (value instanceof Uint64MapEntry) {
     if (typeof value === 'number') {
-        id = new Uint64(value, 0);
+        id = new Uint64(value >>> 0, value < 0 ? 0xffffffff : 0);
     } else if (typeof value === 'string') {
@@ -147,0 +147,0 @@ id = Uint64.parseString(value);

dist/module/neuroglancer/single_mesh/frontend.js

@@ -335,2 +335,9 @@ import _Map from 'babel-runtime/core-js/map';
     }
+    isReady() {
+        let chunk = this.source.chunks.get(SINGLE_MESH_CHUNK_KEY);
+        if (chunk === undefined || chunk.state !== ChunkState.GPU_MEMORY) {
+            return false;
+        }
+        return true;
+    }
     draw(renderContext, attachment) {
@@ -337,0 +344,0 @@ if (!renderContext.emitColor && renderContext.alreadyEmittedPickID) {

dist/module/neuroglancer/webgl/shader_lib.js

@@ -162,3 +162,3 @@ /**
 `];
-export const glsl_int8 = `
+export const glsl_int8 = [glsl_uint64, `
 struct int8_t {
@@ -183,6 +183,12 @@ highp int value;
 highp ivec4 toRaw(int8x4_t x) { return x.value; }
+uint64_t toUint64(int8_t x) {
+  uint64_t result;
+  result.value[0] = uint(x.value);
+  result.value[1] = uint(x.value >> 31);
+  return result;
+}
 int8_t int8FromFloat(highp float x) {
   return int8_t(int(clamp(x, -128.0, 127.0)));
 }
-`;
+`];
 export const glsl_float = `
@@ -222,3 +228,3 @@ highp float toRaw(highp float x) { return x; }
 `];
-export const glsl_int16 = `
+export const glsl_int16 = [glsl_uint64, `
 struct int16_t {
@@ -235,6 +241,12 @@ highp int value;
 highp ivec2 toRaw(int16x2_t x) { return x.value; }
+uint64_t toUint64(int16_t x) {
+  uint64_t result;
+  result.value[0] = uint(x.value);
+  result.value[1] = uint(x.value >> 31);
+  return result;
+}
 int16_t int16FromFloat(highp float x) {
   return int16_t(int(clamp(x, -32768.0, 32767.0)));
 }
-`;
+`];
 export const glsl_uint32 = [glsl_uint64, `
@@ -259,3 +271,3 @@ struct uint32_t {
 `];
-export const glsl_int32 = `
+export const glsl_int32 = [glsl_uint64, `
 struct int32_t {
@@ -268,6 +280,12 @@ highp int value;
 highp int toRaw(int32_t x) { return x.value; }
+uint64_t toUint64(int32_t x) {
+  uint64_t result;
+  result.value[0] = uint(x.value);
+  result.value[1] = uint(x.value >> 31);
+  return result;
+}
 int32_t int32FromFloat(highp float x) {
   return int32_t(int(clamp(x, 2147483648.0, 2147483647.0)));
 }
-`;
+`];
 export var glsl_getFortranOrderIndex = `
@@ -274,0 +292,0 @@ highp int getFortranOrderIndex(ivec3 subscripts, ivec3 size) {

package.json

@@ -5,3 +5,3 @@ {
   "license": "Apache-2.0",
-  "version": "2.33.1",
+  "version": "2.34.0",
   "main": "dist/module/main_module.js",
@@ -8,0 +8,0 @@ "repository": {

src/main_module.ts

@@ -13,2 +13,4 @@ import {bindDefaultCopyHandler, bindDefaultPasteHandler} from 'neuroglancer/ui/default_clipboard_handling';
 import 'neuroglancer/datasource/precomputed/register_default';
+import 'neuroglancer/datasource/n5/register_default';
+import 'neuroglancer/datasource/zarr/register_default';
 import 'neuroglancer/segmentation_user_layer';
@@ -15,0 +17,0 @@ import 'neuroglancer/image_user_layer';

src/neuroglancer/datasource/dvid/api.ts

@@ -67,3 +67,9 @@ /**
 
+export function appendQueryString(url: string, name: string, value: string) {
+  return `${url}${url.includes('?') ? '&' : '?'}${name}=${value}`;
+}
+
 export function appendQueryStringForDvid(url: string, user: string|null|undefined) {
+  let newUrl = appendQueryString(url, 'app', 'Neuroglancer');
+  /*
   if (url.includes('?')) {
@@ -75,6 +81,7 @@ url += '&';
   url += 'app=Neuroglancer';
+  */
   if (user) {
-    url += `&u=${user}`;
+    newUrl += `&u=${user}`;
   }
-  return url;
+  return newUrl;
 }
@@ -81,0 +88,0 @@

src/neuroglancer/datasource/dvid/backend.ts

@@ -30,3 +30,3 @@ /**
 import {WithSharedCredentialsProviderCounterpart} from 'neuroglancer/credentials_provider/shared_counterpart';
-import {DVIDInstance, DVIDToken, makeRequestWithCredentials, appendQueryStringForDvid, fetchMeshDataFromService} from 'neuroglancer/datasource/dvid/api';
+import {DVIDInstance, DVIDToken, makeRequestWithCredentials, appendQueryStringForDvid, fetchMeshDataFromService, appendQueryString} from 'neuroglancer/datasource/dvid/api';
 import {DVIDPointAnnotation, DVIDAnnotation, DVIDAnnotationFacade} from 'neuroglancer/datasource/dvid/utils';
@@ -49,2 +49,6 @@ import {verifyObject, verifyObjectProperty, verifyString, parseIntVec} from 'neuroglancer/util/json';
     const {parameters} = this;
+    if (parameters.supervoxels) {
+      return Promise.reject();
+    }
+
     let bodyid = `${chunk.objectId}`;
@@ -77,6 +81,10 @@ const url = `${parameters.baseUrl}/api/node/${parameters['nodeKey']}` +
   download(chunk: ManifestChunk) {
-    // DVID does not currently store meshes chunked, the main
-    // use-case is for low-resolution 3D views.
-    // for now, fragmentId is the body id
-    chunk.fragmentIds = [`${chunk.objectId}`];
+    if (this.parameters.supervoxels) {
+      chunk.fragmentIds = [];
+    } else {
+      // DVID does not currently store meshes chunked, the main
+      // use-case is for low-resolution 3D views.
+      // for now, fragmentId is the body id
+      chunk.fragmentIds = [`${chunk.objectId}`];
+    }
     return Promise.resolve(undefined);
@@ -338,2 +346,5 @@ }
       path = this.getPath(chunkPosition, chunkDataSize);
+      if (params.supervoxels) {
+        path = appendQueryString(path, 'supervoxels', 'true');
+      }
     }
@@ -340,0 +351,0 @@ const decoder = this.getDecoder(params);

src/neuroglancer/datasource/dvid/base.ts

@@ -37,2 +37,3 @@ /**
   dvidService?: string;
+  supervoxels?: boolean;
 }
@@ -39,0 +40,0 @@

src/neuroglancer/datasource/dvid/frontend.ts

@@ -192,7 +192,6 @@ /**
       let volParameters: VolumeChunkSourceParameters = {
-        'baseUrl': parameters.baseUrl,
-        'nodeKey': parameters.nodeKey,
-        'dataInstanceKey': dataInstanceKey,
-        'dataScale': level.toString(),
-        'encoding': encoding,
+        ...parameters,
+        dataInstanceKey,
+        dataScale: level.toString(),
+        encoding
       };
@@ -498,2 +497,6 @@ const chunkToMultiscaleTransform = mat4.create();
 
+  get supervoxels() {
+    return this.sourceParameters.supervoxels || false;
+  }
+
   constructor(
@@ -508,3 +511,3 @@ chunkManager: ChunkManager, public sourceParameters: DVIDSourceParameters, public info: VolumeDataInstanceInfo, public credentialsProvider: CredentialsProvider<DVIDToken>) {
       // dvid=${dvidConfig.protocol}://${dvidConfig.host}&uuid=${dvidConfig.uuid}&${(user ? `&u=${user}` : '')}
-      return fetch(`${dvidService}/locate-body?dvid=${this.baseUrl}&uuid=${this.nodeKey}&body=${id.toString()}`, {
+      return fetch(`${dvidService}/locate-body?dvid=${this.baseUrl}&uuid=${this.nodeKey}&body=${id.toString()}${this.supervoxels ? '&supervoxels=true' : ''}`, {
         method: 'GET',
@@ -519,9 +522,3 @@ }).then((response) => response.json()).then((location) => new Float32Array(location));
     return this.info.getSources(
-        this.chunkManager, {
-          'baseUrl': this.baseUrl,
-          'nodeKey': this.nodeKey,
-          'dataInstanceKey': this.dataInstanceKey,
-        },
-        volumeSourceOptions,
-        this.credentialsProvider);
+        this.chunkManager, this.sourceParameters, volumeSourceOptions, this.credentialsProvider);
   }
@@ -569,2 +566,4 @@ }
     }
+
+    sourceParameters.supervoxels = (parameters.supervoxels === 'true');
   }
@@ -823,13 +822,11 @@ sourceParameters.authServer = getDefaultAuthServer(sourceParameters.baseUrl);
 export function getDataSource(options: GetDataSourceOptions): Promise<DataSource> {
-  const sourceParameters = parseSourceUrl(options.providerUrl);
-  const {baseUrl, nodeKey, dataInstanceKey} = sourceParameters;
-
   return options.chunkManager.memoize.getUncounted(
       {
         type: 'dvid:MultiscaleVolumeChunkSource',
-        baseUrl,
-        nodeKey: nodeKey,
-        dataInstanceKey,
+        sourceUrl: options.providerUrl,
       },
       async () => {
+        const sourceParameters = parseSourceUrl(options.providerUrl);
+        const {baseUrl, nodeKey, dataInstanceKey} = sourceParameters;
+
         const credentialsProvider = options.credentialsManager.getCredentialsProvider<DVIDToken>(
@@ -836,0 +833,0 @@ credentialsKey,

src/neuroglancer/segmentation_display_state/frontend.ts

@@ -80,4 +80,4 @@ /**
     } else if (typeof value === 'number') {
-      newLow = newBaseLow = value;
-      newHigh = newBaseHigh = 0;
+      newLow = newBaseLow = (value >>> 0);
+      newHigh = newBaseHigh = value < 0 ? 0xffffffff : 0;
       hasSelectedSegment = true;
@@ -185,3 +185,3 @@ } else if (value instanceof Uint64MapEntry) {
   if (typeof value === 'number') {
-    id = new Uint64(value, 0);
+    id = new Uint64((value >>> 0), value < 0 ? 0xffffffff : 0);
   } else if (typeof value === 'string') {
@@ -188,0 +188,0 @@ id = Uint64.parseString(value);

src/neuroglancer/single_mesh/frontend.ts

@@ -398,2 +398,10 @@ /**
 
+  isReady() {
+    let chunk = <SingleMeshChunk|undefined>this.source.chunks.get(SINGLE_MESH_CHUNK_KEY);
+    if (chunk === undefined || chunk.state !== ChunkState.GPU_MEMORY) {
+      return false;
+    }
+    return true;
+  }
+
   draw(
@@ -400,0 +408,0 @@ renderContext: PerspectiveViewRenderContext,

src/neuroglancer/webgl/shader_lib.ts

@@ -64,3 +64,4 @@ /**
 }
-`];
+`
+];
 
@@ -110,3 +111,3 @@ export const glsl_equalUint64 = [
 export const glsl_addSaturateUint64 = [
-  glsl_addUint64, glsl_compareLessThanUint64,  `
+  glsl_addUint64, glsl_compareLessThanUint64, `
 uint64_t addSaturate(uint64_t a, uint64_t b) {
@@ -123,3 +124,3 @@ a = add(a, b);
 export const glsl_subtractSaturateUint64 = [
-  glsl_subtractUint64, glsl_compareLessThanUint64,  `
+  glsl_subtractUint64, glsl_compareLessThanUint64, `
 uint64_t subtractSaturate(uint64_t a, uint64_t b) {
@@ -201,3 +202,4 @@ b = subtract(a, b);
 
-export const glsl_int8 = `
+export const glsl_int8 = [
+  glsl_uint64, `
 struct int8_t {
@@ -222,6 +224,13 @@ highp int value;
 highp ivec4 toRaw(int8x4_t x) { return x.value; }
+uint64_t toUint64(int8_t x) {
+  uint64_t result;
+  result.value[0] = uint(x.value);
+  result.value[1] = uint(x.value >> 31);
+  return result;
+}
 int8_t int8FromFloat(highp float x) {
   return int8_t(int(clamp(x, -128.0, 127.0)));
 }
-`;
+`
+];
 
@@ -267,3 +276,4 @@
 
-export const glsl_int16 = `
+export const glsl_int16 = [
+  glsl_uint64, `
 struct int16_t {
@@ -280,6 +290,13 @@ highp int value;
 highp ivec2 toRaw(int16x2_t x) { return x.value; }
+uint64_t toUint64(int16_t x) {
+  uint64_t result;
+  result.value[0] = uint(x.value);
+  result.value[1] = uint(x.value >> 31);
+  return result;
+}
 int16_t int16FromFloat(highp float x) {
   return int16_t(int(clamp(x, -32768.0, 32767.0)));
 }
-`;
+`
+];
 
@@ -308,3 +325,4 @@ export const glsl_uint32 = [
 
-export const glsl_int32 = `
+export const glsl_int32 = [
+  glsl_uint64, `
 struct int32_t {
@@ -317,6 +335,13 @@ highp int value;
 highp int toRaw(int32_t x) { return x.value; }
+uint64_t toUint64(int32_t x) {
+  uint64_t result;
+  result.value[0] = uint(x.value);
+  result.value[1] = uint(x.value >> 31);
+  return result;
+}
 int32_t int32FromFloat(highp float x) {
   return int32_t(int(clamp(x, 2147483648.0, 2147483647.0)));
 }
-`;
+`
+];
 
@@ -399,3 +424,4 @@ export var glsl_getFortranOrderIndex = `
 
-export const glsl_addSaturateInt32 = [glsl_addSaturateUint32, `
+export const glsl_addSaturateInt32 = [
+  glsl_addSaturateUint32, `
 highp int addSaturate(highp int x, highp uint y) {
@@ -410,5 +436,7 @@ if (x >= 0) {
 }
-`];
+`
+];
 
-export const glsl_subtractSaturateInt32 = [glsl_addSaturateUint32, `
+export const glsl_subtractSaturateInt32 = [
+  glsl_addSaturateUint32, `
 highp int subtractSaturate(highp int x, highp uint y) {
@@ -423,3 +451,4 @@ if (x < 0) {
 }
-`];
+`
+];
 
@@ -426,0 +455,0 @@ export function getShaderType(dataType: DataType, numComponents: number = 1) {

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Improved metrics

Total package byte prevSize

9320179

increased by0.03%

Lines of code

201090

increased by0.05%

No dependency changes