diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3818a12b58192d4816d32defda468a265eef4504..fdaf339b1f73fa568cb8c5aa8a290247a240c500 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
+- Fixed a bug in mesh visualization (show backfaces when opacity < 1)
+
## [v3.28.0] - 2022-12-20
- Show histogram in direct volume control point settings
diff --git a/src/extensions/meshes/choice.ts b/src/extensions/meshes/choice.ts
deleted file mode 100644
index 0da7350eefbd28fa49bbb75816b064bff8573cee..0000000000000000000000000000000000000000
--- a/src/extensions/meshes/choice.ts
+++ /dev/null
@@ -1,35 +0,0 @@
-/**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Adam Midlik <midlik@gmail.com>
- */
-
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-
-
-/**
- * Represents a set of values to choose from, with a default value. Example:
- * ```
- * export const MyChoice = new Choice({ yes: 'I agree', no: 'Nope' }, 'yes');
- * export type MyChoiceType = Choice.Values<typeof MyChoice>; // 'yes'|'no'
- * ```
- */
-export class Choice<T extends string, D extends T> {
- readonly defaultValue: D;
- readonly options: [T, string][];
- private readonly nameDict: { [value in T]: string };
- constructor(opts: { [value in T]: string }, defaultValue: D) {
- this.defaultValue = defaultValue;
- this.options = Object.keys(opts).map(k => [k as T, opts[k as T]]);
- this.nameDict = opts;
- }
- PDSelect(defaultValue?: T, info?: PD.Info): PD.Select<T> {
- return PD.Select<T>(defaultValue ?? this.defaultValue, this.options, info);
- }
- prettyName(value: T): string {
- return this.nameDict[value];
- }
-}
-export namespace Choice {
- export type Values<T extends Choice<any, any>> = T extends Choice<infer R, any> ? R : any;
-}
diff --git a/src/extensions/meshes/examples.ts b/src/extensions/meshes/examples.ts
index 64c2476ce95a19c4a98c0e89aa17a7d6f2e7b208..16956efd8bf9e24dd3d9e9af3ec790df0e3931bd 100644
--- a/src/extensions/meshes/examples.ts
+++ b/src/extensions/meshes/examples.ts
@@ -6,31 +6,28 @@
/** Testing examples for using mesh-extension.ts. */
-import { ParseMeshlistTransformer, MeshShapeTransformer, MeshlistData } from './mesh-extension';
-import * as MeshUtils from './mesh-utils';
-import { BACKGROUND_OPACITY, FOREROUND_OPACITY, InitMeshStreaming } from './mesh-streaming/transformers';
-import { MeshServerInfo } from './mesh-streaming/server-info';
-import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { PluginContext } from '../../mol-plugin/context';
-import { StateObjectRef, StateObjectSelector } from '../../mol-state';
-import { Color } from '../../mol-util/color';
-import { Download } from '../../mol-plugin-state/transforms/data';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { Box3D } from '../../mol-math/geometry';
-import { ShapeRepresentation3D } from '../../mol-plugin-state/transforms/representation';
-import { ParamDefinition } from '../../mol-util/param-definition';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
+import { CIF } from '../../mol-io/reader/cif';
import { Volume } from '../../mol-model/volume';
+import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectSelector } from '../../mol-state';
import { Asset } from '../../mol-util/assets';
-import { CIF } from '../../mol-io/reader/cif';
+import { Color } from '../../mol-util/color';
+import { ParamDefinition } from '../../mol-util/param-definition';
+
+import { createMeshFromUrl } from './mesh-extension';
+import { MeshServerInfo } from './mesh-streaming/server-info';
+import { InitMeshStreaming } from './mesh-streaming/transformers';
+import * as MeshUtils from './mesh-utils';
export const DB_URL = '/db'; // local
-export async function runMeshExtensionExamples(plugin: PluginUIContext, db_url: string = DB_URL) {
+export async function runMeshExtensionExamples(plugin: PluginContext, db_url: string = DB_URL) {
console.time('TIME MESH EXAMPLES');
// await runIsosurfaceExample(plugin, db_url);
// await runMolsurfaceExample(plugin);
@@ -47,7 +44,7 @@ export async function runMeshExtensionExamples(plugin: PluginUIContext, db_url:
}
/** Example for downloading multiple separate segments, each containing 1 mesh. */
-export async function runMeshExample(plugin: PluginUIContext, segments: 'fg' | 'all', db_url: string = DB_URL) {
+export async function runMeshExample(plugin: PluginContext, segments: 'fg' | 'all', db_url: string = DB_URL) {
const detail = 2;
const segmentIds = (segments === 'all') ?
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17] // segment-16 has no detail-2
@@ -59,7 +56,7 @@ export async function runMeshExample(plugin: PluginUIContext, segments: 'fg' | '
}
/** Example for downloading multiple separate segments, each containing 1 mesh. */
-export async function runMeshExample2(plugin: PluginUIContext, segments: 'one' | 'few' | 'fg' | 'all') {
+export async function runMeshExample2(plugin: PluginContext, segments: 'one' | 'few' | 'fg' | 'all') {
const detail = 1;
const segmentIds = (segments === 'one') ? [15]
: (segments === 'few') ? [1, 4, 7, 10, 16]
@@ -72,48 +69,13 @@ export async function runMeshExample2(plugin: PluginUIContext, segments: 'one' |
}
/** Example for downloading a single segment containing multiple meshes. */
-export async function runMultimeshExample(plugin: PluginUIContext, segments: 'fg' | 'all', detailChoice: 'best' | 'worst', db_url: string = DB_URL) {
+export async function runMultimeshExample(plugin: PluginContext, segments: 'fg' | 'all', detailChoice: 'best' | 'worst', db_url: string = DB_URL) {
const urlDetail = (detailChoice === 'best') ? '2' : 'worst';
const numDetail = (detailChoice === 'best') ? 2 : 1000;
await createMeshFromUrl(plugin, `${db_url}/empiar-10070-multimesh-rounded/segments-${segments}/detail-${urlDetail}`, 0, numDetail, false, undefined);
}
-/** Download data and create state tree hierarchy down to visual representation. */
-export async function createMeshFromUrl(plugin: PluginContext, meshDataUrl: string, segmentId: number, detail: number,
- collapseTree: boolean, color?: Color, parent?: StateObjectSelector | StateObjectRef, transparentIfBboxAbove?: number,
- name?: string, ownerId?: string) {
-
- const update = parent ? plugin.build().to(parent) : plugin.build().toRoot();
- const rawDataNodeRef = update.apply(Download,
- { url: meshDataUrl, isBinary: true, label: `Downloaded Data ${segmentId}` },
- { state: { isCollapsed: collapseTree } }
- ).ref;
- const parsedDataNode = await update.to(rawDataNodeRef)
- .apply(StateTransforms.Data.ParseCif)
- .apply(ParseMeshlistTransformer,
- { label: undefined, segmentId: segmentId, segmentName: name ?? `Segment ${segmentId}`, detail: detail, ownerId: ownerId },
- {}
- )
- .commit();
-
- let transparent = false;
- if (transparentIfBboxAbove !== undefined && parsedDataNode.data) {
- const bbox = MeshlistData.bbox(parsedDataNode.data) || Box3D.zero();
- transparent = Box3D.volume(bbox) > transparentIfBboxAbove;
- }
-
- await plugin.build().to(parsedDataNode)
- .apply(MeshShapeTransformer, { color: color },)
- .apply(ShapeRepresentation3D,
- { alpha: transparent ? BACKGROUND_OPACITY : FOREROUND_OPACITY },
- { tags: ['mesh-segment-visual', `segment-${segmentId}`] }
- )
- .commit();
-
- return rawDataNodeRef;
-}
-
-export async function runMeshStreamingExample(plugin: PluginUIContext, source: MeshServerInfo.MeshSource = 'empiar', entryId: string = 'empiar-10070', serverUrl?: string, parent?: StateObjectSelector) {
+export async function runMeshStreamingExample(plugin: PluginContext, source: MeshServerInfo.MeshSource = 'empiar', entryId: string = 'empiar-10070', serverUrl?: string, parent?: StateObjectSelector) {
const params = ParamDefinition.getDefaultValues(MeshServerInfo.Params);
if (serverUrl) params.serverUrl = serverUrl;
params.source = source;
@@ -122,7 +84,7 @@ export async function runMeshStreamingExample(plugin: PluginUIContext, source: M
}
/** Example for downloading a protein structure and visualizing molecular surface. */
-export async function runMolsurfaceExample(plugin: PluginUIContext) {
+export async function runMolsurfaceExample(plugin: PluginContext) {
const entryId = 'pdb-7etq';
// Node "https://www.ebi.ac.uk/pdbe/entry-files/download/7etq.bcif" ("transformer": "ms-plugin.download") -> var data
@@ -151,7 +113,7 @@ export async function runMolsurfaceExample(plugin: PluginUIContext) {
}
/** Example for downloading an EMDB density data and visualizing isosurface. */
-export async function runIsosurfaceExample(plugin: PluginUIContext, db_url: string = DB_URL) {
+export async function runIsosurfaceExample(plugin: PluginContext, db_url: string = DB_URL) {
const entryId = 'emd-1832';
const isoLevel = 2.73;
@@ -203,7 +165,7 @@ export async function runIsosurfaceExample(plugin: PluginUIContext, db_url: stri
}
-export async function runCifMeshExample(plugin: PluginUIContext, api: string = 'http://localhost:9000/v2',
+export async function runCifMeshExample(plugin: PluginContext, api: string = 'http://localhost:9000/v2',
source: MeshServerInfo.MeshSource = 'empiar', entryId: string = 'empiar-10070',
segmentId: number = 1, detail: number = 10,
) {
@@ -211,8 +173,8 @@ export async function runCifMeshExample(plugin: PluginUIContext, api: string = '
getMeshFromBcif(plugin, url);
}
-async function getMeshFromBcif(plugin: PluginUIContext, url: string) {
- const urlAsset = Asset.getUrlAsset(plugin.managers.asset, url); // QUESTION how is urlAsset better than normal `fetch`
+async function getMeshFromBcif(plugin: PluginContext, url: string) {
+ const urlAsset = Asset.getUrlAsset(plugin.managers.asset, url);
const asset = await plugin.runTask(plugin.managers.asset.resolve(urlAsset, 'binary'));
const parsed = await plugin.runTask(CIF.parseBinary(asset.data));
if (parsed.isError) {
diff --git a/src/extensions/meshes/mesh-extension.ts b/src/extensions/meshes/mesh-extension.ts
index be312e602275e677b7e212a35e5cc405d9b25c27..4ff1206572e84637f3bac790807383cb7329591c 100644
--- a/src/extensions/meshes/mesh-extension.ts
+++ b/src/extensions/meshes/mesh-extension.ts
@@ -15,14 +15,20 @@ import { Vec3 } from '../../mol-math/linear-algebra';
import { Shape } from '../../mol-model/shape';
import { ShapeProvider } from '../../mol-model/shape/provider';
import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { StateTransformer } from '../../mol-state';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { Download } from '../../mol-plugin-state/transforms/data';
+import { ShapeRepresentation3D } from '../../mol-plugin-state/transforms/representation';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectRef, StateObjectSelector, StateTransformer } from '../../mol-state';
import { Task } from '../../mol-task';
import { Color } from '../../mol-util/color';
-import { Material } from '../../mol-util/material';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import * as MeshUtils from './mesh-utils';
+export const BACKGROUND_OPACITY = 0.2;
+export const FOREROUND_OPACITY = 1;
+
export const VolsegTransform: StateTransformer.Builder.Root = StateTransformer.builderFactory('volseg');
@@ -106,19 +112,17 @@ export namespace MeshlistData {
}
-
// // // // // // // // // // // // // // // // // // // // // // // //
// Raw Data -> Parsed data
export class MeshlistStateObject extends PluginStateObject.Create<MeshlistData>({ name: 'Parsed Meshlist', typeClass: 'Object' }) { }
-// QUESTION: is typeClass just for color, or does do something?
export const ParseMeshlistTransformer = VolsegTransform({
name: 'meshlist-from-string',
from: PluginStateObject.Format.Cif,
to: MeshlistStateObject,
params: {
- label: PD.Text(MeshlistStateObject.type.name, { isHidden: true }), // QUESTION: Is this the right way to pass a value to apply() without exposing it in GUI?
+ label: PD.Text(MeshlistStateObject.type.name, { isHidden: true }),
segmentId: PD.Numeric(1, {}, { isHidden: true }),
segmentName: PD.Text('Segment'),
detail: PD.Numeric(1, {}, { isHidden: true }),
@@ -148,47 +152,32 @@ namespace MeshShapeProvider {
return {
label: 'Mesh',
data: meshlist,
- params: meshParamDef, // TODO how to pass the real params correctly?
+ params: meshShapeProviderParams,
geometryUtils: Mesh.Utils,
getShape: (ctx, data: MeshlistData) => MeshlistData.getShape(data, theColor),
};
}
}
-/** Params for MeshShapeTransformer */
-const meshShapeParamDef = {
- color: PD.Value<Color | undefined>(undefined), // undefined means random color
-};
-
-const meshParamDef: Mesh.Params = {
- // These are basically original MS.Mesh.Params:
- // BaseGeometry.Params
- alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }, { label: 'Opacity', isEssential: true, description: 'How opaque/transparent the representation is rendered.' }),
+const meshShapeProviderParams: Mesh.Params = {
+ ...Mesh.Params,
quality: PD.Select<VisualQuality>('custom', VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }), // use 'custom' when wanting to apply doubleSided
- material: Material.getParam(),
- clip: Mesh.Params.clip, // PD.Group(MS.Clip.Params),
- instanceGranularity: PD.Boolean(false, { description: 'Use instance granularity for marker, transparency, clipping, overpaint, substance data to save memory.' }),
- // Mesh.Params
- doubleSided: PD.Boolean(true, BaseGeometry.CustomQualityParamInfo), // default: false (set true, to show at least something in weird cases)
- flipSided: PD.Boolean(false, BaseGeometry.ShadingCategory),
- flatShaded: PD.Boolean(false, BaseGeometry.ShadingCategory), // default: false (set true to see the real mesh vertices and triangles)
- ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
- xrayShaded: PD.Boolean(false, BaseGeometry.ShadingCategory), // this is like better opacity (angle-dependent), nice
- transparentBackfaces: PD.Select('off', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory),
- bumpFrequency: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
- bumpAmplitude: PD.Numeric(1, { min: 0, max: 5, step: 0.1 }, BaseGeometry.ShadingCategory),
- // TODO when I change values here, it has effect, but not if I change them in GUI
+ doubleSided: PD.Boolean(true, BaseGeometry.CustomQualityParamInfo),
+ // set `flatShaded`: true to see the real mesh vertices and triangles
+ transparentBackfaces: PD.Select('on', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory), // 'on' means: show backfaces with correct opacity, even when opacity < 1 (requires doubleSided) ÂŻ\_(ă„)_/ÂŻ
};
+
export const MeshShapeTransformer = VolsegTransform({
name: 'shape-from-meshlist',
display: { name: 'Shape from Meshlist', description: 'Create Shape from Meshlist data' },
from: MeshlistStateObject,
to: PluginStateObject.Shape.Provider,
- params: meshShapeParamDef
+ params: {
+ color: PD.Value<Color | undefined>(undefined), // undefined means random color
+ },
})({
apply({ a, params }) {
- // you can look for example at ShapeFromPly in mol-plugin-state/tansforms/model.ts as an example
const shapeProvider = MeshShapeProvider.fromMeshlistData(a.data, params.color);
return new PluginStateObject.Shape.Provider(shapeProvider, { label: PluginStateObject.Shape.Provider.type.name, description: a.description });
}
@@ -196,32 +185,39 @@ export const MeshShapeTransformer = VolsegTransform({
// // // // // // // // // // // // // // // // // // // // // // // //
-// Shape -> Repr
-
-// type MeshRepr = MS.PluginStateObject.Representation3DData<MS.ShapeRepresentation<MS.ShapeProvider<any,any,any>, MS.Mesh, MS.Mesh.Params>, any>;
-
-// export const CustomMeshReprTransformer = VolsegTransform({
-// name: 'custom-repr',
-// from: MS.PluginStateObject.Shape.Provider, // later we can change this
-// to: MS.PluginStateObject.Shape.Representation3D,
-// })({
-// apply({ a }, globalCtx) {
-// const repr: MeshRepr = createRepr(a.data); // TODO implement createRepr
-// // have a look at MS.StateTransforms.Representation.ShapeRepresentation3D if you want to try implementing yourself
-// return new MS.PluginStateObject.Shape.Representation3D(repr)
-// },
-// })
-
-// export async function createMeshRepr(plugin: MS.PluginContext, data: any) {
-// await plugin.build()
-// .toRoot()
-// .apply(CreateMyShapeTransformer, { data })
-// .apply(MS.StateTransforms.Representation.ShapeRepresentation3D) // this should work
-// // or .apply(CustomMeshRepr)
-// .commit();
-// }
-
-// export function createRepr(reprData: MS.ShapeProvider<any,any,any>): MeshRepr {
-// throw new Error('NotImplemented');
-// return {} as MeshRepr;
-// }
+
+
+/** Download data and create state tree hierarchy down to visual representation. */
+export async function createMeshFromUrl(plugin: PluginContext, meshDataUrl: string, segmentId: number, detail: number,
+ collapseTree: boolean, color?: Color, parent?: StateObjectSelector | StateObjectRef, transparentIfBboxAbove?: number,
+ name?: string, ownerId?: string) {
+
+ const update = parent ? plugin.build().to(parent) : plugin.build().toRoot();
+ const rawDataNodeRef = update.apply(Download,
+ { url: meshDataUrl, isBinary: true, label: `Downloaded Data ${segmentId}` },
+ { state: { isCollapsed: collapseTree } }
+ ).ref;
+ const parsedDataNode = await update.to(rawDataNodeRef)
+ .apply(StateTransforms.Data.ParseCif)
+ .apply(ParseMeshlistTransformer,
+ { label: undefined, segmentId: segmentId, segmentName: name ?? `Segment ${segmentId}`, detail: detail, ownerId: ownerId },
+ {}
+ )
+ .commit();
+
+ let transparent = false;
+ if (transparentIfBboxAbove !== undefined && parsedDataNode.data) {
+ const bbox = MeshlistData.bbox(parsedDataNode.data) || Box3D.zero();
+ transparent = Box3D.volume(bbox) > transparentIfBboxAbove;
+ }
+
+ await plugin.build().to(parsedDataNode)
+ .apply(MeshShapeTransformer, { color: color },)
+ .apply(ShapeRepresentation3D,
+ { alpha: transparent ? BACKGROUND_OPACITY : FOREROUND_OPACITY },
+ { tags: ['mesh-segment-visual', `segment-${segmentId}`] }
+ )
+ .commit();
+
+ return rawDataNodeRef;
+}
diff --git a/src/extensions/meshes/mesh-streaming/behavior.ts b/src/extensions/meshes/mesh-streaming/behavior.ts
index a52f0ece1ae5675487d332352fe10edede70d3ae..f24784a80a2bfb997e5727cc22aa576c0ed89e0f 100644
--- a/src/extensions/meshes/mesh-streaming/behavior.ts
+++ b/src/extensions/meshes/mesh-streaming/behavior.ts
@@ -19,9 +19,10 @@ import { Color } from '../../../mol-util/color';
import { ColorNames } from '../../../mol-util/color/names';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { Choice } from '../choice';
+import { Choice } from '../../volumes-and-segmentations/helpers';
+import { MetadataWrapper } from '../../volumes-and-segmentations/volseg-api/utils';
+
import { MeshlistData } from '../mesh-extension';
-import { Metadata } from '../metadata';
import { MeshServerInfo } from './server-info';
@@ -33,8 +34,6 @@ const MAX_DETAIL = 10;
const DEFAULT_DETAIL = 7; // TODO decide a reasonable default
/** Segments whose bounding box volume is above this value (relative to the overall bounding box) are considered as background segments */
export const BACKGROUND_SEGMENT_VOLUME_THRESHOLD = 0.5;
-// const DEBUG_IGNORED_SEGMENTS = new Set([13, 15]); // TODO remove
-const DEBUG_IGNORED_SEGMENTS = new Set(); // TODO remove
export class MeshStreaming extends PluginStateObject.CreateBehavior<MeshStreaming.Behavior>({ name: 'Mesh Streaming' }) { }
@@ -116,7 +115,7 @@ export namespace MeshStreaming {
private id: string;
private ref: string = '';
public parentData: MeshServerInfo.Data;
- private metadata?: Metadata;
+ private metadata?: MetadataWrapper;
public visuals?: { [tag: string]: VisualInfo };
public backgroundSegments: { [segmentId: number]: boolean } = {};
private focusObservable = this.plugin.behaviors.interaction.click.pipe( // QUESTION is this OK way to get focused segment?
@@ -165,7 +164,8 @@ export namespace MeshStreaming {
if (!this.metadata) {
const response = await fetch(this.getMetadataUrl());
- this.metadata = await response.json();
+ const rawMetadata = await response.json();
+ this.metadata = new MetadataWrapper(rawMetadata);
}
if (!this.visuals) {
@@ -209,13 +209,10 @@ export namespace MeshStreaming {
}
private initVisualInfos() {
- const namesAndColors = Metadata.namesAndColorsBySegment(this.metadata!);
-
const visuals: { [tag: string]: VisualInfo } = {};
- for (const segid of Metadata.meshSegments(this.metadata!)) {
- if (DEBUG_IGNORED_SEGMENTS.has(segid)) continue;
- const name = namesAndColors[segid]?.name ?? DEFAULT_SEGMENT_NAME;
- const color = namesAndColors[segid]?.color ?? DEFAULT_SEGMENT_COLOR;
+ for (const segid of this.metadata!.meshSegmentIds) {
+ const name = this.metadata?.getSegment(segid)?.biological_annotation.name ?? DEFAULT_SEGMENT_NAME;
+ const color = this.metadata?.getSegmentColor(segid) ?? DEFAULT_SEGMENT_COLOR;
for (const detailType of VisualInfo.DetailTypes) {
const visual: VisualInfo = {
tag: VisualInfo.tagFor(segid, detailType),
@@ -254,7 +251,7 @@ export namespace MeshStreaming {
const visual = this.visuals[tag];
const preferredDetail = (visual.detailType === 'high') ? highDetail : lowDetail;
if (preferredDetail !== undefined) {
- visual.detail = Metadata.getSufficientDetail(this.metadata!, visual.segmentId, preferredDetail);
+ visual.detail = this.metadata!.getSufficientMeshDetail(visual.segmentId, preferredDetail);
}
}
}
diff --git a/src/extensions/meshes/mesh-streaming/server-info.ts b/src/extensions/meshes/mesh-streaming/server-info.ts
index b85315a1c5618b4b9c2129b7ba52692442f54177..400dd5d51b777c8ce1786d324e2345c1004d420b 100644
--- a/src/extensions/meshes/mesh-streaming/server-info.ts
+++ b/src/extensions/meshes/mesh-streaming/server-info.ts
@@ -7,7 +7,7 @@
import { PluginStateObject } from '../../../mol-plugin-state/objects';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { Choice } from '../choice';
+import { Choice } from '../../volumes-and-segmentations/helpers';
export const DEFAULT_MESH_SERVER = 'http://localhost:9000/v2';
diff --git a/src/extensions/meshes/mesh-streaming/transformers.ts b/src/extensions/meshes/mesh-streaming/transformers.ts
index 6f64eb463d9a744d18b87dd32d3a59c1affc769b..34c43374c69cfeb689d0bfe9a89bf59960eb3b0f 100644
--- a/src/extensions/meshes/mesh-streaming/transformers.ts
+++ b/src/extensions/meshes/mesh-streaming/transformers.ts
@@ -13,15 +13,11 @@ import { Task } from '../../../mol-task';
import { shallowEqualObjects } from '../../../mol-util';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { VolsegTransform, MeshlistData } from '../mesh-extension';
+import { BACKGROUND_OPACITY, FOREROUND_OPACITY, MeshlistData, VolsegTransform } from '../mesh-extension';
import { MeshStreaming, NO_SEGMENT } from './behavior';
import { MeshServerInfo } from './server-info';
-export const BACKGROUND_OPACITY = 0.2;
-export const FOREROUND_OPACITY = 1;
-
-
// // // // // // // // // // // // // // // // // // // // // // // //
export const MeshServerTransformer = VolsegTransform({
diff --git a/src/extensions/meshes/metadata.ts b/src/extensions/meshes/metadata.ts
deleted file mode 100644
index ba43707d7719c8e0519bc18fcde86ee165adef32..0000000000000000000000000000000000000000
--- a/src/extensions/meshes/metadata.ts
+++ /dev/null
@@ -1,135 +0,0 @@
-/**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Adam Midlik <midlik@gmail.com>
- */
-
-
-import { Color } from '../../mol-util/color';
-
-
-// TODO unify with Metadata in Volseg
-
-export interface Metadata {
- grid: {
- general: {
- details: string,
- },
- volumes: Volumes,
- segmentation_lattices: SegmentationLattices,
- segmentation_meshes: SegmentationMeshes,
- },
- annotation: Annotation,
-}
-
-export interface Volumes {
- volume_downsamplings: number[],
- voxel_size: { [downsampling: number]: Vector3 },
- origin: Vector3,
- grid_dimensions: Vector3,
- sampled_grid_dimensions: { [downsampling: number]: Vector3 },
- mean: { [downsampling: number]: number },
- std: { [downsampling: number]: number },
- min: { [downsampling: number]: number },
- max: { [downsampling: number]: number },
- volume_force_dtype: string,
-}
-
-export interface SegmentationLattices {
- segmentation_lattice_ids: number[],
- segmentation_downsamplings: { [lattice: number]: number[] },
-}
-
-export interface Annotation {
- name: string,
- details: string,
- segment_list: Segment[],
-}
-
-export interface Segment {
- id: number,
- colour: number[],
- biological_annotation: BiologicalAnnotation,
-}
-
-export interface BiologicalAnnotation {
- name: string,
- external_references: { id: number, resource: string, accession: string, label: string, description: string }[]
-}
-
-export interface SegmentationMeshes {
- mesh_component_numbers: {
- segment_ids?: {
- [segId: number]: {
- detail_lvls: {
- [detail: number]: {
- mesh_ids: {
- [meshId: number]: {
- num_triangles: number,
- num_vertices: number
- }
- }
- }
- }
- }
- }
- }
- detail_lvl_to_fraction: {
- [lvl: number]: number
- }
-}
-
-type Vector3 = [number, number, number];
-
-
-
-export namespace Metadata {
- export function meshSegments(metadata: Metadata): number[] {
- const segmentIds = metadata.grid.segmentation_meshes.mesh_component_numbers.segment_ids;
- if (segmentIds === undefined) return [];
- return Object.keys(segmentIds).map(s => parseInt(s));
- }
- export function meshSegmentDetails(metadata: Metadata, segmentId: number): number[] {
- const segmentIds = metadata.grid.segmentation_meshes.mesh_component_numbers.segment_ids;
- if (segmentIds === undefined) return [];
- const details = segmentIds[segmentId].detail_lvls;
- return Object.keys(details).map(s => parseInt(s));
- }
- /** Get the worst available detail level that is not worse than preferredDetail.
- * If preferredDetail is null, get the worst detail level overall.
- * (worse = greater number) */
- export function getSufficientDetail(metadata: Metadata, segmentId: number, preferredDetail: number | null) {
- let availDetails = meshSegmentDetails(metadata, segmentId);
- if (preferredDetail !== null) {
- availDetails = availDetails.filter(det => det <= preferredDetail);
- }
- return Math.max(...availDetails);
- }
- export function annotationsBySegment(metadata: Metadata): { [id: number]: Segment } {
- const result: { [id: number]: Segment } = {};
- for (const segment of metadata.annotation.segment_list) {
- if (segment.id in result) {
- throw new Error(`Duplicate segment annotation for segment ${segment.id}`);
- }
- result[segment.id] = segment;
- }
- return result;
- }
- export function dropSegments(metadata: Metadata, segments: number[]): void {
- if (metadata.grid.segmentation_meshes.mesh_component_numbers.segment_ids === undefined) return;
- const dropSet = new Set(segments);
- metadata.annotation.segment_list = metadata.annotation.segment_list.filter(seg => !dropSet.has(seg.id));
- for (const seg of segments) {
- delete metadata.grid.segmentation_meshes.mesh_component_numbers.segment_ids[seg];
- }
- }
- export function namesAndColorsBySegment(metadata: Metadata) {
- const result: { [id: number]: { name: string, color: Color } } = {};
- for (const segment of metadata.annotation.segment_list) {
- if (segment.id in result) throw new Error(`Duplicate segment annotation for segment ${segment.id}`);
- result[segment.id] = { name: segment.biological_annotation.name, color: Color.fromNormalizedArray(segment.colour, 0) };
- }
- return result;
-
- }
-}
\ No newline at end of file
diff --git a/src/extensions/volumes-and-segmentations/entry-meshes.ts b/src/extensions/volumes-and-segmentations/entry-meshes.ts
index 15a75d66c956ac45af5931b13ebe82125d7e6596..bf106ea7abd3425c3900a49fb0294a1ca72ff61f 100644
--- a/src/extensions/volumes-and-segmentations/entry-meshes.ts
+++ b/src/extensions/volumes-and-segmentations/entry-meshes.ts
@@ -12,8 +12,8 @@ import { PluginCommands } from '../../mol-plugin/commands';
import { Color } from '../../mol-util/color';
import { ColorNames } from '../../mol-util/color/names';
-import { createMeshFromUrl } from '../meshes/examples';
import { BACKGROUND_SEGMENT_VOLUME_THRESHOLD } from '../meshes/mesh-streaming/behavior';
+import { createMeshFromUrl } from '../meshes/mesh-extension';
import { Segment } from './volseg-api/data';
import { VolsegEntryData } from './entry-root';
diff --git a/src/extensions/volumes-and-segmentations/volseg-api/utils.ts b/src/extensions/volumes-and-segmentations/volseg-api/utils.ts
index f3576bc71cbcd95c8275799b42c5e76518f42099..d138bf5abe7e3922927a0f8fc7d8621fb64f3361 100644
--- a/src/extensions/volumes-and-segmentations/volseg-api/utils.ts
+++ b/src/extensions/volumes-and-segmentations/volseg-api/utils.ts
@@ -4,6 +4,7 @@
* @author Adam Midlik <midlik@gmail.com>
*/
+import { Color } from '../../../mol-util/color';
import { Metadata, Segment } from './data';
@@ -33,6 +34,11 @@ export class MetadataWrapper {
return this.segmentMap[segmentId];
}
+ getSegmentColor(segmentId: number): Color | undefined {
+ const colorArray = this.getSegment(segmentId)?.colour;
+ return colorArray ? Color.fromNormalizedArray(colorArray, 0) : undefined;
+ }
+
/** Get the list of detail levels available for the given mesh segment. */
getMeshDetailLevels(segmentId: number): number[] {
const segmentIds = this.raw.grid.segmentation_meshes.mesh_component_numbers.segment_ids;
@@ -65,4 +71,4 @@ export class MetadataWrapper {
return vx * vy * vz * gx * gy * gz;
}
-}
\ No newline at end of file
+}