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behavior.ts
behavior.ts 10.78 KiB
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import CIF from 'mol-io/reader/cif';
import { Box3D } from 'mol-math/geometry';
import { Vec3 } from 'mol-math/linear-algebra';
import { volumeFromDensityServerData } from 'mol-model-formats/volume/density-server';
import { StructureElement } from 'mol-model/structure';
import { VolumeData, VolumeIsoValue } from 'mol-model/volume';
import { PluginBehavior } from 'mol-plugin/behavior';
import { PluginContext } from 'mol-plugin/context';
import { PluginStateObject } from 'mol-plugin/state/objects';
import { createIsoValueParam } from 'mol-repr/volume/isosurface';
import { Color } from 'mol-util/color';
import { LRUCache } from 'mol-util/lru-cache';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { urlCombine } from 'mol-util/url';
import { VolumeServerHeader, VolumeServerInfo } from './model';
import { CreateVolumeStreamingBehavior } from './transformers';
import { ButtonsType } from 'mol-util/input/input-observer';
export class VolumeStreaming extends PluginStateObject.CreateBehavior<VolumeStreaming.Behavior>({ name: 'Volume Streaming' }) { }
export namespace VolumeStreaming {
function channelParam(label: string, color: Color, defaultValue: VolumeIsoValue, stats: VolumeData['dataStats']) {
return PD.Group({
isoValue: createIsoValueParam(defaultValue, stats),
color: PD.Color(color),
opacity: PD.Numeric(0.3, { min: 0, max: 1, step: 0.01 })
}, { label, isExpanded: true });
}
const fakeSampling: VolumeServerHeader.Sampling = {
byteOffset: 0,
rate: 1,
sampleCount: [1, 1, 1],
valuesInfo: [{ mean: 0, min: -1, max: 1, sigma: 0.1 }, { mean: 0, min: -1, max: 1, sigma: 0.1 }]
};
export function createParams(data?: VolumeServerInfo.Data) {
// fake the info
const info = data || { kind: 'em', header: { sampling: [fakeSampling], availablePrecisions: [{ precision: 0, maxVoxels: 0 }] }, emDefaultContourLevel: VolumeIsoValue.relative(0) };
const box = (data && data.structure.boundary.box) || Box3D.empty();
return {
view: PD.MappedStatic('selection-box', {
'box': PD.Group({
bottomLeft: PD.Vec3(box.min),
topRight: PD.Vec3(box.max),
}, { description: 'Static box defined by cartesian coords.', isFlat: true }),
'selection-box': PD.Group({
radius: PD.Numeric(5, { min: 0, max: 50, step: 0.5 }),
bottomLeft: PD.Vec3(Vec3.create(0, 0, 0), { isHidden: true }),
topRight: PD.Vec3(Vec3.create(0, 0, 0), { isHidden: true }),
}, { description: 'Box around last-interacted element.', isFlat: true }),
'cell': PD.Group({}),
// 'auto': PD.Group({ }), // based on camera distance/active selection/whatever, show whole structure or slice.
}, { options: [['box', 'Bounded Box'], ['selection-box', 'Selection'], ['cell', 'Whole Structure']] }),
detailLevel: PD.Select<number>(Math.min(1, info.header.availablePrecisions.length - 1),
info.header.availablePrecisions.map((p, i) => [i, `${i + 1} [ ${Math.pow(p.maxVoxels, 1 / 3) | 0}^3 cells ]`] as [number, string])),
channels: info.kind === 'em'
? PD.Group({
'em': channelParam('EM', Color(0x638F8F), info.emDefaultContourLevel || VolumeIsoValue.relative(1), info.header.sampling[0].valuesInfo[0])
}, { isFlat: true })
: PD.Group({
'2fo-fc': channelParam('2Fo-Fc', Color(0x3362B2), VolumeIsoValue.relative(1.5), info.header.sampling[0].valuesInfo[0]),
'fo-fc(+ve)': channelParam('Fo-Fc(+ve)', Color(0x33BB33), VolumeIsoValue.relative(3), info.header.sampling[0].valuesInfo[1]),
'fo-fc(-ve)': channelParam('Fo-Fc(-ve)', Color(0xBB3333), VolumeIsoValue.relative(-3), info.header.sampling[0].valuesInfo[1]),
}, { isFlat: true })
};
}
type RT = typeof createParams extends (...args: any[]) => (infer T) ? T : never
export type Params = RT extends PD.Params ? PD.Values<RT> : {}
type ChannelsInfo = { [name in ChannelType]?: { isoValue: VolumeIsoValue, color: Color, opacity: number } }
type ChannelsData = { [name in 'EM' | '2FO-FC' | 'FO-FC']?: VolumeData }
export type ChannelType = 'em' | '2fo-fc' | 'fo-fc(+ve)' | 'fo-fc(-ve)'
export const ChannelTypeOptions: [ChannelType, string][] = [['em', 'em'], ['2fo-fc', '2fo-fc'], ['fo-fc(+ve)', 'fo-fc(+ve)'], ['fo-fc(-ve)', 'fo-fc(-ve)']]
interface ChannelInfo {
data: VolumeData,
color: Color,
isoValue: VolumeIsoValue.Relative,
opacity: number
}
export type Channels = { [name in ChannelType]?: ChannelInfo }
export class Behavior extends PluginBehavior.WithSubscribers<Params> {
private cache = LRUCache.create<ChannelsData>(25);
private params: Params = {} as any;
// private ref: string = '';
channels: Channels = {}
private async queryData(box?: Box3D) {
let url = urlCombine(this.info.serverUrl, `${this.info.kind}/${this.info.dataId}`);
if (box) {
const { min: a, max: b } = box;
url += `/box`
+ `/${a.map(v => Math.round(1000 * v) / 1000).join(',')}`
+ `/${b.map(v => Math.round(1000 * v) / 1000).join(',')}`;
} else {
url += `/cell`;
}
url += `?detail=${this.params.detailLevel}`;
let data = LRUCache.get(this.cache, url);
if (data) {
return data;
}
const cif = await this.plugin.runTask(this.plugin.fetch({ url, type: 'binary' }));
data = await this.parseCif(cif as Uint8Array);
if (!data) {
return;
}
LRUCache.set(this.cache, url, data);
return data;
}
private async parseCif(data: Uint8Array): Promise<ChannelsData | undefined> {
const parsed = await this.plugin.runTask(CIF.parseBinary(data));
if (parsed.isError) {
this.plugin.log.error('VolumeStreaming, parsing CIF: ' + parsed.toString());
return;
}
if (parsed.result.blocks.length < 2) {
this.plugin.log.error('VolumeStreaming: Invalid data.');
return;
}
const ret: ChannelsData = {};
for (let i = 1; i < parsed.result.blocks.length; i++) {
const block = parsed.result.blocks[i];
const densityServerCif = CIF.schema.densityServer(block);
const volume = await this.plugin.runTask(await volumeFromDensityServerData(densityServerCif));
(ret as any)[block.header as any] = volume;
}
return ret;
}
register(ref: string): void {
// this.ref = ref;
this.subscribeObservable(this.plugin.events.canvas3d.click, ({ current, buttons }) => {
if (buttons !== ButtonsType.Flag.Secondary || this.params.view.name !== 'selection-box') return;
// TODO: support link loci as well?
// Perhaps structure loci too?
if (!StructureElement.isLoci(current.loci)) return;
// TODO: check if it's the related structure
const loci = StructureElement.Loci.extendToWholeResidues(current.loci);
const eR = this.params.view.params.radius;
const box = StructureElement.Loci.getBoundary(loci).box;
const update = this.plugin.state.dataState.build().to(ref).update(CreateVolumeStreamingBehavior, old => ({
...old,
view: {
name: 'selection-box' as 'selection-box',
params: {
radius: eR,
bottomLeft: box.min,
topRight: box.max
}
}
}));
// TODO: create/use command queue here and cancel any ongoing updates.
this.plugin.runTask(this.plugin.state.dataState.updateTree(update));
});
}
async update(params: Params) {
this.params = params;
let box: Box3D | undefined = void 0, emptyData = false;
switch (params.view.name) {
case 'box':
box = Box3D.create(params.view.params.bottomLeft, params.view.params.topRight);
emptyData = Box3D.volume(box) < 0.0001;
break;
case 'selection-box': {
box = Box3D.create(Vec3.clone(params.view.params.bottomLeft), Vec3.clone(params.view.params.topRight));
const r = params.view.params.radius;
emptyData = Box3D.volume(box) < 0.0001;
Box3D.expand(box, box, Vec3.create(r, r, r));
break;
}
case 'cell':
box = this.info.kind === 'x-ray'
? this.info.structure.boundary.box
: void 0;
break;
}
const data = emptyData ? {} : await this.queryData(box);
if (!data) return false;
const info = params.channels as ChannelsInfo;
if (this.info.kind === 'x-ray') {
this.channels['2fo-fc'] = this.createChannel(data['2FO-FC'] || VolumeData.One, info['2fo-fc'], this.info.header.sampling[0].valuesInfo[0]);
this.channels['fo-fc(+ve)'] = this.createChannel(data['FO-FC'] || VolumeData.One, info['fo-fc(+ve)'], this.info.header.sampling[0].valuesInfo[1]);
this.channels['fo-fc(-ve)'] = this.createChannel(data['FO-FC'] || VolumeData.One, info['fo-fc(-ve)'], this.info.header.sampling[0].valuesInfo[1]);
} else {
this.channels['em'] = this.createChannel(data['EM'] || VolumeData.One, info['em'], this.info.header.sampling[0].valuesInfo[0]);
}
return true;
}
private createChannel(data: VolumeData, info: ChannelsInfo['em'], stats: VolumeData['dataStats']): ChannelInfo {
const i = info!;
return {
data,
color: i.color,
opacity: i.opacity,
isoValue: i.isoValue.kind === 'relative' ? i.isoValue : VolumeIsoValue.toRelative(i.isoValue, stats)
};
}
constructor(public plugin: PluginContext, public info: VolumeServerInfo.Data) {
super(plugin);
}
}
}