diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index 621f33fd33ed7c7ada1162639b97c232a1536427..3f9925eb128862d5b5819a61f2d47b3d86dc1b5e 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -6,22 +6,191 @@
import { PluginBehavior } from 'mol-plugin/behavior';
import { PluginStateObject } from 'mol-plugin/state/objects';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { VolumeServerInfo, VolumeServerHeader } from './model';
+import { createIsoValueParam } from 'mol-repr/volume/isosurface';
+import { VolumeIsoValue, VolumeData } from 'mol-model/volume';
+import { Color } from 'mol-util/color';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { PluginContext } from 'mol-plugin/context';
+import { LRUCache } from 'mol-util/lru-cache';
+import CIF from 'mol-io/reader/cif';
+import { Box3D } from 'mol-math/geometry';
+import { urlCombine } from 'mol-util/url';
+import { volumeFromDensityServerData } from 'mol-model-formats/volume/density-server';
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) };
- export interface BehaviorParams {
-
+ return {
+ view: PD.MappedStatic('box', {
+ 'box': PD.Group({
+ bottomLeft: PD.Vec3(Vec3.create(-22.4, -33.4, -21.6)),
+ topRight: PD.Vec3(Vec3.create(-7.1, -10, -0.9)),
+ autoUpdate: PD.Boolean(true, { description: 'Update the box when user clicks an element.' })
+ }, { description: 'Static box defined by cartesian coords.', isFlat: true }),
+ 'cell': PD.Group({}),
+ // 'auto': PD.Group({ }), // based on camera distance/active selection/whatever, show whole structure or slice.
+ }, { options: [['box', 'Bounded Box'], ['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)`] 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 implements PluginBehavior<{}> {
+ 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 {
- throw new Error('Method not implemented.');
+ this.ref = ref;
+ }
+
+ async update(params: Params) {
+ this.params = params;
+
+ let box: Box3D | undefined = void 0;
+
+ switch (params.view.name) {
+ case 'box':
+ box = Box3D.create(params.view.params.bottomLeft, params.view.params.topRight);
+ break;
+ case 'cell':
+ box = this.info.kind === 'x-ray'
+ ? this.info.structure.boundary.box
+ : void 0;
+ break;
+ }
+
+ const data = 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']!, info['2fo-fc'], this.info.header.sampling[0].valuesInfo[0]);
+ this.channels['fo-fc(+ve)'] = this.createChannel(data['FO-FC']!, info['fo-fc(+ve)'], this.info.header.sampling[0].valuesInfo[1]);
+ this.channels['fo-fc(-ve)'] = this.createChannel(data['FO-FC']!, info['fo-fc(-ve)'], this.info.header.sampling[0].valuesInfo[1]);
+ } else {
+ this.channels['em'] = this.createChannel(data['EM']!, 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)
+ };
}
unregister(): void {
- throw new Error('Method not implemented.');
+ // throw new Error('Method not implemented.');
+ }
+
+ constructor(public plugin: PluginContext, public info: VolumeServerInfo.Data) {
+
}
}
}
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts
index c0a6a5f57b748d0cf9b9c258d3ee45b8b78cf217..ba54b666d9f091c8ae407c3fb6d8ff4ad09a2398 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/model.ts
@@ -5,16 +5,21 @@
*/
import { PluginStateObject } from '../../../state/objects';
+import { VolumeIsoValue } from 'mol-model/volume';
+import { Structure } from 'mol-model/structure';
export class VolumeServerInfo extends PluginStateObject.Create<VolumeServerInfo.Data>({ name: 'Volume Streaming', typeClass: 'Object' }) { }
export namespace VolumeServerInfo {
+ export type Kind = 'x-ray' | 'em'
export interface Data {
serverUrl: string,
- kind: 'x-ray' | 'em',
+ kind: Kind,
// for em, the EMDB access code, for x-ray, the PDB id
dataId: string,
- header: VolumeServerHeader
+ header: VolumeServerHeader,
+ emDefaultContourLevel?: VolumeIsoValue,
+ structure: Structure
}
}
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..2ed0f9eff7a8a50936563a56e8b89dff5b866771 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
@@ -0,0 +1,173 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginStateObject as SO, PluginStateTransform } from '../../../state/objects';
+import { VolumeServerInfo, VolumeServerHeader } from './model';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { Task } from 'mol-task';
+import { PluginContext } from 'mol-plugin/context';
+import { urlCombine } from 'mol-util/url';
+import { createIsoValueParam } from 'mol-repr/volume/isosurface';
+import { VolumeIsoValue } from 'mol-model/volume';
+import { StateAction, StateObject, StateTransformer } from 'mol-state';
+import { getStreamingMethod, getEmdbIdAndContourLevel } from './util';
+import { VolumeStreaming } from './behavior';
+import { VolumeRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
+import { BuiltInVolumeRepresentations } from 'mol-repr/volume/registry';
+import { createTheme } from 'mol-theme/theme';
+// import { PluginContext } from 'mol-plugin/context';
+
+export const InitVolumeStreaming = StateAction.build({
+ display: { name: 'Volume Streaming' },
+ from: SO.Molecule.Structure,
+ params(a) {
+ return {
+ method: PD.Select<VolumeServerInfo.Kind>(getStreamingMethod(a && a.data), [['em', 'EM'], ['x-ray', 'X-Ray']]),
+ id: PD.Text((a && a.data.models[0].label) || ''),
+ serverUrl: PD.Text('https://webchem.ncbr.muni.cz/DensityServer')
+ };
+ }
+})(({ ref, state, params }, plugin: PluginContext) => Task.create('Volume Streaming', async taskCtx => {
+ // TODO: custom react view for this and the VolumeStreamingBehavior transformer
+
+ let dataId = params.id, emDefaultContourLevel: number | undefined;
+ if (params.method === 'em') {
+ await taskCtx.update('Getting EMDB info...');
+ const emInfo = await getEmdbIdAndContourLevel(plugin, taskCtx, params.id);
+ dataId = emInfo.emdbId;
+ emDefaultContourLevel = emInfo.contour;
+ }
+
+ const infoTree = state.build().to(ref)
+ .apply(CreateVolumeStreamingInfo, {
+ serverUrl: params.serverUrl,
+ source: params.method === 'em'
+ ? { name: 'em', params: { isoValue: VolumeIsoValue.absolute(emDefaultContourLevel || 0) } }
+ : { name: 'x-ray', params: { } },
+ dataId
+ });
+
+ const infoObj = await state.updateTree(infoTree).runInContext(taskCtx);
+
+ const behTree = state.build().to(infoTree.ref).apply(CreateVolumeStreamingBehavior, PD.getDefaultValues(VolumeStreaming.createParams(infoObj.data)))
+ if (params.method === 'em') {
+ behTree.apply(VolumeStreamingVisual, { channel: 'em' });
+ } else {
+ behTree.apply(VolumeStreamingVisual, { channel: '2fo-fc' });
+ behTree.apply(VolumeStreamingVisual, { channel: 'fo-fc(+ve)' });
+ behTree.apply(VolumeStreamingVisual, { channel: 'fo-fc(-ve)' });
+ }
+ await state.updateTree(behTree).runInContext(taskCtx);
+}));
+
+export { CreateVolumeStreamingInfo }
+type CreateVolumeStreamingInfo = typeof CreateVolumeStreamingInfo
+const CreateVolumeStreamingInfo = PluginStateTransform.BuiltIn({
+ name: 'create-volume-streaming-info',
+ display: { name: 'Volume Streaming Info' },
+ from: SO.Molecule.Structure,
+ to: VolumeServerInfo,
+ params(a) {
+ return {
+ serverUrl: PD.Text('https://webchem.ncbr.muni.cz/DensityServer'),
+ source: PD.MappedStatic('x-ray', {
+ 'em': PD.Group({
+ isoValue: createIsoValueParam(VolumeIsoValue.relative(1))
+ }),
+ 'x-ray': PD.Group({ })
+ }),
+ dataId: PD.Text('')
+ };
+ }
+})({
+ apply: ({ a, params }, plugin: PluginContext) => Task.create('', async taskCtx => {
+ const dataId = params.dataId;
+ const emDefaultContourLevel = params.source.name === 'em' ? params.source.params.isoValue : VolumeIsoValue.relative(1);
+ await taskCtx.update('Getting server header...');
+ const header = await plugin.fetch<VolumeServerHeader>({ url: urlCombine(params.serverUrl, `${params.source.name}/${dataId}`), type: 'json' }).runInContext(taskCtx);
+ const data: VolumeServerInfo.Data = {
+ serverUrl: params.serverUrl,
+ dataId,
+ kind: params.source.name,
+ header,
+ emDefaultContourLevel,
+ structure: a.data
+ };
+ return new VolumeServerInfo(data, { label: `Volume Streaming: ${dataId}` });
+ })
+});
+
+export { CreateVolumeStreamingBehavior }
+type CreateVolumeStreamingBehavior = typeof CreateVolumeStreamingBehavior
+const CreateVolumeStreamingBehavior = PluginStateTransform.BuiltIn({
+ name: 'create-volume-streaming-behavior',
+ display: { name: 'Volume Streaming Behavior' },
+ from: VolumeServerInfo,
+ to: VolumeStreaming,
+ params(a) {
+ return VolumeStreaming.createParams(a && a.data);
+ }
+})({
+ canAutoUpdate: ({ oldParams, newParams }) => {
+ return oldParams.view === newParams.view;
+ },
+ apply: ({ a, params }, plugin: PluginContext) => Task.create('Volume streaming', async _ => {
+ const behavior = new VolumeStreaming.Behavior(plugin, a.data);
+ await behavior.update(params);
+ return new VolumeStreaming(behavior, { label: 'Streaming Controls' });
+ }),
+ update({ b, newParams }) {
+ return Task.create('Update Volume Streaming', async _ => {
+ return await b.data.update(newParams) ? StateTransformer.UpdateResult.Updated : StateTransformer.UpdateResult.Unchanged;
+ });
+ }
+});
+
+
+export { VolumeStreamingVisual }
+type VolumeStreamingVisual = typeof VolumeStreamingVisual
+const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
+ name: 'create-volume-streaming-visual',
+ display: { name: 'Volume Streaming Visual' },
+ from: VolumeStreaming,
+ to: SO.Volume.Representation3D,
+ params: {
+ channel: PD.Select<VolumeStreaming.ChannelType>('em', VolumeStreaming.ChannelTypeOptions, { isHidden: true })
+ }
+})({
+ apply: ({ a, params: srcParams }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
+ const channel = a.data.channels[srcParams.channel];
+ if (!channel) return StateObject.Null;
+
+ const params = createVolumeProps(a.data, srcParams.channel);
+
+ const provider = BuiltInVolumeRepresentations.isosurface;
+ const props = params.type.params || {}
+ const repr = provider.factory({ webgl: plugin.canvas3d.webgl, ...plugin.volumeRepresentation.themeCtx }, provider.getParams)
+ repr.setTheme(createTheme(plugin.volumeRepresentation.themeCtx, { volume: channel.data }, params))
+ await repr.createOrUpdate(props, channel.data).runInContext(ctx);
+ return new SO.Volume.Representation3D(repr, { label: `${Math.round(channel.isoValue.relativeValue * 100) / 100} Ď [${srcParams.channel}]` });
+ }),
+ update: ({ a, b, oldParams, newParams }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
+ // TODO : check if params/underlying data/etc have changed; maybe will need to export "data" or some other "tag" in the Representation for this to work
+
+ const channel = a.data.channels[newParams.channel];
+ // TODO: is this correct behavior?
+ if (!channel) return StateTransformer.UpdateResult.Unchanged;
+
+ const params = createVolumeProps(a.data, newParams.channel);
+ const props = { ...b.data.props, ...params.type.params };
+ b.data.setTheme(createTheme(plugin.volumeRepresentation.themeCtx, { volume: channel.data }, params))
+ await b.data.createOrUpdate(props, channel.data).runInContext(ctx);
+ return StateTransformer.UpdateResult.Updated;
+ })
+});
+
+function createVolumeProps(streaming: VolumeStreaming.Behavior, channelName: VolumeStreaming.ChannelType) {
+ const channel = streaming.channels[channelName]!;
+ return VolumeRepresentation3DHelpers.getDefaultParamsStatic(streaming.plugin, 'isosurface',
+ { isoValue: channel.isoValue, alpha: channel.opacity }, 'uniform', { value: channel.color });
+}
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d3a4dbf87ff3177cad8fd51a36877b5bd01f9724
--- /dev/null
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
@@ -0,0 +1,51 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Structure } from 'mol-model/structure';
+import { VolumeServerInfo } from './model';
+import { PluginContext } from 'mol-plugin/context';
+import { RuntimeContext } from 'mol-task';
+
+export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.Kind = 'x-ray'): VolumeServerInfo.Kind {
+ if (!s) return defaultKind;
+
+ const model = s.models[0];
+ if (model.sourceData.kind !== 'mmCIF') return defaultKind;
+
+ const data = model.sourceData.data.exptl.method;
+ for (let i = 0; i < data.rowCount; i++) {
+ const v = data.value(i).toUpperCase();
+ if (v.indexOf('MICROSCOPY') >= 0) return 'em';
+ }
+ return 'x-ray';
+}
+
+export async function getEmdbIdAndContourLevel(plugin: PluginContext, taskCtx: RuntimeContext, pdbId: string) {
+ // TODO: parametrize to a differnt URL? in plugin settings perhaps
+ const summary = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/${pdbId}`, type: 'json' }).runInContext(taskCtx);
+
+ const summaryEntry = summary && summary[pdbId];
+ let emdbId: string;
+ if (summaryEntry && summaryEntry[0] && summaryEntry[0].related_structures) {
+ const emdb = summaryEntry[0].related_structures.filter((s: any) => s.resource === 'EMDB');
+ if (!emdb.length) {
+ throw new Error(`No related EMDB entry found for '${pdbId}'.`);
+ }
+ emdbId = emdb[0].accession;
+ } else {
+ throw new Error(`No related EMDB entry found for '${pdbId}'.`);
+ }
+
+ // TODO: parametrize to a differnt URL? in plugin settings perhaps
+ const emdb = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/${emdbId}`, type: 'json' }).runInContext(taskCtx);
+ const emdbEntry = emdb && emdb[emdbId];
+ let contour: number | undefined = void 0;
+ if (emdbEntry && emdbEntry[0] && emdbEntry[0].map && emdbEntry[0].map.contour_level && emdbEntry[0].map.contour_level.value !== void 0) {
+ contour = +emdbEntry[0].map.contour_level.value;
+ }
+
+ return { emdbId, contour };
+}
\ No newline at end of file
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 9fb4643bae578f86bc599c5d9bf09f05b9a2deb5..91e102c327bbbdeae1112a966fe3c00ba90a1c6f 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -15,6 +15,7 @@ import { StateTransforms } from './state/transforms';
import { PluginBehaviors } from './behavior';
import { AnimateModelIndex } from './state/animation/built-in';
import { StateActions } from './state/actions';
+import { InitVolumeStreaming } from './behavior/dynamic/volume-streaming/transformers';
function getParam(name: string, regex: string): string {
let r = new RegExp(`${name}=(${regex})[&]?`, 'i');
@@ -29,7 +30,8 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Action(StateActions.Structure.CreateComplexRepresentation),
PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
- PluginSpec.Action(StateActions.Volume.InitVolumeStreaming),
+ // PluginSpec.Action(StateActions.Volume.InitVolumeStreaming),
+ PluginSpec.Action(InitVolumeStreaming),
PluginSpec.Action(StateTransforms.Data.Download),
PluginSpec.Action(StateTransforms.Data.ParseCif),
diff --git a/src/mol-repr/volume/isosurface.ts b/src/mol-repr/volume/isosurface.ts
index 7ebfe7df4ba6f453bcd590045134b82967325380..30c8ba3278f4bb26b0625de9f007c04989294675 100644
--- a/src/mol-repr/volume/isosurface.ts
+++ b/src/mol-repr/volume/isosurface.ts
@@ -19,24 +19,41 @@ import { VisualContext } from 'mol-repr/visual';
import { NullLocation } from 'mol-model/location';
import { Lines } from 'mol-geo/geometry/lines/lines';
-export function createIsoValueParam(defaultValue: VolumeIsoValue) {
+const defaultStats: VolumeData['dataStats'] = { min: -1, max: 1, mean: 0, sigma: 0.1 };
+export function createIsoValueParam(defaultValue: VolumeIsoValue, stats?: VolumeData['dataStats']) {
+ const sts = stats || defaultStats;
+ const { min, max, mean, sigma } = sts;
+
+ // using ceil/floor could lead to "ouf of bounds" when converting
+ const relMin = (min - mean) / sigma;
+ const relMax = (max - mean) / sigma;
+
+ let def = defaultValue;
+ if (defaultValue.kind === 'absolute') {
+ if (defaultValue.absoluteValue < min) def = VolumeIsoValue.absolute(min);
+ else if (defaultValue.absoluteValue > max) def = VolumeIsoValue.absolute(max);
+ } else {
+ if (defaultValue.relativeValue < relMin) def = VolumeIsoValue.relative(relMin);
+ else if (defaultValue.relativeValue > relMax) def = VolumeIsoValue.relative(relMax);
+ }
+
return PD.Conditioned(
- defaultValue,
+ def,
{
'absolute': PD.Converted(
(v: VolumeIsoValue) => VolumeIsoValue.toAbsolute(v, VolumeData.One.dataStats).absoluteValue,
(v: number) => VolumeIsoValue.absolute(v),
- PD.Numeric(0.5, { min: -1, max: 1, step: 0.01 })
+ PD.Numeric(mean, { min, max, step: sigma / 100 })
),
'relative': PD.Converted(
(v: VolumeIsoValue) => VolumeIsoValue.toRelative(v, VolumeData.One.dataStats).relativeValue,
(v: number) => VolumeIsoValue.relative(v),
- PD.Numeric(2, { min: -10, max: 10, step: 0.01 })
+ PD.Numeric(Math.min(1, relMax), { min: relMin, max: relMax, step: Math.round(((max - min) / sigma)) / 100 })
)
},
(v: VolumeIsoValue) => v.kind === 'absolute' ? 'absolute' : 'relative',
- (v: VolumeIsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? VolumeIsoValue.toAbsolute(v, VolumeData.One.dataStats) : VolumeIsoValue.toRelative(v, VolumeData.One.dataStats)
- )
+ (v: VolumeIsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? VolumeIsoValue.toAbsolute(v, sts) : VolumeIsoValue.toRelative(v, sts)
+ );
}
export const IsoValueParam = createIsoValueParam(VolumeIsoValue.relative(2));
@@ -138,27 +155,8 @@ export const IsosurfaceParams = {
}
export type IsosurfaceParams = typeof IsosurfaceParams
export function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: VolumeData) {
- const p = PD.clone(IsosurfaceParams)
- const stats = volume.dataStats
- const { min, max, mean, sigma } = stats
- p.isoValue = PD.Conditioned(
- VolumeIsoValue.relative(2),
- {
- 'absolute': PD.Converted(
- (v: VolumeIsoValue) => VolumeIsoValue.toAbsolute(v, stats).absoluteValue,
- (v: number) => VolumeIsoValue.absolute(v),
- PD.Numeric(mean, { min, max, step: sigma / 100 })
- ),
- 'relative': PD.Converted(
- (v: VolumeIsoValue) => VolumeIsoValue.toRelative(v, stats).relativeValue,
- (v: number) => VolumeIsoValue.relative(v),
- PD.Numeric(2, { min: Math.floor((min - mean) / sigma), max: Math.ceil((max - mean) / sigma), step: Math.ceil((max - min) / sigma) / 100 })
- )
- },
- (v: VolumeIsoValue) => v.kind === 'absolute' ? 'absolute' : 'relative',
- (v: VolumeIsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? VolumeIsoValue.toAbsolute(v, stats) : VolumeIsoValue.toRelative(v, stats)
- )
-
+ const p = PD.clone(IsosurfaceParams);
+ p.isoValue = createIsoValueParam(VolumeIsoValue.relative(2), volume.dataStats);
return p
}
diff --git a/src/mol-util/data-source.ts b/src/mol-util/data-source.ts
index c370cc066a4e64a2c700fecacf2b2a523c70412d..316403070d3fbd5b9170bc18c1ddc02bc71ded3f 100644
--- a/src/mol-util/data-source.ts
+++ b/src/mol-util/data-source.ts
@@ -14,7 +14,7 @@ import { utf8Read } from 'mol-io/common/utf8';
// Gzip
// }
-export interface AjaxGetParams<T extends 'string' | 'binary' = 'string'> {
+export interface AjaxGetParams<T extends 'string' | 'binary' | 'json' = 'string'> {
url: string,
type?: T,
title?: string,
@@ -34,21 +34,14 @@ export function readFromFile(file: File, type: 'string' | 'binary') {
return <Task<Uint8Array | string>>readFromFileInternal(file, type === 'binary');
}
-export function ajaxGetString(url: string, title?: string) {
- return <Task<string>>ajaxGetInternal(title, url, false, false);
-}
-
-export function ajaxGetUint8Array(url: string, title?: string) {
- return <Task<Uint8Array>>ajaxGetInternal(title, url, true, false);
-}
-
export function ajaxGet(url: string): Task<string>
export function ajaxGet(params: AjaxGetParams<'string'>): Task<string>
export function ajaxGet(params: AjaxGetParams<'binary'>): Task<Uint8Array>
-export function ajaxGet(params: AjaxGetParams<'string' | 'binary'>): Task<string | Uint8Array>
-export function ajaxGet(params: AjaxGetParams<'string' | 'binary'> | string) {
- if (typeof params === 'string') return ajaxGetInternal(params, params, false, false);
- return ajaxGetInternal(params.title, params.url, params.type === 'binary', false /* params.compression === DataCompressionMethod.Gzip */, params.body);
+export function ajaxGet<T = any>(params: AjaxGetParams<'json'>): Task<T>
+export function ajaxGet(params: AjaxGetParams<'string' | 'binary' | 'json'>): Task<string | Uint8Array | object>
+export function ajaxGet(params: AjaxGetParams<'string' | 'binary' | 'json'> | string) {
+ if (typeof params === 'string') return ajaxGetInternal(params, params, 'string', false);
+ return ajaxGetInternal(params.title, params.url, params.type || 'string', false /* params.compression === DataCompressionMethod.Gzip */, params.body);
}
export type AjaxTask = typeof ajaxGet
@@ -168,10 +161,11 @@ async function processAjax(ctx: RuntimeContext, asUint8Array: boolean, decompres
}
}
-function ajaxGetInternal(title: string | undefined, url: string, asUint8Array: boolean, decompressGzip: boolean, body?: string): Task<string | Uint8Array> {
+function ajaxGetInternal(title: string | undefined, url: string, type: 'json' | 'string' | 'binary', decompressGzip: boolean, body?: string): Task<string | Uint8Array> {
let xhttp: XMLHttpRequest | undefined = void 0;
return Task.create(title ? title : 'Download', async ctx => {
try {
+ const asUint8Array = type === 'binary';
if (!asUint8Array && decompressGzip) {
throw 'Decompress is only available when downloading binary data.';
}
@@ -185,6 +179,13 @@ function ajaxGetInternal(title: string | undefined, url: string, asUint8Array: b
ctx.update({ message: 'Waiting for server...', canAbort: true });
const e = await readData(ctx, 'Downloading...', xhttp, asUint8Array);
const result = await processAjax(ctx, asUint8Array, decompressGzip, e)
+
+ if (type === 'json') {
+ ctx.update({ message: 'Parsing JSON...', canAbort: false });
+ const data = JSON.parse(result);
+ return data;
+ }
+
return result;
} finally {
xhttp = void 0;
diff --git a/src/mol-util/url-query.ts b/src/mol-util/url.ts
similarity index 72%
rename from src/mol-util/url-query.ts
rename to src/mol-util/url.ts
index a4a10a8371c24b55995ea175df35fb14bc6cec86..3234bdbaea7ff7565eb8f2542c057b314242fd02 100644
--- a/src/mol-util/url-query.ts
+++ b/src/mol-util/url.ts
@@ -9,4 +9,8 @@ export function urlQueryParameter (id: string) {
const a = new RegExp(`${id}=([^&#=]*)`)
const m = a.exec(window.location.search)
return m ? decodeURIComponent(m[1]) : undefined
+}
+
+export function urlCombine(base: string, query: string) {
+ return `${base}${base[base.length - 1] === '/' || query[0] === '/' ? '' : '/'}${query}`;
}
\ No newline at end of file