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-/**
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- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
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- *
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- * @author David Sehnal <david.sehnal@gmail.com>
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- * @author Alexander Rose <alexander.rose@weirdbyte.de>
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- */
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-
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-import { PluginStateObject as SO, PluginStateTransform } from 'molstar/lib/mol-plugin-state/objects';
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-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
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-import { Task } from 'molstar/lib/mol-task';
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-import { PluginContext } from 'molstar/lib/mol-plugin/context';
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-import { Volume } from 'molstar/lib/mol-model/volume';
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-import { StateAction, StateObject, StateTransformer } from 'molstar/lib/mol-state';
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-import { VolumeRepresentation3DHelpers } from 'molstar/lib/mol-plugin-state/transforms/representation';
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-import { VolumeRepresentationRegistry } from 'molstar/lib/mol-repr/volume/registry';
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-import { Theme } from 'molstar/lib/mol-theme/theme';
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-import { Model } from 'molstar/lib/mol-model/structure';
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-import { GlobalModelTransformInfo } from 'molstar/lib/mol-model/structure/model/properties/global-transform';
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-import {
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- getContourLevel,
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- getEmdbIds,
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- getIds,
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- getStreamingMethod
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-} from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/util';
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-import { VolumeStreaming } from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior';
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-import { PluginConfig } from 'molstar/lib/mol-plugin/config';
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-import { VolumeServerInfo } from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/model';
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-import {
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- CreateVolumeStreamingBehavior,
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- CreateVolumeStreamingInfo
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-} from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers';
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-
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-// TODO SMB 6/11/21 - this is a temp impl, safe to remove as soon as the next Mol* version after 2.0.6 is released
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-
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-function addEntry(entries: InfoEntryProps[], method: VolumeServerInfo.Kind, dataId: string, emDefaultContourLevel: number) {
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- entries.push({
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- source: method === 'em'
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- ? { name: 'em', params: { isoValue: Volume.IsoValue.absolute(emDefaultContourLevel || 0) } }
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- : { name: 'x-ray', params: { } },
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- dataId
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- });
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-}
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-
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-export const InitVolumeStreaming = StateAction.build({
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- display: { name: 'Volume Streaming' },
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- from: SO.Molecule.Structure,
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- params(a, plugin: PluginContext) {
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- const method = getStreamingMethod(a && a.data);
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- const ids = getIds(method, a && a.data);
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- return {
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- method: PD.Select<VolumeServerInfo.Kind>(method, [['em', 'EM'], ['x-ray', 'X-Ray']]),
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- entries: PD.ObjectList({ id: PD.Text(ids[0] || '') }, ({ id }) => id, { defaultValue: ids.map(id => ({ id })) }),
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- defaultView: PD.Select<VolumeStreaming.ViewTypes>(method === 'em' ? 'cell' : 'selection-box', VolumeStreaming.ViewTypeOptions as any),
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- options: PD.Group({
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- serverUrl: PD.Text(plugin.config.get(PluginConfig.VolumeStreaming.DefaultServer) || 'https://ds.litemol.org'),
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- behaviorRef: PD.Text('', { isHidden: true }),
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- emContourProvider: PD.Select<'emdb' | 'pdbe'>('emdb', [['emdb', 'EMDB'], ['pdbe', 'PDBe']], { isHidden: true }),
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- channelParams: PD.Value<VolumeStreaming.DefaultChannelParams>({}, { isHidden: true })
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- })
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- };
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- },
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- isApplicable: (a, _, plugin: PluginContext) => {
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- const canStreamTest = plugin.config.get(PluginConfig.VolumeStreaming.CanStream);
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- if (canStreamTest) return canStreamTest(a.data, plugin);
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- return a.data.models.length === 1 && Model.probablyHasDensityMap(a.data.models[0]);
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- }
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-})(({ ref, state, params }, plugin: PluginContext) => Task.create('Volume Streaming', async taskCtx => {
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- const entries: InfoEntryProps[] = [];
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-
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- for (let i = 0, il = params.entries.length; i < il; ++i) {
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- let dataId = params.entries[i].id.toLowerCase();
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- let emDefaultContourLevel: number | undefined;
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-
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- if (params.method === 'em') {
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- // if pdb ids are given for method 'em', get corresponding emd ids
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- // and continue the loop
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- if (!dataId.toUpperCase().startsWith('EMD')) {
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- await taskCtx.update('Getting EMDB info...');
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- const emdbIds = await getEmdbIds(plugin, taskCtx, dataId);
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- for (let j = 0, jl = emdbIds.length; j < jl; ++j) {
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- const emdbId = emdbIds[j];
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- let contourLevel: number | undefined;
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- try {
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- contourLevel = await getContourLevel(params.options.emContourProvider, plugin, taskCtx, emdbId);
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- } catch (e) {
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- console.info(`Could not get map info for ${emdbId}: ${e}`);
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- continue;
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- }
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- addEntry(entries, params.method, emdbId, contourLevel || 0);
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- }
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- continue;
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- }
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- try {
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- emDefaultContourLevel = await getContourLevel(params.options.emContourProvider, plugin, taskCtx, dataId);
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- } catch (e) {
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- console.info(`Could not get map info for ${dataId}: ${e}`);
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- continue;
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- }
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- }
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-
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- addEntry(entries, params.method, dataId, emDefaultContourLevel || 0);
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- }
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-
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- const infoTree = state.build().to(ref)
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- .applyOrUpdateTagged(VolumeStreaming.RootTag, CreateVolumeStreamingInfo, {
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- serverUrl: params.options.serverUrl,
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- entries
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- });
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-
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- await infoTree.commit();
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-
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- const info = infoTree.selector;
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- if (!info.isOk) return;
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-
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- // clear the children in case there were errors
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- const children = state.tree.children.get(info.ref);
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- if (children?.size > 0) await plugin.managers.structure.hierarchy.remove(children?.toArray());
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-
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- const infoObj = info.cell!.obj!;
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-
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- const behTree = state.build().to(infoTree.ref).apply(CreateVolumeStreamingBehavior,
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- PD.getDefaultValues(VolumeStreaming.createParams({ data: infoObj.data, defaultView: params.defaultView, channelParams: params.options.channelParams })),
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- { ref: params.options.behaviorRef ? params.options.behaviorRef : void 0 });
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-
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- if (params.method === 'em') {
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- behTree.apply(VolumeStreamingVisual, { channel: 'em' }, { state: { isGhost: true }, tags: 'em' });
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- } else {
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- behTree.apply(VolumeStreamingVisual, { channel: '2fo-fc' }, { state: { isGhost: true }, tags: '2fo-fc' });
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- behTree.apply(VolumeStreamingVisual, { channel: 'fo-fc(+ve)' }, { state: { isGhost: true }, tags: 'fo-fc(+ve)' });
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- behTree.apply(VolumeStreamingVisual, { channel: 'fo-fc(-ve)' }, { state: { isGhost: true }, tags: 'fo-fc(-ve)' });
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- }
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- await state.updateTree(behTree).runInContext(taskCtx);
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-}));
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-
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-const InfoEntryParams = {
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- dataId: PD.Text(''),
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- source: PD.MappedStatic('x-ray', {
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- 'em': PD.Group({
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- isoValue: Volume.createIsoValueParam(Volume.IsoValue.relative(1))
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- }),
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- 'x-ray': PD.Group({ })
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- })
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-};
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-type InfoEntryProps = PD.Values<typeof InfoEntryParams>
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-
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-export { VolumeStreamingVisual };
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-type VolumeStreamingVisual = typeof VolumeStreamingVisual
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-const VolumeStreamingVisual = PluginStateTransform.BuiltIn({
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- name: 'create-volume-streaming-visual-custom',
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- display: { name: 'Volume Streaming Visual' },
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- from: VolumeStreaming,
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- to: SO.Volume.Representation3D,
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- params: {
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- channel: PD.Select<VolumeStreaming.ChannelType>('em', VolumeStreaming.ChannelTypeOptions, { isHidden: true })
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- }
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-})({
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- apply: ({ a, params: srcParams, spine }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
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- const channel = a.data.channels[srcParams.channel];
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- if (!channel) return StateObject.Null;
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-
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- const params = createVolumeProps(a.data, srcParams.channel);
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- const provider = VolumeRepresentationRegistry.BuiltIn.isosurface;
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- const props = params.type.params || {};
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- const repr = provider.factory({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.volume.themes }, provider.getParams);
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- repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
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- const structure = spine.getAncestorOfType(SO.Molecule.Structure)?.data;
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- const transform = structure?.models.length === 0 ? void 0 : GlobalModelTransformInfo.get(structure?.models[0]!);
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- await repr.createOrUpdate(props, channel.data).runInContext(ctx);
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- if (transform) repr.setState({ transform });
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- return new SO.Volume.Representation3D({ repr, sourceData: channel.data }, { label: `${Math.round(channel.isoValue.relativeValue * 100) / 100} σ [${srcParams.channel}]` });
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- }),
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- update: ({ a, b, newParams, spine }, plugin: PluginContext) => Task.create('Volume Representation', async ctx => {
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- // 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
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-
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- const channel = a.data.channels[newParams.channel];
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- // TODO: is this correct behavior?
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- if (!channel) return StateTransformer.UpdateResult.Unchanged;
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-
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- const visible = b.data.repr.state.visible;
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- const params = createVolumeProps(a.data, newParams.channel);
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- const props = { ...b.data.repr.props, ...params.type.params };
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- b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: channel.data }, params));
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- await b.data.repr.createOrUpdate(props, channel.data).runInContext(ctx);
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- b.data.repr.setState({ visible });
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- b.data.sourceData = channel.data;
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-
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- // TODO: set the transform here as well in case the structure moves?
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- // doing this here now breaks the code for some reason...
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- // const structure = spine.getAncestorOfType(SO.Molecule.Structure)?.data;
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- // const transform = structure?.models.length === 0 ? void 0 : GlobalModelTransformInfo.get(structure?.models[0]!);
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- // if (transform) b.data.repr.setState({ transform });
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-
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- return StateTransformer.UpdateResult.Updated;
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- })
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-});
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-
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-function createVolumeProps(streaming: VolumeStreaming.Behavior, channelName: VolumeStreaming.ChannelType) {
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- const channel = streaming.channels[channelName]!;
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- return VolumeRepresentation3DHelpers.getDefaultParamsStatic(streaming.plugin,
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- 'isosurface', { isoValue: channel.isoValue, alpha: channel.opacity, visuals: channel.wireframe ? ['wireframe'] : ['solid'] },
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- 'uniform', { value: channel.color });
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-}
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JonStargaryen