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Commit c23651c0 authored by Alexander Rose's avatar Alexander Rose
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wip, DscifProvider

parent 171cda89
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src/mol-plugin/state/actions/basic.ts
+ 57
− 28
View file @ c23651c0
......@@ -6,7 +6,7 @@
*/
import { PluginContext } from 'mol-plugin/context';
import { StateTree, Transformer, StateObject } from 'mol-state';
import { StateTree, Transformer, StateObject, State } from 'mol-state';
import { StateAction } from 'mol-state/action';
import { StateSelection } from 'mol-state/state/selection';
import { StateTreeBuilder } from 'mol-state/tree/builder';
......@@ -14,9 +14,11 @@ import { ParamDefinition as PD } from 'mol-util/param-definition';
import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
import { StructureRepresentation3DHelpers } from '../transforms/representation';
import { StructureRepresentation3DHelpers, VolumeRepresentation3DHelpers } from '../transforms/representation';
import { getFileInfo, FileInfo } from 'mol-util/file-info';
import { Task } from 'mol-task';
import { ColorNames } from 'mol-util/color/tables';
import { VolumeIsoValue } from 'mol-model/volume';
// TODO: "structure/volume parser provider"
......@@ -171,8 +173,8 @@ export const UpdateTrajectory = StateAction.build({
//
export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String, M extends StateObject> {
private _list: { name: string, provider: DataFormatProvider<D, M> }[] = []
private _map = new Map<string, DataFormatProvider<D, M>>()
private _list: { name: string, provider: DataFormatProvider<D> }[] = []
private _map = new Map<string, DataFormatProvider<D>>()
get default() { return this._list[0]; }
get types(): [string, string][] {
......@@ -185,7 +187,7 @@ export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | Plugin
this.add('dscif', DscifProvider)
};
add(name: string, provider: DataFormatProvider<D, M>) {
add(name: string, provider: DataFormatProvider<D>) {
this._list.push({ name, provider })
this._map.set(name, provider)
}
......@@ -203,7 +205,7 @@ export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | Plugin
throw new Error('no compatible data format provider available')
}
get(name: string): DataFormatProvider<D, M> {
get(name: string): DataFormatProvider<D> {
if (this._map.has(name)) {
return this._map.get(name)!
} else {
......@@ -216,53 +218,82 @@ export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | Plugin
}
}
interface DataFormatProvider<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String, M extends StateObject> {
interface DataFormatProvider<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String> {
label: string
description: string
fileExtensions: string[]
isApplicable(info: FileInfo, data: string | Uint8Array): boolean
getDefaultBuilder(b: StateTreeBuilder.To<D>): StateTreeBuilder.To<M>
getDefaultBuilder(ctx: PluginContext, data: StateTreeBuilder.To<D>, state?: State): Task<void>
}
const Ccp4Provider: DataFormatProvider<any, any> = {
const Ccp4Provider: DataFormatProvider<any> = {
label: 'CCP4/MRC/BRIX',
description: 'CCP4/MRC/BRIX',
fileExtensions: ['ccp4', 'mrc', 'map'],
isApplicable: (info: FileInfo, data: Uint8Array) => {
return info.ext === 'ccp4' || info.ext === 'mrc' || info.ext === 'map'
},
getDefaultBuilder: (b: StateTreeBuilder.To<PluginStateObject.Data.Binary>) => {
return b.apply(StateTransforms.Data.ParseCcp4)
.apply(StateTransforms.Model.VolumeFromCcp4)
.apply(StateTransforms.Representation.VolumeRepresentation3D)
getDefaultBuilder: (ctx: PluginContext, data: StateTreeBuilder.To<PluginStateObject.Data.Binary>, state: State) => {
return Task.create('CCP4/MRC/BRIX default builder', async taskCtx => {
const tree = data.apply(StateTransforms.Data.ParseCcp4)
.apply(StateTransforms.Model.VolumeFromCcp4)
.apply(StateTransforms.Representation.VolumeRepresentation3D)
await state.updateTree(tree).runInContext(taskCtx)
})
}
}
const Dsn6Provider: DataFormatProvider<any, any> = {
const Dsn6Provider: DataFormatProvider<any> = {
label: 'DSN6/BRIX',
description: 'DSN6/BRIX',
fileExtensions: ['dsn6', 'brix'],
isApplicable: (info: FileInfo, data: Uint8Array) => {
return info.ext === 'dsn6' || info.ext === 'brix'
},
getDefaultBuilder: (b: StateTreeBuilder.To<PluginStateObject.Data.Binary>) => {
return b.apply(StateTransforms.Data.ParseDsn6)
.apply(StateTransforms.Model.VolumeFromDsn6)
.apply(StateTransforms.Representation.VolumeRepresentation3D)
getDefaultBuilder: (ctx: PluginContext, data: StateTreeBuilder.To<PluginStateObject.Data.Binary>, state: State) => {
return Task.create('DSN6/BRIX default builder', async taskCtx => {
const tree = data.apply(StateTransforms.Data.ParseDsn6)
.apply(StateTransforms.Model.VolumeFromDsn6)
.apply(StateTransforms.Representation.VolumeRepresentation3D)
await state.updateTree(tree).runInContext(taskCtx)
})
}
}
const DscifProvider: DataFormatProvider<any, any> = {
const DscifProvider: DataFormatProvider<any> = {
label: 'DensityServer CIF',
description: 'DensityServer CIF',
fileExtensions: ['cif'],
isApplicable: (info: FileInfo, data: Uint8Array) => {
return info.ext === 'cif'
},
getDefaultBuilder: (b: StateTreeBuilder.To<PluginStateObject.Data.Binary>) => {
return b.apply(StateTransforms.Data.ParseCif, { })
.apply(StateTransforms.Model.VolumeFromDensityServerCif)
.apply(StateTransforms.Representation.VolumeRepresentation3D)
getDefaultBuilder: (ctx: PluginContext, data: StateTreeBuilder.To<PluginStateObject.Data.Binary>, state: State) => {
return Task.create('DensityServer CIF default builder', async taskCtx => {
const cifBuilder = data.apply(StateTransforms.Data.ParseCif)
const cifStateObject = await state.updateTree(cifBuilder).runInContext(taskCtx)
const b = state.build().to(cifBuilder.ref);
const blocks = cifStateObject.data.blocks.slice(1); // zero block contains query meta-data
let tree: StateTreeBuilder.To<any>
if (blocks.length === 1) {
tree = b
.apply(StateTransforms.Model.VolumeFromDensityServerCif, { blockHeader: blocks[0].header })
.apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }))
} else if (blocks.length === 2) {
tree = b
.apply(StateTransforms.Model.VolumeFromDensityServerCif, { blockHeader: blocks[0].header })
.apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.blue }))
const vol = tree.to(cifBuilder.ref)
.apply(StateTransforms.Model.VolumeFromDensityServerCif, { blockHeader: blocks[1].header })
const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green })
tree = vol.apply(StateTransforms.Representation.VolumeRepresentation3D, posParams)
const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red })
tree = tree.to(vol.ref).apply(StateTransforms.Representation.VolumeRepresentation3D, negParams)
} else {
throw new Error('unknown number of blocks')
}
await state.updateTree(tree).runInContext(taskCtx);
})
}
}
......@@ -302,9 +333,8 @@ export const OpenVolume = StateAction.build({
const provider = params.format === 'auto' ? ctx.dataFormat.registry.auto(getFileInfo(params.file), dataStateObject) : ctx.dataFormat.registry.get(params.format)
const b = state.build().to(data.ref);
const tree = provider.getDefaultBuilder(b).getTree()
// need to await the 2nd update the so that the enclosing Task finishes after the update is done.
await state.updateTree(tree).runInContext(taskCtx);
await provider.getDefaultBuilder(ctx, b, state).runInContext(taskCtx)
}));
export { DownloadDensity };
......@@ -341,7 +371,7 @@ const DownloadDensity = StateAction.build({
})(({ params, state }, ctx: PluginContext) => Task.create('Download Density', async taskCtx => {
const src = params.source;
let downloadParams: Transformer.Params<Download>;
let provider: DataFormatProvider<any, any>
let provider: DataFormatProvider<any>
switch (src.name) {
case 'url':
......@@ -386,6 +416,5 @@ const DownloadDensity = StateAction.build({
}
const b = state.build().to(data.ref);
const tree = provider.getDefaultBuilder(b).getTree()
await state.updateTree(tree).runInContext(taskCtx);
await provider.getDefaultBuilder(ctx, b, state).runInContext(taskCtx)
}));
\ No newline at end of file
src/mol-plugin/state/transforms/representation.ts
+ 7
− 6
View file @ c23651c0
......@@ -19,6 +19,8 @@ import { ExplodeRepresentation3D } from 'mol-plugin/behavior/dynamic/representat
import { VolumeData } from 'mol-model/volume';
import { BuiltInVolumeRepresentationsName } from 'mol-repr/volume/registry';
import { VolumeParams } from 'mol-repr/volume/representation';
import { BuiltInColorThemeName, ColorTheme } from 'mol-theme/color';
import { BuiltInSizeThemeName, SizeTheme } from 'mol-theme/size';
export namespace StructureRepresentation3DHelpers {
export function getDefaultParams(ctx: PluginContext, name: BuiltInStructureRepresentationsName, structure: Structure, structureParams?: Partial<PD.Values<StructureParams>>): Transformer.Params<StructureRepresentation3D> {
......@@ -162,14 +164,14 @@ export namespace VolumeRepresentation3DHelpers {
})
}
export function getDefaultParamsStatic(ctx: PluginContext, name: BuiltInVolumeRepresentationsName, volumeParams?: Partial<PD.Values<VolumeParams>>): Transformer.Params<VolumeRepresentation3D> {
export function getDefaultParamsStatic(ctx: PluginContext, name: BuiltInVolumeRepresentationsName, volumeParams?: Partial<PD.Values<PD.Params>>, colorName?: BuiltInColorThemeName, colorParams?: Partial<ColorTheme.Props>, sizeName?: BuiltInSizeThemeName, sizeParams?: Partial<SizeTheme.Props>): Transformer.Params<VolumeRepresentation3D> {
const type = ctx.volumeRepresentation.registry.get(name);
const colorParams = ctx.volumeRepresentation.themeCtx.colorThemeRegistry.get(type.defaultColorTheme).defaultValues;
const sizeParams = ctx.volumeRepresentation.themeCtx.sizeThemeRegistry.get(type.defaultSizeTheme).defaultValues
const colorType = ctx.volumeRepresentation.themeCtx.colorThemeRegistry.get(colorName || type.defaultColorTheme);
const sizeType = ctx.volumeRepresentation.themeCtx.sizeThemeRegistry.get(sizeName || type.defaultSizeTheme);
return ({
type: { name, params: volumeParams ? { ...type.defaultValues, ...volumeParams } : type.defaultValues },
colorTheme: { name: type.defaultColorTheme, params: colorParams },
sizeTheme: { name: type.defaultSizeTheme, params: sizeParams }
colorTheme: { name: type.defaultColorTheme, params: colorParams ? { ...colorType.defaultValues, ...colorParams } : colorType.defaultValues },
sizeTheme: { name: type.defaultSizeTheme, params: sizeParams ? { ...sizeType.defaultValues, ...sizeParams } : sizeType.defaultValues }
})
}
}
......@@ -234,7 +236,6 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
repr.setTheme(createTheme(plugin.volumeRepresentation.themeCtx, { volume: a.data }, params))
// TODO set initial state, repr.setState({})
// TODO include isoValue in the label where available
console.log(params.type.params);
await repr.createOrUpdate(props, a.data).runInContext(ctx);
return new SO.Volume.Representation3D(repr, { label: provider.label });
});
......
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