From bd1b07ad8639fe7269956fb8e5627483a5ea333e Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 24 Feb 2019 13:20:52 -0800
Subject: [PATCH] removed gaussian density calc from unit
---
src/mol-model/structure/structure/unit.ts | 17 +--
.../structure/unit/gaussian-density.ts | 76 -----------
.../visual/gaussian-density-point.ts | 4 +-
.../visual/gaussian-density-volume.ts | 57 +-------
.../structure/visual/gaussian-surface-mesh.ts | 4 +-
.../visual/gaussian-surface-wireframe.ts | 4 +-
.../structure/visual/util/gaussian.ts | 124 ++++++++++++++++++
7 files changed, 135 insertions(+), 151 deletions(-)
delete mode 100644 src/mol-model/structure/structure/unit/gaussian-density.ts
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index cbdf58718..725862657 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -7,7 +7,7 @@
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import { Model } from '../model'
-import { GridLookup3D, Lookup3D, DensityData } from 'mol-math/geometry'
+import { GridLookup3D, Lookup3D } from 'mol-math/geometry'
import { IntraUnitLinks, computeIntraUnitBonds } from './unit/links'
import { CoarseElements, CoarseSphereConformation, CoarseGaussianConformation } from '../model/properties/coarse';
import { ValueRef } from 'mol-util';
@@ -18,9 +18,6 @@ import { IntMap, SortedArray } from 'mol-data/int';
import { hash2, hashFnv32a } from 'mol-data/util';
import { getAtomicPolymerElements, getCoarsePolymerElements, getAtomicGapElements, getCoarseGapElements } from './util/polymer';
import { getNucleotideElements } from './util/nucleotide';
-import { GaussianDensityProps, computeUnitGaussianDensityCached } from './unit/gaussian-density';
-import { RuntimeContext } from 'mol-task';
-import { WebGLContext } from 'mol-gl/webgl/context';
/**
* A building block of a structure that corresponds to an atomic or
@@ -191,10 +188,6 @@ namespace Unit {
return this.model.atomicHierarchy.residueAtomSegments.index[this.elements[elementIndex]];
}
- async computeGaussianDensity(props: GaussianDensityProps, ctx: RuntimeContext, webgl?: WebGLContext) {
- return computeUnitGaussianDensityCached(this, props, this.props.gaussianDensities, ctx, webgl);
- }
-
constructor(id: number, invariantId: number, model: Model, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: AtomicProperties) {
this.id = id;
this.invariantId = invariantId;
@@ -215,7 +208,6 @@ namespace Unit {
polymerElements: ValueRef<SortedArray<ElementIndex> | undefined>
gapElements: ValueRef<SortedArray<ElementIndex> | undefined>
nucleotideElements: ValueRef<SortedArray<ElementIndex> | undefined>
- gaussianDensities: Map<string, DensityData>
}
function AtomicProperties(): AtomicProperties {
@@ -226,7 +218,6 @@ namespace Unit {
polymerElements: ValueRef.create(void 0),
gapElements: ValueRef.create(void 0),
nucleotideElements: ValueRef.create(void 0),
- gaussianDensities: new Map()
};
}
@@ -280,10 +271,6 @@ namespace Unit {
return this.kind === Kind.Spheres ? this.model.coarseConformation.spheres : this.model.coarseConformation.gaussians;
}
- async computeGaussianDensity(props: GaussianDensityProps, ctx: RuntimeContext, webgl?: WebGLContext): Promise<DensityData> {
- return computeUnitGaussianDensityCached(this as Unit.Spheres | Unit.Gaussians, props, this.props.gaussianDensities, ctx, webgl); // TODO get rid of casting
- }
-
constructor(id: number, invariantId: number, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties) {
this.kind = kind;
this.id = id;
@@ -299,7 +286,6 @@ namespace Unit {
interface CoarseProperties {
lookup3d: ValueRef<Lookup3D | undefined>,
- gaussianDensities: Map<string, DensityData>
polymerElements: ValueRef<SortedArray<ElementIndex> | undefined>
gapElements: ValueRef<SortedArray<ElementIndex> | undefined>
}
@@ -307,7 +293,6 @@ namespace Unit {
function CoarseProperties(): CoarseProperties {
return {
lookup3d: ValueRef.create(void 0),
- gaussianDensities: new Map(),
polymerElements: ValueRef.create(void 0),
gapElements: ValueRef.create(void 0),
};
diff --git a/src/mol-model/structure/structure/unit/gaussian-density.ts b/src/mol-model/structure/structure/unit/gaussian-density.ts
deleted file mode 100644
index cefbfcd68..000000000
--- a/src/mol-model/structure/structure/unit/gaussian-density.ts
+++ /dev/null
@@ -1,76 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Unit, StructureElement, ElementIndex } from 'mol-model/structure';
-import { GaussianDensity } from 'mol-math/geometry/gaussian-density';
-import { Task, RuntimeContext } from 'mol-task';
-import { DensityData } from 'mol-math/geometry';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { GaussianDensityTexture } from 'mol-math/geometry/gaussian-density/gpu';
-import { Texture } from 'mol-gl/webgl/texture';
-import { WebGLContext } from 'mol-gl/webgl/context';
-import { PhysicalSizeTheme } from 'mol-theme/size/physical';
-
-export const GaussianDensityParams = {
- resolution: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
- radiusOffset: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }),
- smoothness: PD.Numeric(1.5, { min: 0.5, max: 2.5, step: 0.1 }),
- useGpu: PD.Boolean(false),
- ignoreCache: PD.Boolean(false),
-}
-export const DefaultGaussianDensityProps = PD.getDefaultValues(GaussianDensityParams)
-export type GaussianDensityProps = typeof DefaultGaussianDensityProps
-
-function getConformation(unit: Unit) {
- switch (unit.kind) {
- case Unit.Kind.Atomic: return unit.model.atomicConformation
- case Unit.Kind.Spheres: return unit.model.coarseConformation.spheres
- case Unit.Kind.Gaussians: return unit.model.coarseConformation.gaussians
- }
-}
-
-function getConformationAndRadius(unit: Unit) {
- const conformation = getConformation(unit)
- const { elements } = unit
- const position = {
- indices: elements,
- x: conformation.x,
- y: conformation.y,
- z: conformation.z
- }
-
- const l = StructureElement.create(unit)
- const sizeTheme = PhysicalSizeTheme({}, {})
- const radius = (index: number) => {
- l.element = index as ElementIndex
- return sizeTheme.size(l)
- }
-
- return { position, radius }
-}
-
-export function computeUnitGaussianDensity(unit: Unit, props: GaussianDensityProps, webgl?: WebGLContext) {
- const { position, radius } = getConformationAndRadius(unit)
- return Task.create('Gaussian Density', async ctx => {
- return await GaussianDensity(ctx, position, unit.lookup3d.boundary.box, radius, props, webgl);
- });
-}
-
-export function computeUnitGaussianDensityTexture(unit: Unit, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture) {
- const { position, radius } = getConformationAndRadius(unit)
- return Task.create('Gaussian Density', async ctx => {
- return await GaussianDensityTexture(ctx, webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
- });
-}
-
-export async function computeUnitGaussianDensityCached(unit: Unit, props: GaussianDensityProps, cache: Map<string, DensityData>, ctx: RuntimeContext, webgl?: WebGLContext) {
- const key = `${props.radiusOffset}|${props.resolution}|${props.smoothness}`
- let density = cache.get(key)
- if (density && !props.ignoreCache) return density
- density = await computeUnitGaussianDensity(unit, props, webgl).runInContext(ctx)
- if (!props.ignoreCache) cache.set(key, density)
- return density
-}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/gaussian-density-point.ts b/src/mol-repr/structure/visual/gaussian-density-point.ts
index 0be7361e8..c61ae5745 100644
--- a/src/mol-repr/structure/visual/gaussian-density-point.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-point.ts
@@ -11,12 +11,12 @@ import { StructureElementIterator } from './util/element';
import { EmptyLoci } from 'mol-model/loci';
import { Vec3 } from 'mol-math/linear-algebra';
import { UnitsPointsVisual, UnitsPointsParams } from '../units-visual';
-import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Points } from 'mol-geo/geometry/points/points';
import { PointsBuilder } from 'mol-geo/geometry/points/points-builder';
import { VisualContext } from 'mol-repr/visual';
import { Theme } from 'mol-theme/theme';
+import { computeUnitGaussianDensity, GaussianDensityParams, GaussianDensityProps } from './util/gaussian';
export const GaussianDensityPointParams = {
...UnitsPointsParams,
@@ -26,7 +26,7 @@ export const GaussianDensityPointParams = {
export type GaussianDensityPointParams = typeof GaussianDensityPointParams
export async function createGaussianDensityPoint(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, points?: Points) {
- const { transform, field: { space, data } } = await unit.computeGaussianDensity(props, ctx.runtime, ctx.webgl)
+ const { transform, field: { space, data } } = await computeUnitGaussianDensity(unit, props, ctx.webgl).runInContext(ctx.runtime)
const { dimensions, get } = space
const [ xn, yn, zn ] = dimensions
diff --git a/src/mol-repr/structure/visual/gaussian-density-volume.ts b/src/mol-repr/structure/visual/gaussian-density-volume.ts
index 3c928cdb6..51b8b809e 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Structure, StructureElement } from 'mol-model/structure';
+import { Structure } from 'mol-model/structure';
import { VisualUpdateState } from '../../util';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { DirectVolume } from 'mol-geo/geometry/direct-volume/direct-volume';
@@ -14,56 +14,9 @@ import { ComplexVisual, ComplexDirectVolumeVisual, ComplexDirectVolumeParams } f
import { EmptyLoci } from 'mol-model/loci';
import { NullLocation } from 'mol-model/location';
import { LocationIterator } from 'mol-geo/util/location-iterator';
-import { WebGLContext } from 'mol-gl/webgl/context';
-import { Texture } from 'mol-gl/webgl/texture';
-import { GaussianDensityTexture } from 'mol-math/geometry/gaussian-density/gpu';
-import { Task } from 'mol-task';
-import { OrderedSet } from 'mol-data/int';
-import { PhysicalSizeTheme } from 'mol-theme/size/physical';
+import { computeStructureGaussianDensityTexture, GaussianDensityTextureProps, GaussianDensityTextureParams } from './util/gaussian';
-function getConformationAndRadius(structure: Structure) {
- const n = structure.elementCount
-
- const xs = new Float32Array(n)
- const ys = new Float32Array(n)
- const zs = new Float32Array(n)
- const rs = new Float32Array(n)
-
- const l = StructureElement.create()
- const sizeTheme = PhysicalSizeTheme({}, {})
-
- let m = 0
- for (let i = 0, il = structure.units.length; i < il; ++i) {
- const unit = structure.units[i]
- const { elements } = unit
- const { x, y, z } = unit.conformation
- l.unit = unit
- for (let j = 0, jl = elements.length; j < jl; ++j) {
- const eI = elements[j]
- xs[m + j] = x(eI)
- ys[m + j] = y(eI)
- zs[m + j] = z(eI)
- l.element = eI
- rs[m + j] = sizeTheme.size(l)
- }
- m += elements.length
- }
-
- const position = { indices: OrderedSet.ofRange(0, n), x: xs, y: ys, z: zs }
- const radius = (index: number) => rs[index]
-
- return { position, radius }
-}
-
-// TODO calculate by combining unit volumes
-function computeStructureGaussianDensityTexture(structure: Structure, props: PD.Values<GaussianDensityVolumeParams>, webgl: WebGLContext, texture?: Texture) {
- const { position, radius } = getConformationAndRadius(structure)
- return Task.create('Gaussian Density', async ctx => {
- return await GaussianDensityTexture(ctx, webgl, position, structure.lookup3d.boundary.box, radius, props, texture);
- });
-}
-
-async function createGaussianDensityVolume(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<GaussianDensityVolumeParams>, directVolume?: DirectVolume): Promise<DirectVolume> {
+async function createGaussianDensityVolume(ctx: VisualContext, structure: Structure, theme: Theme, props: GaussianDensityTextureProps, directVolume?: DirectVolume): Promise<DirectVolume> {
const { runtime, webgl } = ctx
if (webgl === undefined) throw new Error('createGaussianDensityVolume requires `webgl` object in VisualContext')
@@ -77,9 +30,7 @@ async function createGaussianDensityVolume(ctx: VisualContext, structure: Struct
export const GaussianDensityVolumeParams = {
...ComplexDirectVolumeParams,
- resolution: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
- radiusOffset: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }),
- smoothness: PD.Numeric(1.5, { min: 0.5, max: 2.5, step: 0.1 }),
+ ...GaussianDensityTextureParams
}
export type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index 0c01c3c0f..e39766fd4 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -9,16 +9,16 @@ import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
import { StructureElementIterator, getElementLoci, markElement } from './util/element';
-import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Mesh } from 'mol-geo/geometry/mesh/mesh';
import { computeMarchingCubesMesh } from 'mol-geo/util/marching-cubes/algorithm';
import { VisualContext } from 'mol-repr/visual';
import { Theme } from 'mol-theme/theme';
+import { GaussianDensityProps, computeUnitGaussianDensity, GaussianDensityParams } from './util/gaussian';
async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
const { smoothness } = props
- const { transform, field, idField } = await unit.computeGaussianDensity(props, ctx.runtime, ctx.webgl)
+ const { transform, field, idField } = await computeUnitGaussianDensity(unit, props, ctx.webgl).runInContext(ctx.runtime)
const params = {
isoLevel: Math.exp(-smoothness),
diff --git a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
index e17ebb6e2..68c31c56f 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -9,16 +9,16 @@ import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
import { UnitsLinesVisual, UnitsLinesParams } from '../units-visual';
import { StructureElementIterator, getElementLoci, markElement } from './util/element';
-import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Lines } from 'mol-geo/geometry/lines/lines';
import { computeMarchingCubesLines } from 'mol-geo/util/marching-cubes/algorithm';
import { VisualContext } from 'mol-repr/visual';
import { Theme } from 'mol-theme/theme';
+import { GaussianDensityProps, GaussianDensityParams, computeUnitGaussianDensity } from './util/gaussian';
async function createGaussianWireframe(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, lines?: Lines): Promise<Lines> {
const { smoothness } = props
- const { transform, field, idField } = await unit.computeGaussianDensity(props, ctx.runtime)
+ const { transform, field, idField } = await computeUnitGaussianDensity(unit, props, ctx.webgl).runInContext(ctx.runtime)
const params = {
isoLevel: Math.exp(-smoothness),
diff --git a/src/mol-repr/structure/visual/util/gaussian.ts b/src/mol-repr/structure/visual/util/gaussian.ts
index 54cd72a4b..2f268c983 100644
--- a/src/mol-repr/structure/visual/util/gaussian.ts
+++ b/src/mol-repr/structure/visual/util/gaussian.ts
@@ -3,3 +3,127 @@
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
+
+import { Unit, StructureElement, ElementIndex, Structure } from 'mol-model/structure';
+import { GaussianDensity } from 'mol-math/geometry/gaussian-density';
+import { Task, RuntimeContext } from 'mol-task';
+import { DensityData } from 'mol-math/geometry';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { GaussianDensityTexture } from 'mol-math/geometry/gaussian-density/gpu';
+import { Texture } from 'mol-gl/webgl/texture';
+import { WebGLContext } from 'mol-gl/webgl/context';
+import { PhysicalSizeTheme } from 'mol-theme/size/physical';
+import { OrderedSet } from 'mol-data/int';
+
+export const GaussianDensityParams = {
+ resolution: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
+ radiusOffset: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }),
+ smoothness: PD.Numeric(1.5, { min: 0.5, max: 2.5, step: 0.1 }),
+ useGpu: PD.Boolean(false),
+ ignoreCache: PD.Boolean(false),
+}
+export const DefaultGaussianDensityProps = PD.getDefaultValues(GaussianDensityParams)
+export type GaussianDensityProps = typeof DefaultGaussianDensityProps
+
+function getConformation(unit: Unit) {
+ switch (unit.kind) {
+ case Unit.Kind.Atomic: return unit.model.atomicConformation
+ case Unit.Kind.Spheres: return unit.model.coarseConformation.spheres
+ case Unit.Kind.Gaussians: return unit.model.coarseConformation.gaussians
+ }
+}
+
+function getUnitConformationAndRadius(unit: Unit) {
+ const conformation = getConformation(unit)
+ const { elements } = unit
+ const position = {
+ indices: elements,
+ x: conformation.x,
+ y: conformation.y,
+ z: conformation.z
+ }
+
+ const l = StructureElement.create(unit)
+ const sizeTheme = PhysicalSizeTheme({}, {})
+ const radius = (index: number) => {
+ l.element = index as ElementIndex
+ return sizeTheme.size(l)
+ }
+
+ return { position, radius }
+}
+
+export function computeUnitGaussianDensity(unit: Unit, props: GaussianDensityProps, webgl?: WebGLContext) {
+ const { position, radius } = getUnitConformationAndRadius(unit)
+ return Task.create('Gaussian Density', async ctx => {
+ return await GaussianDensity(ctx, position, unit.lookup3d.boundary.box, radius, props, webgl);
+ });
+}
+
+export function computeUnitGaussianDensityTexture(unit: Unit, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture) {
+ const { position, radius } = getUnitConformationAndRadius(unit)
+ return Task.create('Gaussian Density', async ctx => {
+ return await GaussianDensityTexture(ctx, webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
+ });
+}
+
+export async function computeUnitGaussianDensityCached(unit: Unit, props: GaussianDensityProps, cache: Map<string, DensityData>, ctx: RuntimeContext, webgl?: WebGLContext) {
+ const key = `${props.radiusOffset}|${props.resolution}|${props.smoothness}`
+ let density = cache.get(key)
+ if (density && !props.ignoreCache) return density
+ density = await computeUnitGaussianDensity(unit, props, webgl).runInContext(ctx)
+ if (!props.ignoreCache) cache.set(key, density)
+ return density
+}
+
+//
+
+function getStructureConformationAndRadius(structure: Structure) {
+ const n = structure.elementCount
+
+ const xs = new Float32Array(n)
+ const ys = new Float32Array(n)
+ const zs = new Float32Array(n)
+ const rs = new Float32Array(n)
+
+ const l = StructureElement.create()
+ const sizeTheme = PhysicalSizeTheme({}, {})
+
+ let m = 0
+ for (let i = 0, il = structure.units.length; i < il; ++i) {
+ const unit = structure.units[i]
+ const { elements } = unit
+ const { x, y, z } = unit.conformation
+ l.unit = unit
+ for (let j = 0, jl = elements.length; j < jl; ++j) {
+ const eI = elements[j]
+ xs[m + j] = x(eI)
+ ys[m + j] = y(eI)
+ zs[m + j] = z(eI)
+ l.element = eI
+ rs[m + j] = sizeTheme.size(l)
+ }
+ m += elements.length
+ }
+
+ const position = { indices: OrderedSet.ofRange(0, n), x: xs, y: ys, z: zs }
+ const radius = (index: number) => rs[index]
+
+ return { position, radius }
+}
+
+export const GaussianDensityTextureParams = {
+ resolution: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
+ radiusOffset: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }),
+ smoothness: PD.Numeric(1.5, { min: 0.5, max: 2.5, step: 0.1 }),
+}
+export const DefaultGaussianDensityTextureProps = PD.getDefaultValues(GaussianDensityTextureParams)
+export type GaussianDensityTextureProps = typeof DefaultGaussianDensityTextureProps
+
+// TODO calculate by combining unit volumes
+export function computeStructureGaussianDensityTexture(structure: Structure, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
+ const { position, radius } = getStructureConformationAndRadius(structure)
+ return Task.create('Gaussian Density', async ctx => {
+ return await GaussianDensityTexture(ctx, webgl, position, structure.lookup3d.boundary.box, radius, props, texture);
+ });
+}
\ No newline at end of file
--
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