From f7821b7bad6f3d87e939321db894703221533572 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 20 Nov 2018 16:31:59 -0800
Subject: [PATCH] fixed visual update when only unit transformations have
changed
---
.../structure/structure/structure.ts | 20 ++++++++-
src/mol-model/structure/structure/symmetry.ts | 9 ++++
src/mol-model/structure/structure/unit.ts | 8 +++-
src/mol-repr/structure/complex-visual.ts | 8 ++--
.../structure/units-representation.ts | 23 +++++++---
src/mol-repr/structure/units-visual.ts | 43 ++++++++++---------
src/mol-repr/util.ts | 3 ++
7 files changed, 78 insertions(+), 36 deletions(-)
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index d4e76255b..6eaa79bb0 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -8,7 +8,7 @@ import { IntMap, SortedArray, Iterator, Segmentation } from 'mol-data/int'
import { UniqueArray } from 'mol-data/generic'
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import { Model, ElementIndex } from '../model'
-import { sort, arraySwap, hash1, sortArray, hashString } from 'mol-data/util';
+import { sort, arraySwap, hash1, sortArray, hashString, hashFnv32a } from 'mol-data/util';
import StructureElement from './element'
import Unit from './unit'
import { StructureLookup3D } from './util/lookup3d';
@@ -44,9 +44,11 @@ class Structure {
entityIndices?: ReadonlyArray<EntityIndex>,
uniqueAtomicResidueIndices?: ReadonlyMap<UUID, ReadonlyArray<ResidueIndex>>,
hashCode: number,
+ /** Hash based on all unit.id values in the structure, reflecting the units transformation */
+ transformHash: number,
elementCount: number,
polymerResidueCount: number,
- } = { hashCode: -1, elementCount: 0, polymerResidueCount: 0 };
+ } = { hashCode: -1, transformHash: -1, elementCount: 0, polymerResidueCount: 0 };
subsetBuilder(isSorted: boolean) {
return new StructureSubsetBuilder(this, isSorted);
@@ -74,6 +76,12 @@ class Structure {
return this.computeHash();
}
+ get transformHash() {
+ if (this._props.transformHash !== -1) return this._props.transformHash;
+ this._props.transformHash = hashFnv32a(this.units.map(u => u.id))
+ return this._props.transformHash;
+ }
+
private computeHash() {
let hash = 23;
for (let i = 0, _i = this.units.length; i < _i; i++) {
@@ -389,6 +397,7 @@ namespace Structure {
return s.hashCode;
}
+ /** Hash based on all unit.model conformation values in the structure */
export function conformationHash(s: Structure) {
return hashString(s.units.map(u => Unit.conformationId(u)).join('|'))
}
@@ -409,6 +418,13 @@ namespace Structure {
return true;
}
+ export function areEquivalent(a: Structure, b: Structure) {
+ return a === b || (
+ a.hashCode === b.hashCode &&
+ StructureSymmetry.areTransformGroupsEquivalent(a.unitSymmetryGroups, b.unitSymmetryGroups)
+ )
+ }
+
export class ElementLocationIterator implements Iterator<StructureElement> {
private current = StructureElement.create();
private unitIndex = 0;
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index 1b35f8341..5af14696a 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -78,6 +78,15 @@ namespace StructureSymmetry {
return ret;
}
+
+ /** Checks if transform groups are equal up to their unit's transformations */
+ export function areTransformGroupsEquivalent(a: ReadonlyArray<Unit.SymmetryGroup>, b: ReadonlyArray<Unit.SymmetryGroup>) {
+ if (a.length !== b.length) return false
+ for (let i = 0, il = a.length; i < il; ++i) {
+ if (a[i].hashCode !== b[i].hashCode) return false
+ }
+ return true
+ }
}
function getOperators(symmetry: ModelSymmetry, ijkMin: Vec3, ijkMax: Vec3) {
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index fd41f3db1..a1cd1097e 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -15,7 +15,7 @@ import { UnitRings } from './unit/rings';
import StructureElement from './element'
import { ChainIndex, ResidueIndex, ElementIndex } from '../model/indexing';
import { IntMap, SortedArray } from 'mol-data/int';
-import { hash2 } from 'mol-data/util';
+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';
@@ -48,7 +48,10 @@ namespace Unit {
readonly units: ReadonlyArray<Unit>
/** Maps unit.id to index of unit in units array */
readonly unitIndexMap: IntMap<number>
+ /** Hash based on unit.invariantId which is the same for all units in the group */
readonly hashCode: number
+ /** Hash based on all unit.id values in the group, reflecting the units transformation*/
+ readonly transformHash: number
}
function getUnitIndexMap(units: Unit[]) {
@@ -72,7 +75,8 @@ namespace Unit {
props.unitIndexMap = getUnitIndexMap(units)
return props.unitIndexMap
},
- hashCode: hashUnit(units[0])
+ hashCode: hashUnit(units[0]),
+ transformHash: hashFnv32a(units.map(u => u.id))
}
}
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index 1574648d2..a5adc76f9 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -85,15 +85,15 @@ export function ComplexVisual<P extends ComplexParams>(builder: ComplexVisualGeo
VisualUpdateState.reset(updateState)
setUpdateState(updateState, newProps, currentProps, theme, currentTheme)
+ if (ColorTheme.areEqual(theme.color, currentTheme.color)) updateState.updateColor = true
+ if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createGeometry = true
+
const newConformationHash = Structure.conformationHash(currentStructure)
if (newConformationHash !== conformationHash) {
conformationHash = newConformationHash
updateState.createGeometry = true
}
- if (ColorTheme.areEqual(theme.color, currentTheme.color)) updateState.updateColor = true
- if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createGeometry = true
-
//
if (updateState.createGeometry) {
@@ -129,7 +129,7 @@ export function ComplexVisual<P extends ComplexParams>(builder: ComplexVisualGeo
throw new Error('missing structure')
} else if (structure && (!currentStructure || !renderObject)) {
await create(ctx, structure, theme, props)
- } else if (structure && structure.hashCode !== currentStructure.hashCode) {
+ } else if (structure && !Structure.areEquivalent(structure, currentStructure)) {
await create(ctx, structure, theme, props)
} else {
if (structure && Structure.conformationHash(structure) !== Structure.conformationHash(currentStructure)) {
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index abd56451a..ac47dae9d 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -50,7 +50,7 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, getPar
if (!_structure && !structure) {
throw new Error('missing structure')
} else if (structure && !_structure) {
- // console.log('initial structure')
+ // console.log(label, 'initial structure')
// First call with a structure, create visuals for each group.
_groups = structure.unitSymmetryGroups;
for (let i = 0; i < _groups.length; i++) {
@@ -59,8 +59,8 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, getPar
await visual.createOrUpdate({ ...ctx, runtime }, _theme, _props, { group, structure })
visuals.set(group.hashCode, { visual, group })
}
- } else if (structure && _structure.hashCode !== structure.hashCode) {
- // console.log('_structure.hashCode !== structure.hashCode')
+ } else if (structure && !Structure.areEquivalent(structure, _structure)) {
+ // console.log(label, 'structure not equivalent')
// Tries to re-use existing visuals for the groups of the new structure.
// Creates additional visuals if needed, destroys left-over visuals.
_groups = structure.unitSymmetryGroups;
@@ -71,18 +71,25 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, getPar
const group = _groups[i];
const visualGroup = oldVisuals.get(group.hashCode)
if (visualGroup) {
+ // console.log(label, 'found visualGroup to reuse')
+ // console.log('old', visualGroup.group)
+ // console.log('new', group)
const { visual } = visualGroup
await visual.createOrUpdate({ ...ctx, runtime }, _theme, _props, { group, structure })
visuals.set(group.hashCode, { visual, group })
oldVisuals.delete(group.hashCode)
} else {
+ // console.log(label, 'not found visualGroup to reuse, creating new')
// newGroups.push(group)
const visual = visualCtor()
await visual.createOrUpdate({ ...ctx, runtime }, _theme, _props, { group, structure })
visuals.set(group.hashCode, { visual, group })
}
}
- oldVisuals.forEach(({ visual }) => visual.destroy())
+ oldVisuals.forEach(({ visual }) => {
+ // console.log(label, 'removed unused visual')
+ visual.destroy()
+ })
// TODO review logic
// For new groups, re-use left-over visuals
@@ -94,12 +101,14 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, getPar
// visuals.set(group.hashCode, { visual, group })
// })
// unusedVisuals.forEach(visual => visual.destroy())
- } else if (structure && structure !== _structure && _structure.hashCode === structure.hashCode) {
- // console.log('_structure.hashCode === structure.hashCode')
+ } else if (structure && structure !== _structure && Structure.areEquivalent(structure, _structure)) {
+ console.log(label, 'structures equivalent but not identical')
// Expects that for structures with the same hashCode,
// the unitSymmetryGroups are the same as well.
// Re-uses existing visuals for the groups of the new structure.
_groups = structure.unitSymmetryGroups;
+ // console.log('new', structure.unitSymmetryGroups)
+ // console.log('old', _structure.unitSymmetryGroups)
for (let i = 0; i < _groups.length; i++) {
const group = _groups[i];
const visualGroup = visuals.get(group.hashCode)
@@ -111,7 +120,7 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, getPar
}
}
} else {
- // console.log('no new structure')
+ // console.log(label, 'no new structure')
// No new structure given, just update all visuals with new props.
const visualsList: [ UnitsVisual<P>, Unit.SymmetryGroup ][] = [] // TODO avoid allocation
visuals.forEach(({ visual, group }) => visualsList.push([ visual, group ]))
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index f89364eb9..a80885a74 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -34,13 +34,6 @@ export type StructureGroup = { structure: Structure, group: Unit.SymmetryGroup }
export interface UnitsVisual<P extends RepresentationProps = {}> extends Visual<StructureGroup, P> { }
-function sameGroupConformation(groupA: Unit.SymmetryGroup, groupB: Unit.SymmetryGroup) {
- return (
- groupA.units.length === groupB.units.length &&
- Unit.conformationId(groupA.units[0]) === Unit.conformationId(groupB.units[0])
- )
-}
-
type UnitsRenderObject = MeshRenderObject | LinesRenderObject | PointsRenderObject | DirectVolumeRenderObject
interface UnitsVisualBuilder<P extends UnitsParams, G extends Geometry> {
@@ -88,35 +81,46 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
renderObject = await createRenderObject(ctx, group, geometry, locationIt, theme, currentProps)
}
- async function update(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<P>> = {}) {
+ async function update(ctx: VisualContext, group: Unit.SymmetryGroup, theme: Theme, props: Partial<PD.Values<P>> = {}) {
if (!renderObject) return
const newProps = Object.assign({}, currentProps, props, { structure: currentStructure })
- const unit = currentGroup.units[0]
+ const unit = group.units[0]
locationIt.reset()
VisualUpdateState.reset(updateState)
setUpdateState(updateState, newProps, currentProps, theme, currentTheme)
+ if (ColorTheme.areEqual(theme.color, currentTheme.color)) updateState.updateColor = true
+ if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createGeometry = true
+
+ if (group.transformHash !== currentGroup.transformHash) {
+ if (group.units.length !== currentGroup.units.length || updateState.updateColor) {
+ updateState.updateTransform = true
+ } else {
+ updateState.updateMatrix = true
+ }
+ }
+
+ // check if the conformation of unit.model has changed
const newConformationId = Unit.conformationId(unit)
if (newConformationId !== currentConformationId) {
currentConformationId = newConformationId
updateState.createGeometry = true
}
- if (currentGroup.units.length !== locationIt.instanceCount) updateState.updateTransform = true
-
- if (ColorTheme.areEqual(theme.color, currentTheme.color)) updateState.updateColor = true
- if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createGeometry = true
-
//
if (updateState.updateTransform) {
- locationIt = createLocationIterator(currentGroup)
+ locationIt = createLocationIterator(group)
const { instanceCount, groupCount } = locationIt
- createUnitsTransform(currentGroup, renderObject.values)
createMarkers(instanceCount * groupCount, renderObject.values)
updateState.updateColor = true
+ updateState.updateMatrix = true
+ }
+
+ if (updateState.updateMatrix) {
+ createUnitsTransform(group, renderObject.values)
}
if (updateState.createGeometry) {
@@ -143,6 +147,7 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
currentProps = newProps
currentTheme = theme
+ currentGroup = group
}
return {
@@ -161,11 +166,7 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
await create(ctx, group, theme, props)
} else {
// console.log('unit-visual update')
- if (group && !sameGroupConformation(group, currentGroup)) {
- // console.log('unit-visual new conformation')
- currentGroup = group
- }
- await update(ctx, theme, props)
+ await update(ctx, group || currentGroup, theme, props)
}
},
getLoci(pickingId: PickingId) {
diff --git a/src/mol-repr/util.ts b/src/mol-repr/util.ts
index ad7d10164..dd3acb447 100644
--- a/src/mol-repr/util.ts
+++ b/src/mol-repr/util.ts
@@ -10,6 +10,7 @@ import { VisualQuality } from 'mol-geo/geometry/geometry';
export interface VisualUpdateState {
updateTransform: boolean
+ updateMatrix: boolean
updateColor: boolean
updateSize: boolean
createGeometry: boolean
@@ -18,6 +19,7 @@ export namespace VisualUpdateState {
export function create(): VisualUpdateState {
return {
updateTransform: false,
+ updateMatrix: false,
updateColor: false,
updateSize: false,
createGeometry: false
@@ -25,6 +27,7 @@ export namespace VisualUpdateState {
}
export function reset(state: VisualUpdateState) {
state.updateTransform = false
+ state.updateMatrix = false
state.updateColor = false
state.updateSize = false
state.createGeometry = false
--
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