molstar
Version:
A comprehensive macromolecular library.
272 lines (271 loc) • 14.7 kB
JavaScript
/**
* Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { hashFnv32a } from '../../../mol-data/util';
import { LocationIterator, PositionLocation } from '../../../mol-geo/util/location-iterator';
import { calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
import { createNullTexture } from '../../../mol-gl/webgl/texture';
import { Box3D, Sphere3D } from '../../../mol-math/geometry';
import { Mat4, Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
import { ValueCell } from '../../../mol-util';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Box } from '../../primitive/box';
import { BaseGeometry } from '../base';
import { createColors } from '../color-data';
import { createMarkers } from '../marker-data';
import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';
import { createTransferFunctionTexture, getControlPointsFromVec2Array } from './transfer-function';
import { createEmptyClipping } from '../clipping-data';
import { Grid } from '../../../mol-model/volume';
import { createEmptySubstance } from '../substance-data';
import { createEmptyEmissive } from '../emissive-data';
const VolumeBox = Box();
export var DirectVolume;
(function (DirectVolume) {
function create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, dataType, directVolume) {
return directVolume ?
update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, dataType, directVolume) :
fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, dataType);
}
DirectVolume.create = create;
function hashCode(directVolume) {
return hashFnv32a([
directVolume.bboxSize.ref.version, directVolume.gridDimension.ref.version,
directVolume.gridTexture.ref.version, directVolume.transform.ref.version,
directVolume.gridStats.ref.version
]);
}
function fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, dataType) {
const boundingSphere = Sphere3D();
let currentHash = -1;
const width = texture.getWidth();
const height = texture.getHeight();
const depth = texture.getDepth();
const directVolume = {
kind: 'direct-volume',
gridDimension: ValueCell.create(gridDimension),
gridTexture: ValueCell.create(texture),
gridTextureDim: ValueCell.create(Vec3.create(width, height, depth)),
gridStats: ValueCell.create(Vec4.create(stats.min, stats.max, stats.mean, stats.sigma)),
bboxMin: ValueCell.create(bbox.min),
bboxMax: ValueCell.create(bbox.max),
bboxSize: ValueCell.create(Vec3.sub(Vec3(), bbox.max, bbox.min)),
transform: ValueCell.create(transform),
cellDim: ValueCell.create(cellDim),
unitToCartn: ValueCell.create(unitToCartn),
cartnToUnit: ValueCell.create(Mat4.invert(Mat4(), unitToCartn)),
get boundingSphere() {
const newHash = hashCode(directVolume);
if (newHash !== currentHash) {
const b = getBoundingSphere(directVolume.gridDimension.ref.value, directVolume.transform.ref.value);
Sphere3D.copy(boundingSphere, b);
currentHash = newHash;
}
return boundingSphere;
},
packedGroup: ValueCell.create(packedGroup),
axisOrder: ValueCell.create(axisOrder),
dataType: ValueCell.create(dataType),
setBoundingSphere(sphere) {
Sphere3D.copy(boundingSphere, sphere);
currentHash = hashCode(directVolume);
},
meta: {}
};
return directVolume;
}
function update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, dataType, directVolume) {
const width = texture.getWidth();
const height = texture.getHeight();
const depth = texture.getDepth();
ValueCell.update(directVolume.gridDimension, gridDimension);
ValueCell.update(directVolume.gridTexture, texture);
ValueCell.update(directVolume.gridTextureDim, Vec3.set(directVolume.gridTextureDim.ref.value, width, height, depth));
ValueCell.update(directVolume.gridStats, Vec4.set(directVolume.gridStats.ref.value, stats.min, stats.max, stats.mean, stats.sigma));
ValueCell.update(directVolume.bboxMin, bbox.min);
ValueCell.update(directVolume.bboxMax, bbox.max);
ValueCell.update(directVolume.bboxSize, Vec3.sub(directVolume.bboxSize.ref.value, bbox.max, bbox.min));
ValueCell.update(directVolume.transform, transform);
ValueCell.update(directVolume.cellDim, cellDim);
ValueCell.update(directVolume.unitToCartn, unitToCartn);
ValueCell.update(directVolume.cartnToUnit, Mat4.invert(Mat4(), unitToCartn));
ValueCell.updateIfChanged(directVolume.packedGroup, packedGroup);
ValueCell.updateIfChanged(directVolume.axisOrder, Vec3.fromArray(directVolume.axisOrder.ref.value, axisOrder, 0));
ValueCell.updateIfChanged(directVolume.dataType, dataType);
return directVolume;
}
function createEmpty(directVolume) {
const bbox = Box3D();
const gridDimension = Vec3();
const transform = Mat4.identity();
const unitToCartn = Mat4.identity();
const cellDim = Vec3();
const texture = createNullTexture();
const stats = Grid.One.stats;
const packedGroup = false;
const axisOrder = Vec3.create(0, 1, 2);
const dataType = 'byte';
return create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, dataType, directVolume);
}
DirectVolume.createEmpty = createEmpty;
DirectVolume.Params = {
...BaseGeometry.Params,
ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
celShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
xrayShaded: PD.Select(false, [[false, 'Off'], [true, 'On'], ['inverted', 'Inverted']], BaseGeometry.ShadingCategory),
controlPoints: PD.LineGraph([
Vec2.create(0.19, 0.0), Vec2.create(0.2, 0.05), Vec2.create(0.25, 0.05), Vec2.create(0.26, 0.0),
Vec2.create(0.79, 0.0), Vec2.create(0.8, 0.05), Vec2.create(0.85, 0.05), Vec2.create(0.86, 0.0),
], { isEssential: true }),
stepsPerCell: PD.Numeric(3, { min: 1, max: 10, step: 1 }),
jumpLength: PD.Numeric(0, { min: 0, max: 20, step: 0.1 }),
};
DirectVolume.Utils = {
Params: DirectVolume.Params,
createEmpty,
createValues,
createValuesSimple,
updateValues,
updateBoundingSphere,
createRenderableState,
updateRenderableState,
createPositionIterator
};
function createPositionIterator(directVolume, transform) {
const t = directVolume.transform.ref.value;
const [x, y, z] = directVolume.gridDimension.ref.value;
const groupCount = x * y * z;
const instanceCount = transform.instanceCount.ref.value;
const location = PositionLocation();
const p = location.position;
const m = transform.aTransform.ref.value;
const getLocation = (groupIndex, instanceIndex) => {
const k = Math.floor(groupIndex / z);
p[0] = Math.floor(k / y);
p[1] = k % y;
p[2] = groupIndex % z;
Vec3.transformMat4(p, p, t);
if (instanceIndex >= 0) {
Vec3.transformMat4Offset(p, p, m, 0, 0, instanceIndex * 16);
}
return location;
};
return LocationIterator(groupCount, instanceCount, 1, getLocation);
}
function getMaxSteps(gridDim, stepsPerCell) {
return Math.ceil(Vec3.magnitude(gridDim) * stepsPerCell);
}
function getStepScale(cellDim, stepsPerCell) {
return Math.min(...cellDim) * (1 / stepsPerCell);
}
function getTransferScale(stepsPerCell) {
return (1 / stepsPerCell);
}
function createValues(directVolume, transform, locationIt, theme, props) {
const { gridTexture, gridTextureDim, gridStats } = directVolume;
const { bboxSize, bboxMin, bboxMax, gridDimension, transform: gridTransform } = directVolume;
const { instanceCount, groupCount } = locationIt;
const positionIt = createPositionIterator(directVolume, transform);
const color = createColors(locationIt, positionIt, theme.color);
const marker = props.instanceGranularity
? createMarkers(instanceCount, 'instance')
: createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const emissive = createEmptyEmissive();
const material = createEmptySubstance();
const clipping = createEmptyClipping();
const [x, y, z] = gridDimension.ref.value;
const counts = { drawCount: VolumeBox.indices.length, vertexCount: x * y * z, groupCount, instanceCount };
const invariantBoundingSphere = Sphere3D.clone(directVolume.boundingSphere);
const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
const controlPoints = getControlPointsFromVec2Array(props.controlPoints);
const transferTex = createTransferFunctionTexture(controlPoints);
return {
dGeometryType: ValueCell.create('directVolume'),
...color,
...marker,
...overpaint,
...transparency,
...emissive,
...material,
...clipping,
...transform,
...BaseGeometry.createValues(props, counts),
aPosition: ValueCell.create(VolumeBox.vertices),
elements: ValueCell.create(VolumeBox.indices),
boundingSphere: ValueCell.create(boundingSphere),
invariantBoundingSphere: ValueCell.create(invariantBoundingSphere),
uInvariantBoundingSphere: ValueCell.create(Vec4.ofSphere(invariantBoundingSphere)),
uBboxMin: bboxMin,
uBboxMax: bboxMax,
uBboxSize: bboxSize,
uMaxSteps: ValueCell.create(getMaxSteps(gridDimension.ref.value, props.stepsPerCell)),
uStepScale: ValueCell.create(getStepScale(directVolume.cellDim.ref.value, props.stepsPerCell)),
uJumpLength: ValueCell.create(props.jumpLength),
uTransform: gridTransform,
uGridDim: gridDimension,
tTransferTex: transferTex,
uTransferScale: ValueCell.create(getTransferScale(props.stepsPerCell)),
dGridTexType: ValueCell.create(gridTexture.ref.value.getDepth() > 0 ? '3d' : '2d'),
uGridTexDim: gridTextureDim,
tGridTex: gridTexture,
uGridStats: gridStats,
uCellDim: directVolume.cellDim,
uCartnToUnit: directVolume.cartnToUnit,
uUnitToCartn: directVolume.unitToCartn,
dPackedGroup: directVolume.packedGroup,
dAxisOrder: ValueCell.create(directVolume.axisOrder.ref.value.join('')),
dIgnoreLight: ValueCell.create(props.ignoreLight),
dCelShaded: ValueCell.create(props.celShaded),
dXrayShaded: ValueCell.create(props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off'),
meta: ValueCell.create(directVolume.meta),
};
}
function createValuesSimple(directVolume, props, colorValue, sizeValue, transform) {
const s = BaseGeometry.createSimple(colorValue, sizeValue, transform);
const p = { ...PD.getDefaultValues(DirectVolume.Params), ...props };
return createValues(directVolume, s.transform, s.locationIterator, s.theme, p);
}
function updateValues(values, props) {
BaseGeometry.updateValues(values, props);
ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
ValueCell.updateIfChanged(values.dCelShaded, props.celShaded);
ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off');
const controlPoints = getControlPointsFromVec2Array(props.controlPoints);
createTransferFunctionTexture(controlPoints, values.tTransferTex);
ValueCell.updateIfChanged(values.uMaxSteps, getMaxSteps(values.uGridDim.ref.value, props.stepsPerCell));
ValueCell.updateIfChanged(values.uStepScale, getStepScale(values.uCellDim.ref.value, props.stepsPerCell));
ValueCell.updateIfChanged(values.uTransferScale, getTransferScale(props.stepsPerCell));
ValueCell.updateIfChanged(values.uJumpLength, props.jumpLength);
}
function updateBoundingSphere(values, directVolume) {
const invariantBoundingSphere = Sphere3D.clone(directVolume.boundingSphere);
const boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value, 0);
if (!Sphere3D.equals(boundingSphere, values.boundingSphere.ref.value)) {
ValueCell.update(values.boundingSphere, boundingSphere);
}
if (!Sphere3D.equals(invariantBoundingSphere, values.invariantBoundingSphere.ref.value)) {
ValueCell.update(values.invariantBoundingSphere, invariantBoundingSphere);
ValueCell.update(values.uInvariantBoundingSphere, Vec4.fromSphere(values.uInvariantBoundingSphere.ref.value, invariantBoundingSphere));
}
}
function createRenderableState(props) {
const state = BaseGeometry.createRenderableState(props);
state.opaque = false;
state.writeDepth = false;
return state;
}
function updateRenderableState(state, props) {
BaseGeometry.updateRenderableState(state, props);
state.opaque = false;
state.writeDepth = false;
}
})(DirectVolume || (DirectVolume = {}));
//
function getBoundingSphere(gridDimension, gridTransform) {
return Sphere3D.fromDimensionsAndTransform(Sphere3D(), gridDimension, gridTransform);
}