molstar
Version:
A comprehensive macromolecular library.
261 lines • 16.9 kB
JavaScript
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __assign } from "tslib";
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, Volume } from '../../../mol-model/volume';
import { ColorNames } from '../../../mol-util/color/names';
var VolumeBox = Box();
export var DirectVolume;
(function (DirectVolume) {
function create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume) {
return directVolume ?
update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume) :
fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup);
}
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) {
var boundingSphere = Sphere3D();
var currentHash = -1;
var width = texture.getWidth();
var height = texture.getHeight();
var depth = texture.getDepth();
var 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() {
var newHash = hashCode(directVolume);
if (newHash !== currentHash) {
var b = getBoundingSphere(directVolume.gridDimension.ref.value, directVolume.transform.ref.value);
Sphere3D.copy(boundingSphere, b);
currentHash = newHash;
}
return boundingSphere;
},
packedGroup: ValueCell.create(packedGroup),
setBoundingSphere: function (sphere) {
Sphere3D.copy(boundingSphere, sphere);
currentHash = hashCode(directVolume);
}
};
return directVolume;
}
function update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume) {
var width = texture.getWidth();
var height = texture.getHeight();
var 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);
return directVolume;
}
function createEmpty(directVolume) {
var bbox = Box3D();
var gridDimension = Vec3();
var transform = Mat4.identity();
var unitToCartn = Mat4.identity();
var cellDim = Vec3();
var texture = createNullTexture();
var stats = Grid.One.stats;
var packedGroup = false;
return create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume);
}
DirectVolume.createEmpty = createEmpty;
function createRenderModeParam(stats) {
var isoValueParam = stats
? Volume.createIsoValueParam(Volume.IsoValue.relative(2), stats)
: Volume.IsoValueParam;
return PD.MappedStatic('volume', {
isosurface: PD.Group({
isoValue: isoValueParam,
singleLayer: PD.Boolean(false, { isEssential: true }),
}, { isFlat: true }),
volume: PD.Group({
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),
]),
list: PD.ColorList({
kind: 'interpolate',
colors: [
[ColorNames.white, 0],
[ColorNames.red, 0.25],
[ColorNames.white, 0.5],
[ColorNames.blue, 0.75],
[ColorNames.white, 1]
]
}, { offsets: true }),
}, { isFlat: true })
}, { isEssential: true });
}
DirectVolume.createRenderModeParam = createRenderModeParam;
DirectVolume.Params = __assign(__assign({}, BaseGeometry.Params), { doubleSided: PD.Boolean(false, BaseGeometry.CustomQualityParamInfo), flipSided: PD.Boolean(false, BaseGeometry.ShadingCategory), flatShaded: PD.Boolean(false, BaseGeometry.ShadingCategory), ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory), xrayShaded: PD.Boolean(false, BaseGeometry.ShadingCategory), renderMode: createRenderModeParam(), stepsPerCell: PD.Numeric(5, { min: 1, max: 20, step: 1 }), jumpLength: PD.Numeric(0, { min: 0, max: 20, step: 0.1 }) });
DirectVolume.Utils = {
Params: DirectVolume.Params,
createEmpty: createEmpty,
createValues: createValues,
createValuesSimple: createValuesSimple,
updateValues: updateValues,
updateBoundingSphere: updateBoundingSphere,
createRenderableState: createRenderableState,
updateRenderableState: updateRenderableState,
createPositionIterator: createPositionIterator
};
function createPositionIterator(directVolume, transform) {
var t = directVolume.transform.ref.value;
var _a = directVolume.gridDimension.ref.value, x = _a[0], y = _a[1], z = _a[2];
var groupCount = x * y * z;
var instanceCount = transform.instanceCount.ref.value;
var location = PositionLocation();
var p = location.position;
var m = transform.aTransform.ref.value;
var getLocation = function (groupIndex, instanceIndex) {
var 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 getNormalizedIsoValue(out, isoValue, stats) {
var min = stats[0], max = stats[1], mean = stats[2], sigma = stats[3];
var value = Volume.IsoValue.toAbsolute(isoValue, { min: min, max: max, mean: mean, sigma: sigma }).absoluteValue;
Vec2.set(out, (value - min) / (max - min), (0 - min) / (max - min));
return out;
}
function getMaxSteps(gridDim, stepsPerCell) {
return Math.ceil(Vec3.magnitude(gridDim) * stepsPerCell);
}
function getStepScale(cellDim, stepsPerCell) {
return Math.min.apply(Math, cellDim) * (1 / stepsPerCell);
}
function getTransferScale(stepsPerCell) {
return (1 / stepsPerCell);
}
function createValues(directVolume, transform, locationIt, theme, props) {
var gridTexture = directVolume.gridTexture, gridTextureDim = directVolume.gridTextureDim, gridStats = directVolume.gridStats;
var bboxSize = directVolume.bboxSize, bboxMin = directVolume.bboxMin, bboxMax = directVolume.bboxMax, gridDimension = directVolume.gridDimension, gridTransform = directVolume.transform;
var instanceCount = locationIt.instanceCount, groupCount = locationIt.groupCount;
var positionIt = DirectVolume.Utils.createPositionIterator(directVolume, transform);
var color = createColors(locationIt, positionIt, theme.color);
var marker = createMarkers(instanceCount * groupCount);
var overpaint = createEmptyOverpaint();
var transparency = createEmptyTransparency();
var clipping = createEmptyClipping();
var _a = gridDimension.ref.value, x = _a[0], y = _a[1], z = _a[2];
var counts = { drawCount: VolumeBox.indices.length, vertexCount: x * y * z, groupCount: groupCount, instanceCount: instanceCount };
var invariantBoundingSphere = Sphere3D.clone(directVolume.boundingSphere);
var boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
var controlPoints = props.renderMode.name === 'volume' ? getControlPointsFromVec2Array(props.renderMode.params.controlPoints) : [];
var transferTex = createTransferFunctionTexture(controlPoints, props.renderMode.name === 'volume' ? props.renderMode.params.list.colors : []);
var isoValue = props.renderMode.name === 'isosurface'
? props.renderMode.params.isoValue
: Volume.IsoValue.relative(2);
var singleLayer = props.renderMode.name === 'isosurface'
? props.renderMode.params.singleLayer
: false;
return __assign(__assign(__assign(__assign(__assign(__assign(__assign(__assign({}, color), marker), overpaint), transparency), 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)), uIsoValue: ValueCell.create(getNormalizedIsoValue(Vec2(), isoValue, directVolume.gridStats.ref.value)), 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, dRenderMode: ValueCell.create(props.renderMode.name), 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, dSingleLayer: ValueCell.create(singleLayer), dDoubleSided: ValueCell.create(props.doubleSided), dFlatShaded: ValueCell.create(props.flatShaded), dFlipSided: ValueCell.create(props.flipSided), dIgnoreLight: ValueCell.create(props.ignoreLight), dXrayShaded: ValueCell.create(props.xrayShaded) });
}
function createValuesSimple(directVolume, props, colorValue, sizeValue, transform) {
var s = BaseGeometry.createSimple(colorValue, sizeValue, transform);
var p = __assign(__assign({}, PD.getDefaultValues(DirectVolume.Params)), props);
return createValues(directVolume, s.transform, s.locationIterator, s.theme, p);
}
function updateValues(values, props) {
ValueCell.updateIfChanged(values.alpha, props.alpha);
ValueCell.updateIfChanged(values.uAlpha, props.alpha);
ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded);
ValueCell.updateIfChanged(values.dFlipSided, props.flipSided);
ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
ValueCell.updateIfChanged(values.dRenderMode, props.renderMode.name);
if (props.renderMode.name === 'isosurface') {
ValueCell.updateIfChanged(values.uIsoValue, getNormalizedIsoValue(values.uIsoValue.ref.value, props.renderMode.params.isoValue, values.uGridStats.ref.value));
ValueCell.updateIfChanged(values.dSingleLayer, props.renderMode.params.singleLayer);
}
else if (props.renderMode.name === 'volume') {
var controlPoints = getControlPointsFromVec2Array(props.renderMode.params.controlPoints);
createTransferFunctionTexture(controlPoints, props.renderMode.params.list.colors, 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) {
var invariantBoundingSphere = Sphere3D.clone(directVolume.boundingSphere);
var boundingSphere = calculateTransformBoundingSphere(invariantBoundingSphere, values.aTransform.ref.value, values.instanceCount.ref.value);
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) {
var state = BaseGeometry.createRenderableState(props);
state.opaque = false;
state.writeDepth = props.renderMode.name === 'isosurface';
return state;
}
function updateRenderableState(state, props) {
BaseGeometry.updateRenderableState(state, props);
state.opaque = false;
state.writeDepth = props.renderMode.name === 'isosurface';
}
})(DirectVolume || (DirectVolume = {}));
//
function getBoundingSphere(gridDimension, gridTransform) {
return Sphere3D.fromDimensionsAndTransform(Sphere3D(), gridDimension, gridTransform);
}
//# sourceMappingURL=direct-volume.js.map