molstar
Version:
A comprehensive macromolecular library.
298 lines (297 loc) • 14.6 kB
JavaScript
"use strict";
/**
* Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Gianluca Tomasello <giagitom@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.DotRepresentationProvider = exports.DotParams = exports.VolumePointParams = exports.VolumeSphereParams = exports.VolumeDotParams = void 0;
exports.VolumeSphereVisual = VolumeSphereVisual;
exports.VolumeSphereImpostorVisual = VolumeSphereImpostorVisual;
exports.VolumeSphereMeshVisual = VolumeSphereMeshVisual;
exports.createVolumeSphereImpostor = createVolumeSphereImpostor;
exports.createVolumeSphereMesh = createVolumeSphereMesh;
exports.VolumePointVisual = VolumePointVisual;
exports.createVolumePoint = createVolumePoint;
exports.getDotParams = getDotParams;
exports.DotRepresentation = DotRepresentation;
const param_definition_1 = require("../../mol-util/param-definition.js");
const volume_1 = require("../../mol-model/volume.js");
const mesh_1 = require("../../mol-geo/geometry/mesh/mesh.js");
const representation_1 = require("./representation.js");
const representation_2 = require("../representation.js");
const picking_1 = require("../../mol-geo/geometry/picking.js");
const loci_1 = require("../../mol-model/loci.js");
const util_1 = require("./util.js");
const base_1 = require("../../mol-geo/geometry/base.js");
const spheres_1 = require("../../mol-geo/geometry/spheres/spheres.js");
const mesh_builder_1 = require("../../mol-geo/geometry/mesh/mesh-builder.js");
const spheres_builder_1 = require("../../mol-geo/geometry/spheres/spheres-builder.js");
const vec3_1 = require("../../mol-math/linear-algebra/3d/vec3.js");
const sphere_1 = require("../../mol-geo/geometry/mesh/builder/sphere.js");
const sphere_2 = require("../../mol-geo/primitive/sphere.js");
const points_1 = require("../../mol-geo/geometry/points/points.js");
const points_builder_1 = require("../../mol-geo/geometry/points/points-builder.js");
const linear_algebra_1 = require("../../mol-math/linear-algebra.js");
const interval_1 = require("../../mol-data/int/interval.js");
const ordered_set_1 = require("../../mol-data/int/ordered-set.js");
exports.VolumeDotParams = {
isoValue: volume_1.Volume.IsoValueParam,
perturbPositions: param_definition_1.ParamDefinition.Boolean(false)
};
//
exports.VolumeSphereParams = {
...spheres_1.Spheres.Params,
...mesh_1.Mesh.Params,
...exports.VolumeDotParams,
tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true),
detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo),
};
function VolumeSphereVisual(materialId, volume, key, props, webgl) {
return props.tryUseImpostor && webgl && webgl.extensions.fragDepth && webgl.extensions.textureFloat
? VolumeSphereImpostorVisual(materialId)
: VolumeSphereMeshVisual(materialId);
}
function VolumeSphereImpostorVisual(materialId) {
return (0, representation_1.VolumeVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.VolumeSphereParams),
createGeometry: createVolumeSphereImpostor,
createLocationIterator: util_1.createVolumeCellLocationIterator,
getLoci: getDotLoci,
eachLocation: eachDot,
setUpdateState: (state, volume, newProps, currentProps, newTheme, currentTheme) => {
state.createGeometry = (!volume_1.Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats) ||
newProps.perturbPositions !== currentProps.perturbPositions);
},
geometryUtils: spheres_1.Spheres.Utils,
mustRecreate: (volumekey, props, webgl) => {
return !props.tryUseImpostor || !webgl;
}
}, materialId);
}
function VolumeSphereMeshVisual(materialId) {
return (0, representation_1.VolumeVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.VolumeSphereParams),
createGeometry: createVolumeSphereMesh,
createLocationIterator: util_1.createVolumeCellLocationIterator,
getLoci: getDotLoci,
eachLocation: eachDot,
setUpdateState: (state, volume, newProps, currentProps, newTheme, currentTheme) => {
state.createGeometry = (!volume_1.Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats) ||
newProps.perturbPositions !== currentProps.perturbPositions ||
newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.detail !== currentProps.detail);
},
geometryUtils: mesh_1.Mesh.Utils,
mustRecreate: (volumekey, props, webgl) => {
return props.tryUseImpostor && !!webgl;
}
}, materialId);
}
function getBasis(m) {
return {
...linear_algebra_1.Mat4.extractBasis(m),
maxScale: linear_algebra_1.Mat4.getMaxScaleOnAxis(m)
};
}
const offset = (0, vec3_1.Vec3)();
function getRandomOffsetFromBasis({ x, y, z, maxScale }) {
const rx = (Math.random() - 0.5) * maxScale;
const ry = (Math.random() - 0.5) * maxScale;
const rz = (Math.random() - 0.5) * maxScale;
vec3_1.Vec3.scale(offset, x, rx);
vec3_1.Vec3.scaleAndAdd(offset, offset, y, ry);
vec3_1.Vec3.scaleAndAdd(offset, offset, z, rz);
return offset;
}
function createVolumeSphereImpostor(ctx, volume, key, theme, props, spheres) {
const { cells: { space, data }, stats } = volume.grid;
const gridToCartn = volume_1.Grid.getGridToCartesianTransform(volume.grid);
const isoVal = volume_1.Volume.IsoValue.toAbsolute(props.isoValue, stats).absoluteValue;
const p = (0, vec3_1.Vec3)();
const [xn, yn, zn] = space.dimensions;
const count = Math.ceil((xn * yn * zn) / 10);
const builder = spheres_builder_1.SpheresBuilder.create(count, Math.ceil(count / 2), spheres);
const invert = isoVal < 0;
// Precompute basis vectors and largest cell axis length
const basis = props.perturbPositions ? getBasis(gridToCartn) : undefined;
for (let z = 0; z < zn; ++z) {
for (let y = 0; y < yn; ++y) {
for (let x = 0; x < xn; ++x) {
const value = space.get(data, x, y, z);
if (!invert && value < isoVal || invert && value > isoVal)
continue;
const cellIdx = space.dataOffset(x, y, z);
if (basis) {
vec3_1.Vec3.set(p, x, y, z);
vec3_1.Vec3.transformMat4(p, p, gridToCartn);
const offset = getRandomOffsetFromBasis(basis);
vec3_1.Vec3.add(p, p, offset);
}
else {
vec3_1.Vec3.set(p, x, y, z);
vec3_1.Vec3.transformMat4(p, p, gridToCartn);
}
builder.add(p[0], p[1], p[2], cellIdx);
}
}
}
const s = builder.getSpheres();
s.setBoundingSphere(volume_1.Volume.Isosurface.getBoundingSphere(volume, props.isoValue));
return s;
}
function createVolumeSphereMesh(ctx, volume, key, theme, props, mesh) {
const { detail, sizeFactor } = props;
const { cells: { space, data }, stats } = volume.grid;
const gridToCartn = volume_1.Grid.getGridToCartesianTransform(volume.grid);
const isoVal = volume_1.Volume.IsoValue.toAbsolute(props.isoValue, stats).absoluteValue;
const p = (0, vec3_1.Vec3)();
const [xn, yn, zn] = space.dimensions;
const count = Math.ceil((xn * yn * zn) / 10);
const vertexCount = count * (0, sphere_2.sphereVertexCount)(detail);
const builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, Math.ceil(vertexCount / 2), mesh);
const l = volume_1.Volume.Cell.Location(volume);
const themeSize = theme.size.size;
const invert = isoVal < 0;
// Precompute basis vectors and largest cell axis length
const basis = props.perturbPositions ? getBasis(gridToCartn) : undefined;
for (let z = 0; z < zn; ++z) {
for (let y = 0; y < yn; ++y) {
for (let x = 0; x < xn; ++x) {
const value = space.get(data, x, y, z);
if (!invert && value < isoVal || invert && value > isoVal)
continue;
const cellIdx = space.dataOffset(x, y, z);
l.cell = cellIdx;
const size = themeSize(l) * sizeFactor;
if (basis) {
vec3_1.Vec3.set(p, x, y, z);
vec3_1.Vec3.transformMat4(p, p, gridToCartn);
const offset = getRandomOffsetFromBasis(basis);
vec3_1.Vec3.add(p, p, offset);
}
else {
vec3_1.Vec3.set(p, x, y, z);
vec3_1.Vec3.transformMat4(p, p, gridToCartn);
}
builderState.currentGroup = cellIdx;
(0, sphere_1.addSphere)(builderState, p, size, detail);
}
}
}
const m = mesh_builder_1.MeshBuilder.getMesh(builderState);
m.setBoundingSphere(volume_1.Volume.Isosurface.getBoundingSphere(volume, props.isoValue));
return m;
}
//
exports.VolumePointParams = {
...points_1.Points.Params,
...exports.VolumeDotParams,
};
function VolumePointVisual(materialId) {
return (0, representation_1.VolumeVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.VolumePointParams),
createGeometry: createVolumePoint,
createLocationIterator: util_1.createVolumeCellLocationIterator,
getLoci: getDotLoci,
eachLocation: eachDot,
setUpdateState: (state, volume, newProps, currentProps, newTheme, currentTheme) => {
state.createGeometry = (!volume_1.Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats) ||
newProps.perturbPositions !== currentProps.perturbPositions);
},
geometryUtils: points_1.Points.Utils,
}, materialId);
}
function createVolumePoint(ctx, volume, key, theme, props, points) {
const { cells: { space, data }, stats } = volume.grid;
const gridToCartn = volume_1.Grid.getGridToCartesianTransform(volume.grid);
const isoVal = volume_1.Volume.IsoValue.toAbsolute(props.isoValue, stats).absoluteValue;
const p = (0, vec3_1.Vec3)();
const [xn, yn, zn] = space.dimensions;
const count = Math.ceil((xn * yn * zn) / 10);
const builder = points_builder_1.PointsBuilder.create(count, Math.ceil(count / 2), points);
const invert = isoVal < 0;
// Precompute basis vectors and largest cell axis length
const basis = props.perturbPositions ? getBasis(gridToCartn) : undefined;
for (let z = 0; z < zn; ++z) {
for (let y = 0; y < yn; ++y) {
for (let x = 0; x < xn; ++x) {
const value = space.get(data, x, y, z);
if (!invert && value < isoVal || invert && value > isoVal)
continue;
const cellIdx = space.dataOffset(x, y, z);
if (basis) {
vec3_1.Vec3.set(p, x, y, z);
vec3_1.Vec3.transformMat4(p, p, gridToCartn);
const offset = getRandomOffsetFromBasis(basis);
vec3_1.Vec3.add(p, p, offset);
}
else {
vec3_1.Vec3.set(p, x, y, z);
vec3_1.Vec3.transformMat4(p, p, gridToCartn);
}
builder.add(p[0], p[1], p[2], cellIdx);
}
}
}
const pt = builder.getPoints();
pt.setBoundingSphere(volume_1.Volume.Isosurface.getBoundingSphere(volume, props.isoValue));
return pt;
}
//
function getLoci(volume, props) {
const instances = interval_1.Interval.ofLength(volume.instances.length);
return volume_1.Volume.Isosurface.Loci(volume, props.isoValue, instances);
}
function getDotLoci(pickingId, volume, key, props, id) {
const { objectId, groupId, instanceId } = pickingId;
if (id === objectId) {
const granularity = volume_1.Volume.PickingGranularity.get(volume);
const instances = ordered_set_1.OrderedSet.ofSingleton(instanceId);
if (granularity === 'volume') {
return volume_1.Volume.Loci(volume, instances);
}
else if (granularity === 'object' || groupId === picking_1.PickingId.Null) {
return volume_1.Volume.Isosurface.Loci(volume, props.isoValue, instances);
}
else {
const indices = interval_1.Interval.ofSingleton(groupId);
return volume_1.Volume.Cell.Loci(volume, [{ indices, instances }]);
}
}
return loci_1.EmptyLoci;
}
function eachDot(loci, volume, key, props, apply) {
return (0, util_1.eachVolumeLoci)(loci, volume, { isoValue: props.isoValue }, apply);
}
//
const DotVisuals = {
'sphere': (ctx, getParams) => (0, representation_1.VolumeRepresentation)('Dot sphere', ctx, getParams, VolumeSphereVisual, getLoci),
'point': (ctx, getParams) => (0, representation_1.VolumeRepresentation)('Dot point', ctx, getParams, VolumePointVisual, getLoci),
};
exports.DotParams = {
...exports.VolumeSphereParams,
...exports.VolumePointParams,
visuals: param_definition_1.ParamDefinition.MultiSelect(['sphere'], param_definition_1.ParamDefinition.objectToOptions(DotVisuals)),
bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory),
};
function getDotParams(ctx, volume) {
const p = param_definition_1.ParamDefinition.clone(exports.DotParams);
p.isoValue = volume_1.Volume.createIsoValueParam(volume_1.Volume.IsoValue.relative(2), volume.grid.stats);
return p;
}
function DotRepresentation(ctx, getParams) {
return representation_2.Representation.createMulti('Dot', ctx, getParams, representation_2.Representation.StateBuilder, DotVisuals);
}
exports.DotRepresentationProvider = (0, representation_1.VolumeRepresentationProvider)({
name: 'dot',
label: 'Dot',
description: 'Displays dots of volumetric data.',
factory: DotRepresentation,
getParams: getDotParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.DotParams),
defaultColorTheme: { name: 'uniform' },
defaultSizeTheme: { name: 'uniform' },
isApplicable: (volume) => !volume_1.Volume.isEmpty(volume) && !volume_1.Volume.Segmentation.get(volume)
});