molstar
Version:
A comprehensive macromolecular library.
257 lines • 16.1 kB
JavaScript
;
/**
* Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.IsosurfaceRepresentationProvider = exports.IsosurfaceRepresentation = exports.getIsosurfaceParams = exports.IsosurfaceParams = exports.IsosurfaceWireframeVisual = exports.IsosurfaceWireframeParams = exports.createVolumeIsosurfaceWireframe = exports.IsosurfaceTextureMeshVisual = exports.IsosurfaceMeshVisual = exports.IsosurfaceMeshParams = exports.createVolumeIsosurfaceMesh = exports.eachIsosurface = exports.IsosurfaceVisual = exports.VolumeIsosurfaceParams = void 0;
var tslib_1 = require("tslib");
var param_definition_1 = require("../../mol-util/param-definition");
var volume_1 = require("../../mol-model/volume");
var mesh_1 = require("../../mol-geo/geometry/mesh/mesh");
var algorithm_1 = require("../../mol-geo/util/marching-cubes/algorithm");
var representation_1 = require("./representation");
var location_iterator_1 = require("../../mol-geo/util/location-iterator");
var location_1 = require("../../mol-model/location");
var lines_1 = require("../../mol-geo/geometry/lines/lines");
var representation_2 = require("../representation");
var loci_1 = require("../../mol-model/loci");
var int_1 = require("../../mol-data/int");
var linear_algebra_1 = require("../../mol-math/linear-algebra");
var array_1 = require("../../mol-util/array");
var util_1 = require("./util");
var texture_mesh_1 = require("../../mol-geo/geometry/texture-mesh/texture-mesh");
var isosurface_1 = require("../../mol-gl/compute/marching-cubes/isosurface");
var custom_property_1 = require("../../mol-model/custom-property");
exports.VolumeIsosurfaceParams = {
isoValue: volume_1.Volume.IsoValueParam
};
function gpuSupport(webgl) {
return webgl.extensions.colorBufferFloat && webgl.extensions.textureFloat && webgl.extensions.drawBuffers;
}
var Padding = 1;
function suitableForGpu(volume, webgl) {
var gridDim = volume.grid.cells.space.dimensions;
var powerOfTwoSize = (0, util_1.getVolumeTexture2dLayout)(gridDim, Padding).powerOfTwoSize;
return powerOfTwoSize <= webgl.maxTextureSize / 2;
}
function IsosurfaceVisual(materialId, volume, props, webgl) {
if (props.tryUseGpu && webgl && gpuSupport(webgl) && suitableForGpu(volume, webgl)) {
return IsosurfaceTextureMeshVisual(materialId);
}
return IsosurfaceMeshVisual(materialId);
}
exports.IsosurfaceVisual = IsosurfaceVisual;
function getLoci(volume, props) {
return volume_1.Volume.Isosurface.Loci(volume, props.isoValue);
}
function getIsosurfaceLoci(pickingId, volume, props, id) {
var objectId = pickingId.objectId, groupId = pickingId.groupId;
if (id === objectId) {
return volume_1.Volume.Cell.Loci(volume, int_1.Interval.ofSingleton(groupId));
}
return loci_1.EmptyLoci;
}
function eachIsosurface(loci, volume, props, apply) {
return (0, util_1.eachVolumeLoci)(loci, volume, props.isoValue, apply);
}
exports.eachIsosurface = eachIsosurface;
//
function createVolumeIsosurfaceMesh(ctx, volume, theme, props, mesh) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var ids, surface, transform;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
ctx.runtime.update({ message: 'Marching cubes...' });
ids = (0, array_1.fillSerial)(new Int32Array(volume.grid.cells.data.length));
return [4 /*yield*/, (0, algorithm_1.computeMarchingCubesMesh)({
isoLevel: volume_1.Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue,
scalarField: volume.grid.cells,
idField: linear_algebra_1.Tensor.create(volume.grid.cells.space, linear_algebra_1.Tensor.Data1(ids))
}, mesh).runAsChild(ctx.runtime)];
case 1:
surface = _a.sent();
transform = volume_1.Grid.getGridToCartesianTransform(volume.grid);
mesh_1.Mesh.transform(surface, transform);
if (ctx.webgl && !ctx.webgl.isWebGL2) {
// 2nd arg means not to split triangles based on group id. Splitting triangles
// is too expensive if each cell has its own group id as is the case here.
mesh_1.Mesh.uniformTriangleGroup(surface, false);
}
surface.setBoundingSphere(volume_1.Volume.getBoundingSphere(volume));
return [2 /*return*/, surface];
}
});
});
}
exports.createVolumeIsosurfaceMesh = createVolumeIsosurfaceMesh;
exports.IsosurfaceMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), texture_mesh_1.TextureMesh.Params), exports.VolumeIsosurfaceParams), { quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params.quality), { isEssential: false }), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true) });
function IsosurfaceMeshVisual(materialId) {
return (0, representation_1.VolumeVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IsosurfaceMeshParams),
createGeometry: createVolumeIsosurfaceMesh,
createLocationIterator: function (volume) { return (0, location_iterator_1.LocationIterator)(volume.grid.cells.data.length, 1, 1, function () { return location_1.NullLocation; }); },
getLoci: getIsosurfaceLoci,
eachLocation: eachIsosurface,
setUpdateState: function (state, volume, newProps, currentProps) {
if (!volume_1.Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats))
state.createGeometry = true;
},
geometryUtils: mesh_1.Mesh.Utils,
mustRecreate: function (volume, props, webgl) {
return props.tryUseGpu && !!webgl && suitableForGpu(volume, webgl);
}
}, materialId);
}
exports.IsosurfaceMeshVisual = IsosurfaceMeshVisual;
//
var VolumeIsosurfaceTexture;
(function (VolumeIsosurfaceTexture) {
var name = 'volume-isosurface-texture';
VolumeIsosurfaceTexture.descriptor = (0, custom_property_1.CustomPropertyDescriptor)({ name: name });
function get(volume, webgl) {
var resources = webgl.resources;
var transform = volume_1.Grid.getGridToCartesianTransform(volume.grid);
var gridDimension = linear_algebra_1.Vec3.clone(volume.grid.cells.space.dimensions);
var _a = (0, util_1.getVolumeTexture2dLayout)(gridDimension, Padding), width = _a.width, height = _a.height, texDim = _a.powerOfTwoSize;
var gridTexDim = linear_algebra_1.Vec3.create(width, height, 0);
var gridTexScale = linear_algebra_1.Vec2.create(width / texDim, height / texDim);
// console.log({ texDim, width, height, gridDimension });
if (texDim > webgl.maxTextureSize / 2) {
throw new Error('volume too large for gpu isosurface extraction');
}
if (!volume._propertyData[name]) {
volume._propertyData[name] = resources.texture('image-uint8', 'alpha', 'ubyte', 'linear');
var texture_1 = volume._propertyData[name];
texture_1.define(texDim, texDim);
// load volume into sub-section of texture
texture_1.load((0, util_1.createVolumeTexture2d)(volume, 'data', Padding), true);
volume.customProperties.add(VolumeIsosurfaceTexture.descriptor);
volume.customProperties.assets(VolumeIsosurfaceTexture.descriptor, [{ dispose: function () { return texture_1.destroy(); } }]);
}
gridDimension[0] += Padding;
gridDimension[1] += Padding;
return {
texture: volume._propertyData[name],
transform: transform,
gridDimension: gridDimension,
gridTexDim: gridTexDim,
gridTexScale: gridTexScale
};
}
VolumeIsosurfaceTexture.get = get;
})(VolumeIsosurfaceTexture || (VolumeIsosurfaceTexture = {}));
function createVolumeIsosurfaceTextureMesh(ctx, volume, theme, props, textureMesh) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var _a, max, min, diff, value, isoLevel, _b, texture, gridDimension, gridTexDim, gridTexScale, transform, buffer, gv, surface;
return (0, tslib_1.__generator)(this, function (_c) {
if (!ctx.webgl)
throw new Error('webgl context required to create volume isosurface texture-mesh');
_a = volume.grid.stats, max = _a.max, min = _a.min;
diff = max - min;
value = volume_1.Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue;
isoLevel = ((value - min) / diff);
_b = VolumeIsosurfaceTexture.get(volume, ctx.webgl), texture = _b.texture, gridDimension = _b.gridDimension, gridTexDim = _b.gridTexDim, gridTexScale = _b.gridTexScale, transform = _b.transform;
buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
gv = (0, isosurface_1.extractIsosurface)(ctx.webgl, texture, gridDimension, gridTexDim, gridTexScale, transform, isoLevel, value < 0, false, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, volume_1.Volume.getBoundingSphere(volume), textureMesh);
return [2 /*return*/, surface];
});
});
}
function IsosurfaceTextureMeshVisual(materialId) {
return (0, representation_1.VolumeVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IsosurfaceMeshParams),
createGeometry: createVolumeIsosurfaceTextureMesh,
createLocationIterator: function (volume) { return (0, location_iterator_1.LocationIterator)(volume.grid.cells.data.length, 1, 1, function () { return location_1.NullLocation; }); },
getLoci: getIsosurfaceLoci,
eachLocation: eachIsosurface,
setUpdateState: function (state, volume, newProps, currentProps) {
if (!volume_1.Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats))
state.createGeometry = true;
},
geometryUtils: texture_mesh_1.TextureMesh.Utils,
mustRecreate: function (volume, props, webgl) {
return !props.tryUseGpu || !webgl || !suitableForGpu(volume, webgl);
},
dispose: function (geometry) {
geometry.vertexTexture.ref.value.destroy();
geometry.groupTexture.ref.value.destroy();
geometry.normalTexture.ref.value.destroy();
geometry.doubleBuffer.destroy();
}
}, materialId);
}
exports.IsosurfaceTextureMeshVisual = IsosurfaceTextureMeshVisual;
//
function createVolumeIsosurfaceWireframe(ctx, volume, theme, props, lines) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var ids, wireframe, transform;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
ctx.runtime.update({ message: 'Marching cubes...' });
ids = (0, array_1.fillSerial)(new Int32Array(volume.grid.cells.data.length));
return [4 /*yield*/, (0, algorithm_1.computeMarchingCubesLines)({
isoLevel: volume_1.Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue,
scalarField: volume.grid.cells,
idField: linear_algebra_1.Tensor.create(volume.grid.cells.space, linear_algebra_1.Tensor.Data1(ids))
}, lines).runAsChild(ctx.runtime)];
case 1:
wireframe = _a.sent();
transform = volume_1.Grid.getGridToCartesianTransform(volume.grid);
lines_1.Lines.transform(wireframe, transform);
wireframe.setBoundingSphere(volume_1.Volume.getBoundingSphere(volume));
return [2 /*return*/, wireframe];
}
});
});
}
exports.createVolumeIsosurfaceWireframe = createVolumeIsosurfaceWireframe;
exports.IsosurfaceWireframeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, lines_1.Lines.Params), exports.VolumeIsosurfaceParams), { quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, lines_1.Lines.Params.quality), { isEssential: false }), sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0, max: 10, step: 0.1 }) });
function IsosurfaceWireframeVisual(materialId) {
return (0, representation_1.VolumeVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IsosurfaceWireframeParams),
createGeometry: createVolumeIsosurfaceWireframe,
createLocationIterator: function (volume) { return (0, location_iterator_1.LocationIterator)(volume.grid.cells.data.length, 1, 1, function () { return location_1.NullLocation; }); },
getLoci: getIsosurfaceLoci,
eachLocation: eachIsosurface,
setUpdateState: function (state, volume, newProps, currentProps) {
if (!volume_1.Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats))
state.createGeometry = true;
},
geometryUtils: lines_1.Lines.Utils
}, materialId);
}
exports.IsosurfaceWireframeVisual = IsosurfaceWireframeVisual;
//
var IsosurfaceVisuals = {
'solid': function (ctx, getParams) { return (0, representation_1.VolumeRepresentation)('Isosurface mesh', ctx, getParams, IsosurfaceVisual, getLoci); },
'wireframe': function (ctx, getParams) { return (0, representation_1.VolumeRepresentation)('Isosurface wireframe', ctx, getParams, IsosurfaceWireframeVisual, getLoci); },
};
exports.IsosurfaceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.IsosurfaceMeshParams), exports.IsosurfaceWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['solid'], param_definition_1.ParamDefinition.objectToOptions(IsosurfaceVisuals)) });
function getIsosurfaceParams(ctx, volume) {
var p = param_definition_1.ParamDefinition.clone(exports.IsosurfaceParams);
p.isoValue = volume_1.Volume.createIsoValueParam(volume_1.Volume.IsoValue.relative(2), volume.grid.stats);
return p;
}
exports.getIsosurfaceParams = getIsosurfaceParams;
function IsosurfaceRepresentation(ctx, getParams) {
return representation_2.Representation.createMulti('Isosurface', ctx, getParams, representation_2.Representation.StateBuilder, IsosurfaceVisuals);
}
exports.IsosurfaceRepresentation = IsosurfaceRepresentation;
exports.IsosurfaceRepresentationProvider = (0, representation_1.VolumeRepresentationProvider)({
name: 'isosurface',
label: 'Isosurface',
description: 'Displays a triangulated isosurface of volumetric data.',
factory: IsosurfaceRepresentation,
getParams: getIsosurfaceParams,
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.IsosurfaceParams),
defaultColorTheme: { name: 'uniform' },
defaultSizeTheme: { name: 'uniform' },
isApplicable: function (volume) { return !volume_1.Volume.isEmpty(volume); }
});
//# sourceMappingURL=isosurface.js.map