molstar 3.0.0-dev.7 → 3.0.0-dev.8

package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Texture } from '../../../mol-gl/webgl/texture';
 import { Box3D, Sphere3D } from '../../../mol-math/geometry';
-import { Mat4, Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
+import { Mat4, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
 import { ValueCell } from '../../../mol-util';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { GeometryUtils } from '../geometry';
@@ -24,51 +24,18 @@ export interface DirectVolume {
     readonly unitToCartn: ValueCell<Mat4>;
     readonly cartnToUnit: ValueCell<Mat4>;
     readonly packedGroup: ValueCell<boolean>;
+    readonly axisOrder: ValueCell<Vec3>;
     /** Bounding sphere of the volume */
     readonly boundingSphere: Sphere3D;
     setBoundingSphere(boundingSphere: Sphere3D): void;
 }
 export declare namespace DirectVolume {
-    function create(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, directVolume?: DirectVolume): DirectVolume;
+    function create(bbox: Box3D, gridDimension: Vec3, transform: Mat4, unitToCartn: Mat4, cellDim: Vec3, texture: Texture, stats: Grid['stats'], packedGroup: boolean, axisOrder: Vec3, directVolume?: DirectVolume): DirectVolume;
     function createEmpty(directVolume?: DirectVolume): DirectVolume;
-    function createRenderModeParam(stats?: Grid['stats']): PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: Vec2[];
-        list: {
-            kind: "set" | "interpolate";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
     const Params: {
-        doubleSided: PD.BooleanParam;
-        flipSided: PD.BooleanParam;
-        flatShaded: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
-        renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-            controlPoints: Vec2[];
-            list: {
-                kind: "set" | "interpolate";
-                colors: import("../../../mol-util/color/color").ColorListEntry[];
-            };
-        }>, "volume"> | PD.NamedParams<PD.Normalize<{
-            isoValue: Readonly<{
-                kind: "absolute";
-                absoluteValue: number;
-            }> | Readonly<{
-                kind: "relative";
-                relativeValue: number;
-            }>;
-            singleLayer: boolean;
-        }>, "isosurface">>;
+        controlPoints: PD.LineGraph;
         stepsPerCell: PD.Numeric;
         jumpLength: PD.Numeric;
         alpha: PD.Numeric;

package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -24,15 +24,14 @@ var transparency_data_1 = require("../transparency-data");
 var transfer_function_1 = require("./transfer-function");
 var clipping_data_1 = require("../clipping-data");
 var volume_1 = require("../../../mol-model/volume");
-var names_1 = require("../../../mol-util/color/names");
 var substance_data_1 = require("../substance-data");
 var VolumeBox = (0, box_1.Box)();
 var DirectVolume;
 (function (DirectVolume) {
-    function create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume) {
+    function create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, directVolume) {
         return directVolume ?
-            update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume) :
-            fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup);
+            update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, directVolume) :
+            fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder);
     }
     DirectVolume.create = create;
     function hashCode(directVolume) {
@@ -42,7 +41,7 @@ var DirectVolume;
             directVolume.gridStats.ref.version
         ]);
     }
-    function fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup) {
+    function fromData(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder) {
         var boundingSphere = (0, geometry_1.Sphere3D)();
         var currentHash = -1;
         var width = texture.getWidth();
@@ -71,6 +70,7 @@ var DirectVolume;
                 return boundingSphere;
             },
             packedGroup: mol_util_1.ValueCell.create(packedGroup),
+            axisOrder: mol_util_1.ValueCell.create(axisOrder),
             setBoundingSphere: function (sphere) {
                 geometry_1.Sphere3D.copy(boundingSphere, sphere);
                 currentHash = hashCode(directVolume);
@@ -78,7 +78,7 @@ var DirectVolume;
         };
         return directVolume;
     }
-    function update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume) {
+    function update(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, directVolume) {
         var width = texture.getWidth();
         var height = texture.getHeight();
         var depth = texture.getDepth();
@@ -94,6 +94,7 @@ var DirectVolume;
         mol_util_1.ValueCell.update(directVolume.unitToCartn, unitToCartn);
         mol_util_1.ValueCell.update(directVolume.cartnToUnit, linear_algebra_1.Mat4.invert((0, linear_algebra_1.Mat4)(), unitToCartn));
         mol_util_1.ValueCell.updateIfChanged(directVolume.packedGroup, packedGroup);
+        mol_util_1.ValueCell.updateIfChanged(directVolume.axisOrder, linear_algebra_1.Vec3.fromArray(directVolume.axisOrder.ref.value, axisOrder, 0));
         return directVolume;
     }
     function createEmpty(directVolume) {
@@ -105,38 +106,14 @@ var DirectVolume;
         var texture = (0, texture_1.createNullTexture)();
         var stats = volume_1.Grid.One.stats;
         var packedGroup = false;
-        return create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume);
+        var axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
+        return create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, axisOrder, directVolume);
     }
     DirectVolume.createEmpty = createEmpty;
-    function createRenderModeParam(stats) {
-        var isoValueParam = stats
-            ? volume_1.Volume.createIsoValueParam(volume_1.Volume.IsoValue.relative(2), stats)
-            : volume_1.Volume.IsoValueParam;
-        return param_definition_1.ParamDefinition.MappedStatic('volume', {
-            isosurface: param_definition_1.ParamDefinition.Group({
-                isoValue: isoValueParam,
-                singleLayer: param_definition_1.ParamDefinition.Boolean(false, { isEssential: true }),
-            }, { isFlat: true }),
-            volume: param_definition_1.ParamDefinition.Group({
-                controlPoints: param_definition_1.ParamDefinition.LineGraph([
-                    linear_algebra_1.Vec2.create(0.19, 0.0), linear_algebra_1.Vec2.create(0.2, 0.05), linear_algebra_1.Vec2.create(0.25, 0.05), linear_algebra_1.Vec2.create(0.26, 0.0),
-                    linear_algebra_1.Vec2.create(0.79, 0.0), linear_algebra_1.Vec2.create(0.8, 0.05), linear_algebra_1.Vec2.create(0.85, 0.05), linear_algebra_1.Vec2.create(0.86, 0.0),
-                ]),
-                list: param_definition_1.ParamDefinition.ColorList({
-                    kind: 'interpolate',
-                    colors: [
-                        [names_1.ColorNames.white, 0],
-                        [names_1.ColorNames.red, 0.25],
-                        [names_1.ColorNames.white, 0.5],
-                        [names_1.ColorNames.blue, 0.75],
-                        [names_1.ColorNames.white, 1]
-                    ]
-                }, { offsets: true }),
-            }, { isFlat: true })
-        }, { isEssential: true });
-    }
-    DirectVolume.createRenderModeParam = createRenderModeParam;
-    DirectVolume.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), flipSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), flatShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), renderMode: createRenderModeParam(), stepsPerCell: param_definition_1.ParamDefinition.Numeric(5, { min: 1, max: 20, step: 1 }), jumpLength: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 20, step: 0.1 }) });
+    DirectVolume.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), controlPoints: param_definition_1.ParamDefinition.LineGraph([
+            linear_algebra_1.Vec2.create(0.19, 0.0), linear_algebra_1.Vec2.create(0.2, 0.05), linear_algebra_1.Vec2.create(0.25, 0.05), linear_algebra_1.Vec2.create(0.26, 0.0),
+            linear_algebra_1.Vec2.create(0.79, 0.0), linear_algebra_1.Vec2.create(0.8, 0.05), linear_algebra_1.Vec2.create(0.85, 0.05), linear_algebra_1.Vec2.create(0.86, 0.0),
+        ], { isEssential: true }), stepsPerCell: param_definition_1.ParamDefinition.Numeric(3, { min: 1, max: 10, step: 1 }), jumpLength: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 20, step: 0.1 }) });
     DirectVolume.Utils = {
         Params: DirectVolume.Params,
         createEmpty: createEmpty,
@@ -169,12 +146,6 @@ var DirectVolume;
         };
         return (0, location_iterator_1.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_1.Volume.IsoValue.toAbsolute(isoValue, { min: min, max: max, mean: mean, sigma: sigma }).absoluteValue;
-        linear_algebra_1.Vec2.set(out, (value - min) / (max - min), (0 - min) / (max - min));
-        return out;
-    }
     function getMaxSteps(gridDim, stepsPerCell) {
         return Math.ceil(linear_algebra_1.Vec3.magnitude(gridDim) * stepsPerCell);
     }
@@ -199,15 +170,9 @@ var DirectVolume;
         var counts = { drawCount: VolumeBox.indices.length, vertexCount: x * y * z, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(directVolume.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        var controlPoints = props.renderMode.name === 'volume' ? (0, transfer_function_1.getControlPointsFromVec2Array)(props.renderMode.params.controlPoints) : [];
-        var transferTex = (0, transfer_function_1.createTransferFunctionTexture)(controlPoints, props.renderMode.name === 'volume' ? props.renderMode.params.list.colors : []);
-        var isoValue = props.renderMode.name === 'isosurface'
-            ? props.renderMode.params.isoValue
-            : volume_1.Volume.IsoValue.relative(2);
-        var singleLayer = props.renderMode.name === 'isosurface'
-            ? props.renderMode.params.singleLayer
-            : false;
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { aPosition: mol_util_1.ValueCell.create(VolumeBox.vertices), elements: mol_util_1.ValueCell.create(VolumeBox.indices), boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)), uIsoValue: mol_util_1.ValueCell.create(getNormalizedIsoValue((0, linear_algebra_1.Vec2)(), isoValue, directVolume.gridStats.ref.value)), uBboxMin: bboxMin, uBboxMax: bboxMax, uBboxSize: bboxSize, uMaxSteps: mol_util_1.ValueCell.create(getMaxSteps(gridDimension.ref.value, props.stepsPerCell)), uStepScale: mol_util_1.ValueCell.create(getStepScale(directVolume.cellDim.ref.value, props.stepsPerCell)), uJumpLength: mol_util_1.ValueCell.create(props.jumpLength), uTransform: gridTransform, uGridDim: gridDimension, dRenderMode: mol_util_1.ValueCell.create(props.renderMode.name), tTransferTex: transferTex, uTransferScale: mol_util_1.ValueCell.create(getTransferScale(props.stepsPerCell)), dGridTexType: mol_util_1.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: mol_util_1.ValueCell.create(singleLayer), uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded) });
+        var controlPoints = (0, transfer_function_1.getControlPointsFromVec2Array)(props.controlPoints);
+        var transferTex = (0, transfer_function_1.createTransferFunctionTexture)(controlPoints);
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ dGeometryType: mol_util_1.ValueCell.create('directVolume') }, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { aPosition: mol_util_1.ValueCell.create(VolumeBox.vertices), elements: mol_util_1.ValueCell.create(VolumeBox.indices), boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)), uBboxMin: bboxMin, uBboxMax: bboxMax, uBboxSize: bboxSize, uMaxSteps: mol_util_1.ValueCell.create(getMaxSteps(gridDimension.ref.value, props.stepsPerCell)), uStepScale: mol_util_1.ValueCell.create(getStepScale(directVolume.cellDim.ref.value, props.stepsPerCell)), uJumpLength: mol_util_1.ValueCell.create(props.jumpLength), uTransform: gridTransform, uGridDim: gridDimension, tTransferTex: transferTex, uTransferScale: mol_util_1.ValueCell.create(getTransferScale(props.stepsPerCell)), dGridTexType: mol_util_1.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: mol_util_1.ValueCell.create(directVolume.axisOrder.ref.value.join('')), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded) });
     }
     function createValuesSimple(directVolume, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -216,20 +181,10 @@ var DirectVolume;
     }
     function updateValues(values, props) {
         base_1.BaseGeometry.updateValues(values, props);
-        mol_util_1.ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
-        mol_util_1.ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded);
-        mol_util_1.ValueCell.updateIfChanged(values.dFlipSided, props.flipSided);
         mol_util_1.ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         mol_util_1.ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
-        mol_util_1.ValueCell.updateIfChanged(values.dRenderMode, props.renderMode.name);
-        if (props.renderMode.name === 'isosurface') {
-            mol_util_1.ValueCell.updateIfChanged(values.uIsoValue, getNormalizedIsoValue(values.uIsoValue.ref.value, props.renderMode.params.isoValue, values.uGridStats.ref.value));
-            mol_util_1.ValueCell.updateIfChanged(values.dSingleLayer, props.renderMode.params.singleLayer);
-        }
-        else if (props.renderMode.name === 'volume') {
-            var controlPoints = (0, transfer_function_1.getControlPointsFromVec2Array)(props.renderMode.params.controlPoints);
-            (0, transfer_function_1.createTransferFunctionTexture)(controlPoints, props.renderMode.params.list.colors, values.tTransferTex);
-        }
+        var controlPoints = (0, transfer_function_1.getControlPointsFromVec2Array)(props.controlPoints);
+        (0, transfer_function_1.createTransferFunctionTexture)(controlPoints, values.tTransferTex);
         mol_util_1.ValueCell.updateIfChanged(values.uMaxSteps, getMaxSteps(values.uGridDim.ref.value, props.stepsPerCell));
         mol_util_1.ValueCell.updateIfChanged(values.uStepScale, getStepScale(values.uCellDim.ref.value, props.stepsPerCell));
         mol_util_1.ValueCell.updateIfChanged(values.uTransferScale, getTransferScale(props.stepsPerCell));
@@ -249,13 +204,13 @@ var DirectVolume;
     function createRenderableState(props) {
         var state = base_1.BaseGeometry.createRenderableState(props);
         state.opaque = false;
-        state.writeDepth = props.renderMode.name === 'isosurface';
+        state.writeDepth = false;
         return state;
     }
     function updateRenderableState(state, props) {
         base_1.BaseGeometry.updateRenderableState(state, props);
         state.opaque = false;
-        state.writeDepth = props.renderMode.name === 'isosurface';
+        state.writeDepth = false;
     }
 })(DirectVolume = exports.DirectVolume || (exports.DirectVolume = {}));
 //

package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.d.ts

@@ -1,17 +1,15 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { TextureImage } from '../../../mol-gl/renderable/util';
 import { ValueCell } from '../../../mol-util';
 import { Vec2 } from '../../../mol-math/linear-algebra';
-import { ColorListName } from '../../../mol-util/color/lists';
-import { ColorListEntry } from '../../../mol-util/color/color';
 export interface ControlPoint {
     x: number;
     alpha: number;
 }
 export declare function getControlPointsFromString(s: string): ControlPoint[];
 export declare function getControlPointsFromVec2Array(array: Vec2[]): ControlPoint[];
-export declare function createTransferFunctionTexture(controlPoints: ControlPoint[], listOrName: ColorListEntry[] | ColorListName, texture?: ValueCell<TextureImage<Uint8Array>>): ValueCell<TextureImage<Uint8Array>>;
+export declare function createTransferFunctionTexture(controlPoints: ControlPoint[], texture?: ValueCell<TextureImage<Uint8Array>>): ValueCell<TextureImage<Uint8Array>>;

package/lib/commonjs/mol-geo/geometry/direct-volume/transfer-function.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -8,7 +8,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.createTransferFunctionTexture = exports.getControlPointsFromVec2Array = exports.getControlPointsFromString = void 0;
 var tslib_1 = require("tslib");
 var interpolate_1 = require("../../../mol-math/interpolate");
-var color_1 = require("../../../mol-util/color");
 var mol_util_1 = require("../../../mol-util");
 function getControlPointsFromString(s) {
     return s.split(/\s*,\s*/).map(function (p) {
@@ -21,7 +20,7 @@ function getControlPointsFromVec2Array(array) {
     return array.map(function (v) { return ({ x: v[0], alpha: v[1] }); });
 }
 exports.getControlPointsFromVec2Array = getControlPointsFromVec2Array;
-function createTransferFunctionTexture(controlPoints, listOrName, texture) {
+function createTransferFunctionTexture(controlPoints, texture) {
     var cp = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
         { x: 0, alpha: 0 },
         { x: 0, alpha: 0 }
@@ -29,9 +28,8 @@ function createTransferFunctionTexture(controlPoints, listOrName, texture) {
         { x: 1, alpha: 0 },
         { x: 1, alpha: 0 },
     ], false);
-    var scale = color_1.ColorScale.create({ domain: [0, 1], listOrName: listOrName });
     var n = 256;
-    var array = texture ? texture.ref.value.array : new Uint8Array(n * 4);
+    var array = texture ? texture.ref.value.array : new Uint8Array(n);
     var k = 0;
     var x1, x2;
     var a0, a1, a2, a3;
@@ -46,8 +44,7 @@ function createTransferFunctionTexture(controlPoints, listOrName, texture) {
         var jl = Math.round((x2 - x1) * n);
         for (var j = 0; j < jl; ++j) {
             var t = j / jl;
-            array[k * 4 + 3] = Math.max(0, (0, interpolate_1.spline)(a0, a1, a2, a3, t, 0.5) * 255);
-            scale.colorToArray(k / 255, array, k * 4);
+            array[k] = Math.max(0, (0, interpolate_1.spline)(a0, a1, a2, a3, t, 0.5) * 255);
             ++k;
         }
     }

package/lib/commonjs/mol-geo/geometry/image/image.js

@@ -117,7 +117,7 @@ var Image;
         var counts = { drawCount: QuadIndices.length, vertexCount: util_3.QuadPositions.length / 3, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(image.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { aPosition: image.cornerBuffer, aUv: mol_util_1.ValueCell.create(QuadUvs), elements: mol_util_1.ValueCell.create(QuadIndices), 
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ dGeometryType: mol_util_1.ValueCell.create('image') }, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { aPosition: image.cornerBuffer, aUv: mol_util_1.ValueCell.create(QuadUvs), elements: mol_util_1.ValueCell.create(QuadIndices), 
             // aGroup is used as a vertex index here, group id is in tGroupTex
             aGroup: mol_util_1.ValueCell.create((0, array_1.fillSerial)(new Float32Array(4))), boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)), dInterpolation: mol_util_1.ValueCell.create(props.interpolation), uImageTexDim: image.imageTextureDim, tImageTex: image.imageTexture, tGroupTex: image.groupTexture });
     }

package/lib/commonjs/mol-geo/geometry/lines/lines.js

@@ -168,7 +168,7 @@ var Lines;
         var counts = { drawCount: lines.lineCount * 2 * 3, vertexCount: lines.lineCount * 4, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(lines.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aMapping: lines.mappingBuffer, aGroup: lines.groupBuffer, aStart: lines.startBuffer, aEnd: lines.endBuffer, elements: lines.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), dLineSizeAttenuation: mol_util_1.ValueCell.create(props.lineSizeAttenuation), uDoubleSided: mol_util_1.ValueCell.create(true), dFlipSided: mol_util_1.ValueCell.create(false) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ dGeometryType: mol_util_1.ValueCell.create('lines'), aMapping: lines.mappingBuffer, aGroup: lines.groupBuffer, aStart: lines.startBuffer, aEnd: lines.endBuffer, elements: lines.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), dLineSizeAttenuation: mol_util_1.ValueCell.create(props.lineSizeAttenuation), uDoubleSided: mol_util_1.ValueCell.create(true), dFlipSided: mol_util_1.ValueCell.create(false) });
     }
     function createValuesSimple(lines, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);

package/lib/commonjs/mol-geo/geometry/marker-data.js

@@ -38,12 +38,20 @@ function getMarkersAverage(array, count) {
     var viewEnd = (count - 4) >> 2;
     var backStart = 4 * viewEnd;
     var sum = 0;
-    for (var i = 0; i < viewEnd; ++i) {
-        var v = view[i];
-        sum += MarkerCountLut[v & 0xFFFF] + MarkerCountLut[v >> 16];
+    if (viewEnd < 0) {
+        // avoid edge cases with small arrays
+        for (var i = 0; i < count; ++i) {
+            sum += array[i] && 1;
+        }
     }
-    for (var i = backStart; i < count; ++i) {
-        sum += array[i] && 1;
+    else {
+        for (var i = 0; i < viewEnd; ++i) {
+            var v = view[i];
+            sum += MarkerCountLut[v & 0xFFFF] + MarkerCountLut[v >> 16];
+        }
+        for (var i = backStart; i < count; ++i) {
+            sum += array[i] && 1;
+        }
     }
     return sum / count;
 }

package/lib/commonjs/mol-geo/geometry/mesh/mesh.js

@@ -596,7 +596,7 @@ var Mesh;
         var counts = { drawCount: mesh.triangleCount * 3, vertexCount: mesh.vertexCount, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(mesh.boundingSphere);
         var boundingSphere = (0, util_3.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aPosition: mesh.vertexBuffer, aNormal: mesh.normalBuffer, aGroup: mesh.groupBuffer, elements: mesh.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude), meta: mol_util_1.ValueCell.create(mesh.meta) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ dGeometryType: mol_util_1.ValueCell.create('mesh'), aPosition: mesh.vertexBuffer, aNormal: mesh.normalBuffer, aGroup: mesh.groupBuffer, elements: mesh.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude), meta: mol_util_1.ValueCell.create(mesh.meta) });
     }
     function createValuesSimple(mesh, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);

package/lib/commonjs/mol-geo/geometry/points/points.js

@@ -137,7 +137,7 @@ var Points;
         var counts = { drawCount: points.pointCount, vertexCount: points.pointCount, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(points.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aPosition: points.centerBuffer, aGroup: points.groupBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), dPointSizeAttenuation: mol_util_1.ValueCell.create(props.pointSizeAttenuation), dPointStyle: mol_util_1.ValueCell.create(props.pointStyle) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ dGeometryType: mol_util_1.ValueCell.create('points'), aPosition: points.centerBuffer, aGroup: points.groupBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), dPointSizeAttenuation: mol_util_1.ValueCell.create(props.pointSizeAttenuation), dPointStyle: mol_util_1.ValueCell.create(props.pointStyle) });
     }
     function createValuesSimple(points, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);

package/lib/commonjs/mol-geo/geometry/size-data.js

@@ -12,7 +12,7 @@ var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var util_1 = require("../../mol-gl/renderable/util");
 var location_1 = require("../../mol-model/location");
 var geometry_1 = require("./geometry");
-var float_packing_1 = require("../../mol-util/float-packing");
+var number_packing_1 = require("../../mol-util/number-packing");
 function createSizes(locationIt, sizeTheme, sizeData) {
     switch (geometry_1.Geometry.getGranularity(locationIt, sizeTheme.granularity)) {
         case 'uniform': return createUniformSize(locationIt, sizeTheme.size, sizeData);
@@ -34,7 +34,7 @@ function getMaxSize(sizeData) {
             var maxSize = 0;
             var array = sizeData.tSize.ref.value.array;
             for (var i = 0, il = array.length; i < il; i += 3) {
-                var value = (0, float_packing_1.decodeFloatRGB)(array[i], array[i + 1], array[i + 2]);
+                var value = (0, number_packing_1.unpackRGBToInt)(array[i], array[i + 1], array[i + 2]);
                 if (maxSize < value)
                     maxSize = value;
             }
@@ -89,7 +89,7 @@ function createInstanceSize(locationIt, sizeFn, sizeData) {
     locationIt.reset();
     while (locationIt.hasNext && !locationIt.isNextNewInstance) {
         var v = locationIt.move();
-        (0, float_packing_1.encodeFloatRGBtoArray)(sizeFn(v.location) * exports.sizeDataFactor, sizes.array, v.instanceIndex * 3);
+        (0, number_packing_1.packIntToRGBArray)(sizeFn(v.location) * exports.sizeDataFactor, sizes.array, v.instanceIndex * 3);
         locationIt.skipInstance();
     }
     return createTextureSize(sizes, 'instance', sizeData);
@@ -102,7 +102,7 @@ function createGroupSize(locationIt, sizeFn, sizeData) {
     locationIt.reset();
     while (locationIt.hasNext && !locationIt.isNextNewInstance) {
         var v = locationIt.move();
-        (0, float_packing_1.encodeFloatRGBtoArray)(sizeFn(v.location) * exports.sizeDataFactor, sizes.array, v.groupIndex * 3);
+        (0, number_packing_1.packIntToRGBArray)(sizeFn(v.location) * exports.sizeDataFactor, sizes.array, v.groupIndex * 3);
     }
     return createTextureSize(sizes, 'group', sizeData);
 }
@@ -115,7 +115,7 @@ function createGroupInstanceSize(locationIt, sizeFn, sizeData) {
     locationIt.reset();
     while (locationIt.hasNext) {
         var v = locationIt.move();
-        (0, float_packing_1.encodeFloatRGBtoArray)(sizeFn(v.location) * exports.sizeDataFactor, sizes.array, v.index * 3);
+        (0, number_packing_1.packIntToRGBArray)(sizeFn(v.location) * exports.sizeDataFactor, sizes.array, v.index * 3);
     }
     return createTextureSize(sizes, 'groupInstance', sizeData);
 }

package/lib/commonjs/mol-geo/geometry/spheres/spheres.js

@@ -135,7 +135,7 @@ var Spheres;
         var padding = spheres.boundingSphere.radius ? (0, size_data_1.getMaxSize)(size) * props.sizeFactor : 0;
         var invariantBoundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), spheres.boundingSphere, padding);
         var boundingSphere = (0, util_1.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aPosition: spheres.centerBuffer, aMapping: spheres.mappingBuffer, aGroup: spheres.groupBuffer, elements: spheres.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ dGeometryType: mol_util_1.ValueCell.create('spheres'), aPosition: spheres.centerBuffer, aMapping: spheres.mappingBuffer, aGroup: spheres.groupBuffer, elements: spheres.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude) });
     }
     function createValuesSimple(spheres, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);

package/lib/commonjs/mol-geo/geometry/text/text.js

@@ -151,7 +151,7 @@ var Text;
         var padding = getPadding(text.mappingBuffer.ref.value, text.depthBuffer.ref.value, text.charCount, (0, size_data_1.getMaxSize)(size));
         var invariantBoundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), text.boundingSphere, padding);
         var boundingSphere = (0, util_1.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aPosition: text.centerBuffer, aMapping: text.mappingBuffer, aDepth: text.depthBuffer, aGroup: text.groupBuffer, elements: text.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), substance), clipping), transform), { aTexCoord: text.tcoordBuffer, tFont: text.fontTexture, padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), uBorderWidth: mol_util_1.ValueCell.create((0, interpolate_1.clamp)(props.borderWidth, 0, 0.5)), uBorderColor: mol_util_1.ValueCell.create(color_1.Color.toArrayNormalized(props.borderColor, linear_algebra_1.Vec3.zero(), 0)), uOffsetX: mol_util_1.ValueCell.create(props.offsetX), uOffsetY: mol_util_1.ValueCell.create(props.offsetY), uOffsetZ: mol_util_1.ValueCell.create(props.offsetZ), uBackgroundColor: mol_util_1.ValueCell.create(color_1.Color.toArrayNormalized(props.backgroundColor, linear_algebra_1.Vec3.zero(), 0)), uBackgroundOpacity: mol_util_1.ValueCell.create(props.backgroundOpacity) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ dGeometryType: mol_util_1.ValueCell.create('text'), aPosition: text.centerBuffer, aMapping: text.mappingBuffer, aDepth: text.depthBuffer, aGroup: text.groupBuffer, elements: text.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), substance), clipping), transform), { aTexCoord: text.tcoordBuffer, tFont: text.fontTexture, padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), uBorderWidth: mol_util_1.ValueCell.create((0, interpolate_1.clamp)(props.borderWidth, 0, 0.5)), uBorderColor: mol_util_1.ValueCell.create(color_1.Color.toArrayNormalized(props.borderColor, linear_algebra_1.Vec3.zero(), 0)), uOffsetX: mol_util_1.ValueCell.create(props.offsetX), uOffsetY: mol_util_1.ValueCell.create(props.offsetY), uOffsetZ: mol_util_1.ValueCell.create(props.offsetZ), uBackgroundColor: mol_util_1.ValueCell.create(color_1.Color.toArrayNormalized(props.backgroundColor, linear_algebra_1.Vec3.zero(), 0)), uBackgroundOpacity: mol_util_1.ValueCell.create(props.backgroundOpacity) });
     }
     function createValuesSimple(text, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);

package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.js

@@ -113,7 +113,7 @@ var TextureMesh;
         var counts = { drawCount: textureMesh.vertexCount, vertexCount: textureMesh.vertexCount, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(textureMesh.boundingSphere);
         var boundingSphere = (0, util_1.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ uGeoTexDim: textureMesh.geoTextureDim, tPosition: textureMesh.vertexTexture, tGroup: textureMesh.groupTexture, tNormal: textureMesh.normalTexture, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), marker), overpaint), transparency), substance), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude), dGeoTexture: mol_util_1.ValueCell.create(true), meta: mol_util_1.ValueCell.create(textureMesh.meta) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ dGeometryType: mol_util_1.ValueCell.create('textureMesh'), uGeoTexDim: textureMesh.geoTextureDim, tPosition: textureMesh.vertexTexture, tGroup: textureMesh.groupTexture, tNormal: textureMesh.normalTexture, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), marker), overpaint), transparency), substance), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude), meta: mol_util_1.ValueCell.create(textureMesh.meta) });
     }
     function createValuesSimple(textureMesh, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);

package/lib/commonjs/mol-gl/compute/histogram-pyramid/sum.js

@@ -12,7 +12,7 @@ var render_item_1 = require("../../webgl/render-item");
 var schema_1 = require("../../renderable/schema");
 var shader_code_1 = require("../../../mol-gl/shader-code");
 var mol_util_1 = require("../../../mol-util");
-var float_packing_1 = require("../../../mol-util/float-packing");
+var number_packing_1 = require("../../../mol-util/number-packing");
 var util_1 = require("../util");
 var quad_vert_1 = require("../../../mol-gl/shader/quad.vert");
 var sum_frag_1 = require("../../../mol-gl/shader/histogram-pyramid/sum.frag");
@@ -73,7 +73,7 @@ function getHistopyramidSum(ctx, pyramidTopTexture) {
     ctx.unbindFramebuffer();
     return (0, compat_1.isWebGL2)(gl)
         ? sumInts[0]
-        : (0, float_packing_1.decodeFloatRGB)(sumBytes[0], sumBytes[1], sumBytes[2]);
+        : (0, number_packing_1.unpackRGBToInt)(sumBytes[0], sumBytes[1], sumBytes[2]);
 }
 exports.getHistopyramidSum = getHistopyramidSum;
 //# sourceMappingURL=sum.js.map

package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.d.ts

@@ -7,7 +7,7 @@ import { WebGLContext } from '../../webgl/context';
 import { Texture } from '../../../mol-gl/webgl/texture';
 import { Vec3, Vec2, Mat4 } from '../../../mol-math/linear-algebra';
 import { HistogramPyramid } from '../histogram-pyramid/reduction';
-export declare function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Texture, volumeData: Texture, histogramPyramid: HistogramPyramid, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture): {
+export declare function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Texture, volumeData: Texture, histogramPyramid: HistogramPyramid, gridDim: Vec3, gridTexDim: Vec3, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, axisOrder: Vec3, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture): {
     vertexTexture: Texture;
     groupTexture: Texture;
     normalTexture: Texture;
@@ -22,7 +22,7 @@ export declare function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsB
  *
  * Implementation based on http://www.miaumiau.cat/2016/10/stream-compaction-in-webgl/
  */
-export declare function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture): {
+export declare function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, invert: boolean, packedGroup: boolean, axisOrder: Vec3, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture): {
     vertexTexture: Texture;
     groupTexture: Texture;
     normalTexture: Texture;

package/lib/commonjs/mol-gl/compute/marching-cubes/isosurface.js

@@ -19,9 +19,9 @@ var quad_vert_1 = require("../../../mol-gl/shader/quad.vert");
 var isosurface_frag_1 = require("../../../mol-gl/shader/marching-cubes/isosurface.frag");
 var active_voxels_1 = require("./active-voxels");
 var compat_1 = require("../../webgl/compat");
-var IsosurfaceSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tTriIndices: (0, schema_1.TextureSpec)('image-uint8', 'alpha', 'ubyte', 'nearest'), tActiveVoxelsPyramid: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest'), tActiveVoxelsBase: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest'), tVolumeData: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uIsoValue: (0, schema_1.UniformSpec)('f'), uSize: (0, schema_1.UniformSpec)('f'), uLevels: (0, schema_1.UniformSpec)('f'), uCount: (0, schema_1.UniformSpec)('f'), uInvert: (0, schema_1.UniformSpec)('b'), uGridDim: (0, schema_1.UniformSpec)('v3'), uGridTexDim: (0, schema_1.UniformSpec)('v3'), uGridTransform: (0, schema_1.UniformSpec)('m4'), uScale: (0, schema_1.UniformSpec)('v2'), dPackedGroup: (0, schema_1.DefineSpec)('boolean') });
+var IsosurfaceSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tTriIndices: (0, schema_1.TextureSpec)('image-uint8', 'alpha', 'ubyte', 'nearest'), tActiveVoxelsPyramid: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest'), tActiveVoxelsBase: (0, schema_1.TextureSpec)('texture', 'rgba', 'float', 'nearest'), tVolumeData: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uIsoValue: (0, schema_1.UniformSpec)('f'), uSize: (0, schema_1.UniformSpec)('f'), uLevels: (0, schema_1.UniformSpec)('f'), uCount: (0, schema_1.UniformSpec)('f'), uInvert: (0, schema_1.UniformSpec)('b'), uGridDim: (0, schema_1.UniformSpec)('v3'), uGridTexDim: (0, schema_1.UniformSpec)('v3'), uGridTransform: (0, schema_1.UniformSpec)('m4'), uScale: (0, schema_1.UniformSpec)('v2'), dPackedGroup: (0, schema_1.DefineSpec)('boolean'), dAxisOrder: (0, schema_1.DefineSpec)('string', ['012', '021', '102', '120', '201', '210']) });
 var IsosurfaceName = 'isosurface';
-function getIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup) {
+function getIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup, axisOrder) {
     if (ctx.namedComputeRenderables[IsosurfaceName]) {
         var v = ctx.namedComputeRenderables[IsosurfaceName].values;
         mol_util_1.ValueCell.update(v.tActiveVoxelsPyramid, activeVoxelsPyramid);
@@ -37,16 +37,17 @@ function getIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, vol
         mol_util_1.ValueCell.update(v.uGridTransform, transform);
         mol_util_1.ValueCell.update(v.uScale, scale);
         mol_util_1.ValueCell.update(v.dPackedGroup, packedGroup);
+        mol_util_1.ValueCell.updateIfChanged(v.dAxisOrder, axisOrder.join(''));
         ctx.namedComputeRenderables[IsosurfaceName].update();
     }
     else {
-        ctx.namedComputeRenderables[IsosurfaceName] = createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup);
+        ctx.namedComputeRenderables[IsosurfaceName] = createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup, axisOrder);
     }
     return ctx.namedComputeRenderables[IsosurfaceName];
 }
-function createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup) {
+function createIsosurfaceRenderable(ctx, activeVoxelsPyramid, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup, axisOrder) {
     // console.log('uSize', Math.pow(2, levels))
-    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tTriIndices: mol_util_1.ValueCell.create((0, tables_1.getTriIndices)()), tActiveVoxelsPyramid: mol_util_1.ValueCell.create(activeVoxelsPyramid), tActiveVoxelsBase: mol_util_1.ValueCell.create(activeVoxelsBase), tVolumeData: mol_util_1.ValueCell.create(volumeData), uIsoValue: mol_util_1.ValueCell.create(isoValue), uSize: mol_util_1.ValueCell.create(Math.pow(2, levels)), uLevels: mol_util_1.ValueCell.create(levels), uCount: mol_util_1.ValueCell.create(count), uInvert: mol_util_1.ValueCell.create(invert), uGridDim: mol_util_1.ValueCell.create(gridDim), uGridTexDim: mol_util_1.ValueCell.create(gridTexDim), uGridTransform: mol_util_1.ValueCell.create(transform), uScale: mol_util_1.ValueCell.create(scale), dPackedGroup: mol_util_1.ValueCell.create(packedGroup) });
+    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tTriIndices: mol_util_1.ValueCell.create((0, tables_1.getTriIndices)()), tActiveVoxelsPyramid: mol_util_1.ValueCell.create(activeVoxelsPyramid), tActiveVoxelsBase: mol_util_1.ValueCell.create(activeVoxelsBase), tVolumeData: mol_util_1.ValueCell.create(volumeData), uIsoValue: mol_util_1.ValueCell.create(isoValue), uSize: mol_util_1.ValueCell.create(Math.pow(2, levels)), uLevels: mol_util_1.ValueCell.create(levels), uCount: mol_util_1.ValueCell.create(count), uInvert: mol_util_1.ValueCell.create(invert), uGridDim: mol_util_1.ValueCell.create(gridDim), uGridTexDim: mol_util_1.ValueCell.create(gridTexDim), uGridTransform: mol_util_1.ValueCell.create(transform), uScale: mol_util_1.ValueCell.create(scale), dPackedGroup: mol_util_1.ValueCell.create(packedGroup), dAxisOrder: mol_util_1.ValueCell.create(axisOrder.join('')) });
     var schema = (0, tslib_1.__assign)({}, IsosurfaceSchema);
     var shaderCode = (0, shader_code_1.ShaderCode)('isosurface', quad_vert_1.quad_vert, isosurface_frag_1.isosurface_frag, { drawBuffers: 'required' });
     var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', shaderCode, schema, values);
@@ -62,7 +63,7 @@ function setRenderingDefaults(ctx) {
     state.colorMask(true, true, true, true);
     state.clearColor(0, 0, 0, 0);
 }
-function createIsosurfaceBuffers(ctx, activeVoxelsBase, volumeData, histogramPyramid, gridDim, gridTexDim, transform, isoValue, invert, packedGroup, vertexTexture, groupTexture, normalTexture) {
+function createIsosurfaceBuffers(ctx, activeVoxelsBase, volumeData, histogramPyramid, gridDim, gridTexDim, transform, isoValue, invert, packedGroup, axisOrder, vertexTexture, groupTexture, normalTexture) {
     var drawBuffers = ctx.extensions.drawBuffers;
     if (!drawBuffers)
         throw new Error('need WebGL draw buffers');
@@ -110,7 +111,7 @@ function createIsosurfaceBuffers(ctx, activeVoxelsBase, volumeData, histogramPyr
     vertexTexture.attachFramebuffer(framebuffer, 0);
     groupTexture.attachFramebuffer(framebuffer, 1);
     normalTexture.attachFramebuffer(framebuffer, 2);
-    var renderable = getIsosurfaceRenderable(ctx, pyramidTex, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup);
+    var renderable = getIsosurfaceRenderable(ctx, pyramidTex, activeVoxelsBase, volumeData, gridDim, gridTexDim, transform, isoValue, levels, scale, count, invert, packedGroup, axisOrder);
     ctx.state.currentRenderItemId = -1;
     framebuffer.bind();
     drawBuffers.drawBuffers([
@@ -136,7 +137,7 @@ exports.createIsosurfaceBuffers = createIsosurfaceBuffers;
  *
  * Implementation based on http://www.miaumiau.cat/2016/10/stream-compaction-in-webgl/
  */
-function extractIsosurface(ctx, volumeData, gridDim, gridTexDim, gridTexScale, transform, isoValue, invert, packedGroup, vertexTexture, groupTexture, normalTexture) {
+function extractIsosurface(ctx, volumeData, gridDim, gridTexDim, gridTexScale, transform, isoValue, invert, packedGroup, axisOrder, vertexTexture, groupTexture, normalTexture) {
     // console.time('calcActiveVoxels');
     var activeVoxelsTex = (0, active_voxels_1.calcActiveVoxels)(ctx, volumeData, gridDim, gridTexDim, isoValue, gridTexScale);
     // ctx.waitForGpuCommandsCompleteSync();
@@ -146,7 +147,7 @@ function extractIsosurface(ctx, volumeData, gridDim, gridTexDim, gridTexScale, t
     // ctx.waitForGpuCommandsCompleteSync();
     // console.timeEnd('createHistogramPyramid');
     // console.time('createIsosurfaceBuffers');
-    var gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, invert, packedGroup, vertexTexture, groupTexture, normalTexture);
+    var gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, invert, packedGroup, axisOrder, vertexTexture, groupTexture, normalTexture);
     // ctx.waitForGpuCommandsCompleteSync();
     // console.timeEnd('createIsosurfaceBuffers');
     return gv;

package/lib/commonjs/mol-gl/renderable/cylinders.d.ts

@@ -92,6 +92,7 @@ export declare const CylindersSchema: {
     tColorGrid: import("./schema").TextureSpec<"texture">;
     dColorType: DefineSpec<"string">;
     dUsePalette: DefineSpec<"boolean">;
+    dGeometryType: DefineSpec<"string">;
 };
 export declare type CylindersSchema = typeof CylindersSchema;
 export declare type CylindersValues = Values<CylindersSchema>;