molstar 2.3.7 → 2.4.1

package/lib/commonjs/extensions/geo-export/controls.js

@@ -42,7 +42,7 @@ var GeometryControls = /** @class */ (function (_super) {
         var uniqueIds = new Set();
         models.forEach(function (m) { return uniqueIds.add(m.entryId.toUpperCase()); });
         var idString = set_1.SetUtils.toArray(uniqueIds).join('-');
-        return "" + (idString || 'molstar-model');
+        return "".concat(idString || 'molstar-model');
     };
     GeometryControls.prototype.exportGeometry = function () {
         var _this = this;
@@ -78,7 +78,7 @@ var GeometryControls = /** @class */ (function (_super) {
                         _e.label = 1;
                     case 1:
                         if (!(i < il)) return [3 /*break*/, 5];
-                        return [4 /*yield*/, ctx.update({ message: "Exporting object " + i + "/" + il })];
+                        return [4 /*yield*/, ctx.update({ message: "Exporting object ".concat(i, "/").concat(il) })];
                     case 2:
                         _e.sent();
                         return [4 /*yield*/, renderObjectExporter.add(renderObjects[i], (_d = this.plugin.canvas3d) === null || _d === void 0 ? void 0 : _d.webgl, ctx)];
@@ -97,7 +97,7 @@ var GeometryControls = /** @class */ (function (_super) {
                             }];
                     case 7:
                         e_1 = _e.sent();
-                        this.plugin.log.error('' + e_1);
+                        this.plugin.log.error('Error during geometry export');
                         throw e_1;
                     case 8: return [2 /*return*/];
                 }

package/lib/commonjs/extensions/geo-export/controls.js.map

@@ -1 +1 @@
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+{"version":3,"file":"controls.js","sourceRoot":"","sources":["../../../../src/extensions/geo-export/controls.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;;AAEH,kDAAiD;AACjD,oDAAgD;AAChD,8DAAmE;AAEnE,2CAAsC;AACtC,0DAAmE;AACnE,6CAAiD;AACjD,oEAAwE;AACxE,0CAA8C;AAC9C,+CAA6C;AAC7C,+CAA6C;AAC7C,+CAA6C;AAC7C,iDAA+C;AAElC,QAAA,cAAc,GAAG;IAC1B,MAAM,EAAE,kCAAE,CAAC,MAAM,CAAC,KAAK,EAAE;QACrB,CAAC,KAAK,EAAE,wBAAwB,CAAC;QACjC,CAAC,KAAK,EAAE,YAAY,CAAC;QACrB,CAAC,KAAK,EAAE,kBAAkB,CAAC;QAC3B,CAAC,MAAM,EAAE,qCAAqC,CAAC;KAClD,CAAC;CACL,CAAC;AAEF;IAAsC,iDAAe;IA0DjD,0BAAoB,MAAqB;QAAzC,YACI,iBAAO,SACV;QAFmB,YAAM,GAAN,MAAM,CAAe;QAzDhC,eAAS,GAAG;YACjB,MAAM,EAAE,KAAI,CAAC,EAAE,CAAC,QAAQ,CAAmC,kCAAE,CAAC,gBAAgB,CAAC,sBAAc,CAAC,CAAC;SAClG,CAAA;;IAyDD,CAAC;IAvDO,sCAAW,GAAnB;QACI,IAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,0BAAc,CAAC,UAAU,CAAC,WAAW,CAAC,2BAAiB,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,GAAI,CAAC,IAAI,EAAX,CAAW,CAAC,CAAC;QAC5I,IAAM,SAAS,GAAG,IAAI,GAAG,EAAU,CAAC;QACpC,MAAM,CAAC,OAAO,CAAC,UAAA,CAAC,IAAI,OAAA,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,EAAtC,CAAsC,CAAC,CAAC;QAC5D,IAAM,QAAQ,GAAG,cAAQ,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QACvD,OAAO,UAAG,QAAQ,IAAI,eAAe,CAAE,CAAC;IAC5C,CAAC;IAED,yCAAc,GAAd;QAAA,iBA2CC;QA1CG,IAAM,IAAI,GAAG,eAAI,CAAC,MAAM,CAAC,iBAAiB,EAAE,UAAM,GAAG;;;;;;;wBAEvC,aAAa,GAAG,MAAA,IAAI,CAAC,MAAM,CAAC,QAAQ,0CAAE,gBAAgB,EAAG,CAAC;wBAC1D,QAAQ,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;wBAE9B,KAAK,GAAG,IAAA,mBAAQ,EAAC,MAAA,IAAI,CAAC,MAAM,CAAC,QAAQ,0CAAE,KAAK,CAAC,QAAQ,CAAC,KAAM,CAAC,CAAC;wBAC9D,cAAc,GAAG,MAAA,IAAI,CAAC,MAAM,CAAC,QAAQ,0CAAE,qBAAsB,CAAC;wBAC9D,WAAW,GAAG,gBAAK,CAAC,YAAY,CAAC,IAAA,gBAAK,GAAE,EAAE,cAAc,CAAC,CAAC;wBAC5D,oBAAoB,SAAwD,CAAC;wBACjF,QAAQ,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE;4BACxC,KAAK,KAAK;gCACN,oBAAoB,GAAG,IAAI,0BAAW,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC;gCAC3D,MAAM;4BACV,KAAK,KAAK;gCACN,oBAAoB,GAAG,IAAI,0BAAW,CAAC,QAAQ,EAAE,WAAW,CAAC,CAAC;gCAC9D,MAAM;4BACV,KAAK,KAAK;gCACN,oBAAoB,GAAG,IAAI,0BAAW,CAAC,WAAW,CAAC,CAAC;gCACpD,MAAM;4BACV,KAAK,MAAM;gCACP,oBAAoB,GAAG,IAAI,4BAAY,CAAC,KAAK,EAAE,WAAW,EAAE,cAAc,CAAC,MAAM,CAAC,CAAC;gCACnF,MAAM;4BACV,OAAO,CAAC,CAAC,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;yBACnD;wBAEQ,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM;;;6BAAE,CAAA,CAAC,GAAG,EAAE,CAAA;wBAC7C,qBAAM,GAAG,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,2BAAoB,CAAC,cAAI,EAAE,CAAE,EAAE,CAAC,EAAA;;wBAA5D,SAA4D,CAAC;wBAC7D,qBAAM,oBAAoB,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,MAAA,IAAI,CAAC,MAAM,CAAC,QAAQ,0CAAE,KAAM,EAAE,GAAG,CAAC,EAAA;;wBAAnF,SAAmF,CAAC;;;wBAFrC,EAAE,CAAC,CAAA;;4BAKzC,qBAAM,oBAAoB,CAAC,OAAO,CAAC,GAAG,CAAC,EAAA;;wBAA9C,IAAI,GAAG,SAAuC;wBACpD,sBAAO;gCACH,IAAI,MAAA;gCACJ,QAAQ,EAAE,QAAQ,GAAG,GAAG,GAAG,oBAAoB,CAAC,aAAa;6BAChE,EAAC;;;wBAEF,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,8BAA8B,CAAC,CAAC;wBACtD,MAAM,GAAC,CAAC;;;;aAEf,CAAC,CAAC;QAEH,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC;IAC3D,CAAC;IAKL,uBAAC;AAAD,CAAC,AA7DD,CAAsC,2BAAe,GA6DpD;AA7DY,4CAAgB"}

package/lib/commonjs/extensions/geo-export/glb-exporter.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Style } from '../../mol-gl/renderer';
 import { Box3D } from '../../mol-math/geometry';

package/lib/commonjs/extensions/geo-export/glb-exporter.js

@@ -3,6 +3,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.GlbExporter = void 0;
@@ -24,6 +25,11 @@ var UNSIGNED_INT = 5125;
 var FLOAT = 5126;
 var ARRAY_BUFFER = 34962;
 var ELEMENT_ARRAY_BUFFER = 34963;
+var GLTF_MAGIC_BYTE = 0x46546C67;
+var JSON_CHUNK_TYPE = 0x4E4F534A;
+var BIN_CHUNK_TYPE = 0x004E4942;
+var JSON_PAD_CHAR = 0x20;
+var BIN_PAD_CHAR = 0x00;
 var GlbExporter = /** @class */ (function (_super) {
     (0, tslib_1.__extends)(GlbExporter, _super);
     function GlbExporter(style, boundingBox) {
@@ -113,20 +119,14 @@ var GlbExporter = /** @class */ (function (_super) {
             indexAccessorIndex: isGeoTexture ? undefined : this.addBuffer(indexBuffer, UNSIGNED_INT, 'SCALAR', drawCount, ELEMENT_ARRAY_BUFFER)
         };
     };
-    GlbExporter.prototype.addColorBuffer = function (values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors) {
-        var groupCount = values.uGroupCount.ref.value;
+    GlbExporter.prototype.addColorBuffer = function (geoData, interpolatedColors, interpolatedOverpaint, interpolatedTransparency) {
+        var values = geoData.values, vertexCount = geoData.vertexCount;
         var uAlpha = values.uAlpha.ref.value;
-        var dTransparency = values.dTransparency.ref.value;
-        var tTransparency = values.tTransparency.ref.value;
         var colorArray = new Uint8Array(vertexCount * 4);
         for (var i = 0; i < vertexCount; ++i) {
-            var color = GlbExporter.getColor(values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors, i);
-            var alpha = uAlpha;
-            if (dTransparency) {
-                var group = isGeoTexture ? GlbExporter.getGroup(groups, i) : groups[i];
-                var transparency = tTransparency.array[instanceIndex * groupCount + group] / 255;
-                alpha *= 1 - transparency;
-            }
+            var color = GlbExporter.getColor(i, geoData, interpolatedColors, interpolatedOverpaint);
+            var transparency = GlbExporter.getTransparency(i, geoData, interpolatedTransparency);
+            var alpha = uAlpha * (1 - transparency);
             color = color_1.Color.sRGBToLinear(color);
             color_1.Color.toArray(color, colorArray, i * 4);
             colorArray[i * 4 + 3] = Math.round(alpha * 255);
@@ -139,19 +139,29 @@ var GlbExporter = /** @class */ (function (_super) {
     };
     GlbExporter.prototype.addMeshWithColors = function (input) {
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var mesh, values, isGeoTexture, webgl, ctx, t, colorType, dTransparency, aTransform, instanceCount, interpolatedColors, stride, sameGeometryBuffers, sameColorBuffer, vertexAccessorIndex, normalAccessorIndex, indexAccessorIndex, colorAccessorIndex, meshIndex, instanceIndex, _a, vertices, normals, indices, groups, vertexCount, drawCount, accessorIndices, node;
+            var mesh, values, isGeoTexture, webgl, ctx, t, colorType, overpaintType, transparencyType, dTransparency, aTransform, instanceCount, interpolatedColors, stride, interpolatedOverpaint, stride, interpolatedTransparency, stride, sameGeometryBuffers, sameColorBuffer, vertexAccessorIndex, normalAccessorIndex, indexAccessorIndex, colorAccessorIndex, meshIndex, instanceIndex, _a, vertices, normals, indices, groups, vertexCount, drawCount, accessorIndices, node;
             return (0, tslib_1.__generator)(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         mesh = input.mesh, values = input.values, isGeoTexture = input.isGeoTexture, webgl = input.webgl, ctx = input.ctx;
                         t = (0, linear_algebra_1.Mat4)();
                         colorType = values.dColorType.ref.value;
+                        overpaintType = values.dOverpaintType.ref.value;
+                        transparencyType = values.dTransparencyType.ref.value;
                         dTransparency = values.dTransparency.ref.value;
                         aTransform = values.aTransform.ref.value;
                         instanceCount = values.uInstanceCount.ref.value;
                         if (colorType === 'volume' || colorType === 'volumeInstance') {
                             stride = isGeoTexture ? 4 : 3;
-                            interpolatedColors = GlbExporter.getInterpolatedColors(mesh.vertices, mesh.vertexCount, values, stride, colorType, webgl);
+                            interpolatedColors = GlbExporter.getInterpolatedColors(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride, colorType: colorType });
+                        }
+                        if (overpaintType === 'volumeInstance') {
+                            stride = isGeoTexture ? 4 : 3;
+                            interpolatedOverpaint = GlbExporter.getInterpolatedOverpaint(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride, colorType: overpaintType });
+                        }
+                        if (transparencyType === 'volumeInstance') {
+                            stride = isGeoTexture ? 4 : 3;
+                            interpolatedTransparency = GlbExporter.getInterpolatedTransparency(webgl, { vertices: mesh.vertices, vertexCount: mesh.vertexCount, values: values, stride: stride, colorType: transparencyType });
                         }
                         sameGeometryBuffers = mesh !== undefined;
                         sameColorBuffer = sameGeometryBuffers && colorType !== 'instance' && !colorType.endsWith('Instance') && !dTransparency;
@@ -180,7 +190,7 @@ var GlbExporter = /** @class */ (function (_super) {
                             }
                             // create a color buffer if needed
                             if (instanceIndex === 0 || !sameColorBuffer) {
-                                colorAccessorIndex = this.addColorBuffer(values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors);
+                                colorAccessorIndex = this.addColorBuffer({ values: values, groups: groups, vertexCount: vertexCount, instanceIndex: instanceIndex, isGeoTexture: isGeoTexture }, interpolatedColors, interpolatedOverpaint, interpolatedTransparency);
                             }
                             // glTF mesh
                             meshIndex = this.meshes.length;
@@ -221,7 +231,7 @@ var GlbExporter = /** @class */ (function (_super) {
                 gltf = {
                     asset: {
                         version: '2.0',
-                        generator: "Mol* " + version_1.PLUGIN_VERSION
+                        generator: "Mol* ".concat(version_1.PLUGIN_VERSION)
                     },
                     scenes: [{
                             nodes: (0, array_1.fillSerial)(new Array(this.nodes.length))
@@ -262,12 +272,12 @@ var GlbExporter = /** @class */ (function (_super) {
                 jsonString = JSON.stringify(gltf);
                 jsonBuffer = new Uint8Array(jsonString.length);
                 (0, ascii_1.asciiWrite)(jsonBuffer, jsonString);
-                _a = createChunk(0x4E4F534A, [jsonBuffer.buffer], jsonBuffer.length, 0x20), jsonChunk = _a[0], jsonChunkLength = _a[1];
-                _b = createChunk(0x004E4942, this.binaryBuffer, binaryBufferLength, 0x00), binaryChunk = _b[0], binaryChunkLength = _b[1];
+                _a = createChunk(JSON_CHUNK_TYPE, [jsonBuffer.buffer], jsonBuffer.length, JSON_PAD_CHAR), jsonChunk = _a[0], jsonChunkLength = _a[1];
+                _b = createChunk(BIN_CHUNK_TYPE, this.binaryBuffer, binaryBufferLength, BIN_PAD_CHAR), binaryChunk = _b[0], binaryChunkLength = _b[1];
                 glbBufferLength = 12 + jsonChunkLength + binaryChunkLength;
                 header = new ArrayBuffer(12);
                 headerDataView = new DataView(header);
-                headerDataView.setUint32(0, 0x46546C67, true); // magic number "glTF"
+                headerDataView.setUint32(0, GLTF_MAGIC_BYTE, true); // magic number "glTF"
                 headerDataView.setUint32(4, 2, true); // version
                 headerDataView.setUint32(8, glbBufferLength, true); // length
                 glbBuffer = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([header], jsonChunk, true), binaryChunk, true);

package/lib/commonjs/extensions/geo-export/glb-exporter.js.map

@@ -1 +1 @@
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package/lib/commonjs/extensions/geo-export/mesh-exporter.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { GraphicsRenderObject } from '../../mol-gl/render-object';
 import { BaseValues } from '../../mol-gl/renderable/schema';
@@ -25,12 +26,39 @@ export interface AddMeshInput {
     webgl: WebGLContext | undefined;
     ctx: RuntimeContext;
 }
+export declare type MeshGeoData = {
+    values: BaseValues;
+    groups: Float32Array | Uint8Array;
+    vertexCount: number;
+    instanceIndex: number;
+    isGeoTexture: boolean;
+};
 export declare abstract class MeshExporter<D extends RenderObjectExportData> implements RenderObjectExporter<D> {
     abstract readonly fileExtension: string;
     private static getSizeFromTexture;
     private static getSize;
     protected static getGroup(groups: Float32Array | Uint8Array, i: number): number;
-    protected static getInterpolatedColors(vertices: Float32Array, vertexCount: number, values: BaseValues, stride: number, colorType: 'volume' | 'volumeInstance', webgl: WebGLContext): Uint8Array;
+    protected static getInterpolatedColors(webgl: WebGLContext, input: {
+        vertices: Float32Array;
+        vertexCount: number;
+        values: BaseValues;
+        stride: 3 | 4;
+        colorType: 'volume' | 'volumeInstance';
+    }): Uint8Array;
+    protected static getInterpolatedOverpaint(webgl: WebGLContext, input: {
+        vertices: Float32Array;
+        vertexCount: number;
+        values: BaseValues;
+        stride: 3 | 4;
+        colorType: 'volumeInstance';
+    }): Uint8Array;
+    protected static getInterpolatedTransparency(webgl: WebGLContext, input: {
+        vertices: Float32Array;
+        vertexCount: number;
+        values: BaseValues;
+        stride: 3 | 4;
+        colorType: 'volumeInstance';
+    }): Uint8Array;
     protected static quantizeColors(colorArray: Uint8Array, vertexCount: number): void;
     protected static getInstance(input: AddMeshInput, instanceIndex: number): {
         vertices: Float32Array;
@@ -40,7 +68,8 @@ export declare abstract class MeshExporter<D extends RenderObjectExportData> imp
         vertexCount: number;
         drawCount: number;
     };
-    protected static getColor(values: BaseValues, groups: Float32Array | Uint8Array, vertexCount: number, instanceIndex: number, isGeoTexture: boolean, interpolatedColors: Uint8Array | undefined, vertexIndex: number): Color;
+    protected static getColor(vertexIndex: number, geoData: MeshGeoData, interpolatedColors?: Uint8Array, interpolatedOverpaint?: Uint8Array): Color;
+    protected static getTransparency(vertexIndex: number, geoData: MeshGeoData, interpolatedTransparency?: Uint8Array): number;
     protected abstract addMeshWithColors(input: AddMeshInput): void;
     private addMesh;
     private addLines;

package/lib/commonjs/extensions/geo-export/mesh-exporter.js

@@ -3,6 +3,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MeshExporter = void 0;
@@ -17,6 +18,7 @@ var size_data_1 = require("../../mol-geo/geometry/size-data");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var color_1 = require("../../mol-util/color/color");
 var float_packing_1 = require("../../mol-util/float-packing");
+var util_2 = require("../../mol-gl/compute/util");
 var GeoExportName = 'geo-export';
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 var v3fromArray = linear_algebra_1.Vec3.fromArray;
@@ -59,22 +61,37 @@ var MeshExporter = /** @class */ (function () {
         }
         return (0, float_packing_1.decodeFloatRGB)(r, g, b);
     };
-    MeshExporter.getInterpolatedColors = function (vertices, vertexCount, values, stride, colorType, webgl) {
+    MeshExporter.getInterpolatedColors = function (webgl, input) {
+        var values = input.values, vertexCount = input.vertexCount, vertices = input.vertices, colorType = input.colorType, stride = input.stride;
         var colorGridTransform = values.uColorGridTransform.ref.value;
         var colorGridDim = values.uColorGridDim.ref.value;
         var colorTexDim = values.uColorTexDim.ref.value;
         var aTransform = values.aTransform.ref.value;
         var instanceCount = values.uInstanceCount.ref.value;
-        if (!webgl.namedFramebuffers[GeoExportName]) {
-            webgl.namedFramebuffers[GeoExportName] = webgl.resources.framebuffer();
-        }
-        var framebuffer = webgl.namedFramebuffers[GeoExportName];
-        var width = colorTexDim[0], height = colorTexDim[1];
-        var colorGrid = new Uint8Array(width * height * 4);
-        framebuffer.bind();
-        values.tColorGrid.ref.value.attachFramebuffer(framebuffer, 0);
-        webgl.readPixels(0, 0, width, height, colorGrid);
-        var interpolated = (0, color_smoothing_1.getTrilinearlyInterpolated)({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: aTransform, positionBuffer: vertices, colorType: colorType, grid: colorGrid, gridDim: colorGridDim, gridTexDim: colorTexDim, gridTransform: colorGridTransform, vertexStride: stride, colorStride: 4 });
+        var colorGrid = (0, util_2.readTexture)(webgl, values.tColorGrid.ref.value).array;
+        var interpolated = (0, color_smoothing_1.getTrilinearlyInterpolated)({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: aTransform, positionBuffer: vertices, colorType: colorType, grid: colorGrid, gridDim: colorGridDim, gridTexDim: colorTexDim, gridTransform: colorGridTransform, vertexStride: stride, colorStride: 4, outputStride: 3 });
+        return interpolated.array;
+    };
+    MeshExporter.getInterpolatedOverpaint = function (webgl, input) {
+        var values = input.values, vertexCount = input.vertexCount, vertices = input.vertices, colorType = input.colorType, stride = input.stride;
+        var overpaintGridTransform = values.uOverpaintGridTransform.ref.value;
+        var overpaintGridDim = values.uOverpaintGridDim.ref.value;
+        var overpaintTexDim = values.uOverpaintTexDim.ref.value;
+        var aTransform = values.aTransform.ref.value;
+        var instanceCount = values.uInstanceCount.ref.value;
+        var overpaintGrid = (0, util_2.readTexture)(webgl, values.tOverpaintGrid.ref.value).array;
+        var interpolated = (0, color_smoothing_1.getTrilinearlyInterpolated)({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: aTransform, positionBuffer: vertices, colorType: colorType, grid: overpaintGrid, gridDim: overpaintGridDim, gridTexDim: overpaintTexDim, gridTransform: overpaintGridTransform, vertexStride: stride, colorStride: 4, outputStride: 4 });
+        return interpolated.array;
+    };
+    MeshExporter.getInterpolatedTransparency = function (webgl, input) {
+        var values = input.values, vertexCount = input.vertexCount, vertices = input.vertices, colorType = input.colorType, stride = input.stride;
+        var transparencyGridTransform = values.uTransparencyGridTransform.ref.value;
+        var transparencyGridDim = values.uTransparencyGridDim.ref.value;
+        var transparencyTexDim = values.uTransparencyTexDim.ref.value;
+        var aTransform = values.aTransform.ref.value;
+        var instanceCount = values.uInstanceCount.ref.value;
+        var transparencyGrid = (0, util_2.readAlphaTexture)(webgl, values.tTransparencyGrid.ref.value).array;
+        var interpolated = (0, color_smoothing_1.getTrilinearlyInterpolated)({ vertexCount: vertexCount, instanceCount: instanceCount, transformBuffer: aTransform, positionBuffer: vertices, colorType: colorType, grid: transparencyGrid, gridDim: transparencyGridDim, gridTexDim: transparencyTexDim, gridTransform: transparencyGridTransform, vertexStride: stride, colorStride: 4, outputStride: 1, itemOffset: 3 });
         return interpolated.array;
     };
     MeshExporter.quantizeColors = function (colorArray, vertexCount) {
@@ -156,11 +173,13 @@ var MeshExporter = /** @class */ (function () {
             };
         }
     };
-    MeshExporter.getColor = function (values, groups, vertexCount, instanceIndex, isGeoTexture, interpolatedColors, vertexIndex) {
+    MeshExporter.getColor = function (vertexIndex, geoData, interpolatedColors, interpolatedOverpaint) {
+        var values = geoData.values, instanceIndex = geoData.instanceIndex, isGeoTexture = geoData.isGeoTexture, groups = geoData.groups, vertexCount = geoData.vertexCount;
         var groupCount = values.uGroupCount.ref.value;
         var colorType = values.dColorType.ref.value;
         var uColor = values.uColor.ref.value;
         var tColor = values.tColor.ref.value.array;
+        var overpaintType = values.dOverpaintType.ref.value;
         var dOverpaint = values.dOverpaint.ref.value;
         var tOverpaint = values.tOverpaint.ref.value.array;
         var color;
@@ -196,13 +215,66 @@ var MeshExporter = /** @class */ (function () {
             default: throw new Error('Unsupported color type.');
         }
         if (dOverpaint) {
-            var group = isGeoTexture ? MeshExporter.getGroup(groups, vertexIndex) : groups[vertexIndex];
-            var overpaintColor = color_1.Color.fromArray(tOverpaint, (instanceIndex * groupCount + group) * 4);
-            var overpaintAlpha = tOverpaint[(instanceIndex * groupCount + group) * 4 + 3] / 255;
+            var overpaintColor = void 0;
+            var overpaintAlpha = void 0;
+            switch (overpaintType) {
+                case 'groupInstance': {
+                    var group = isGeoTexture ? MeshExporter.getGroup(groups, vertexIndex) : groups[vertexIndex];
+                    var idx = (instanceIndex * groupCount + group) * 4;
+                    overpaintColor = color_1.Color.fromArray(tOverpaint, idx);
+                    overpaintAlpha = tOverpaint[idx + 3] / 255;
+                    break;
+                }
+                case 'vertexInstance': {
+                    var idx = (instanceIndex * vertexCount + vertexIndex) * 4;
+                    overpaintColor = color_1.Color.fromArray(tOverpaint, idx);
+                    overpaintAlpha = tOverpaint[idx + 3] / 255;
+                    break;
+                }
+                case 'volumeInstance': {
+                    var idx = (instanceIndex * vertexCount + vertexIndex) * 4;
+                    overpaintColor = color_1.Color.fromArray(interpolatedOverpaint, idx);
+                    overpaintAlpha = interpolatedOverpaint[idx + 3] / 255;
+                    break;
+                }
+                default: throw new Error('Unsupported overpaint type.');
+            }
+            // interpolate twice to avoid darkening due to empty overpaint
+            overpaintColor = color_1.Color.interpolate(color, overpaintColor, overpaintAlpha);
             color = color_1.Color.interpolate(color, overpaintColor, overpaintAlpha);
         }
         return color;
     };
+    MeshExporter.getTransparency = function (vertexIndex, geoData, interpolatedTransparency) {
+        var values = geoData.values, instanceIndex = geoData.instanceIndex, isGeoTexture = geoData.isGeoTexture, groups = geoData.groups, vertexCount = geoData.vertexCount;
+        var groupCount = values.uGroupCount.ref.value;
+        var dTransparency = values.dTransparency.ref.value;
+        var tTransparency = values.tTransparency.ref.value.array;
+        var transparencyType = values.dTransparencyType.ref.value;
+        var transparency = 0;
+        if (dTransparency) {
+            switch (transparencyType) {
+                case 'groupInstance': {
+                    var group = isGeoTexture ? MeshExporter.getGroup(groups, vertexIndex) : groups[vertexIndex];
+                    var idx = (instanceIndex * groupCount + group);
+                    transparency = tTransparency[idx] / 255;
+                    break;
+                }
+                case 'vertexInstance': {
+                    var idx = (instanceIndex * vertexCount + vertexIndex);
+                    transparency = tTransparency[idx] / 255;
+                    break;
+                }
+                case 'volumeInstance': {
+                    var idx = (instanceIndex * vertexCount + vertexIndex);
+                    transparency = interpolatedTransparency[idx] / 255;
+                    break;
+                }
+                default: throw new Error('Unsupported transparency type.');
+            }
+        }
+        return transparency;
+    };
     MeshExporter.prototype.addMesh = function (values, webgl, ctx) {
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
             var aPosition, aNormal, aGroup, originalData, indices, vertexCount, drawCount;

package/lib/commonjs/extensions/geo-export/mesh-exporter.js.map

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package/lib/commonjs/extensions/geo-export/obj-exporter.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Box3D } from '../../mol-math/geometry';
 import { RuntimeContext } from '../../mol-task';