From 8f1b3b7b0648502243d1045db29d43b851d8e6c0 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 1 May 2018 17:48:58 +0200
Subject: [PATCH] VolumeData, mesh, tweaks
---
src/apps/render-test/utils/mcubes.ts | 4 +-
src/apps/structure-info/volume.ts | 63 ++++++++++++++++---
src/mol-geo/representation/volume/Mesh.ts | 29 +++++++++
src/mol-geo/util/marching-cubes/algorithm.ts | 2 +-
src/mol-math/geometry/primitives/box3d.ts | 2 +-
.../geometry/spacegroup/construction.ts | 11 +---
src/mol-model/volume/_spec/data.spec.ts | 6 --
src/mol-model/volume/data.ts | 34 +++++++++-
.../volume/formats/density-server.ts | 4 +-
9 files changed, 126 insertions(+), 29 deletions(-)
create mode 100644 src/mol-geo/representation/volume/Mesh.ts
delete mode 100644 src/mol-model/volume/_spec/data.spec.ts
diff --git a/src/apps/render-test/utils/mcubes.ts b/src/apps/render-test/utils/mcubes.ts
index 350cdc9e5..92905c7b6 100644
--- a/src/apps/render-test/utils/mcubes.ts
+++ b/src/apps/render-test/utils/mcubes.ts
@@ -5,7 +5,7 @@
*/
import { Run } from 'mol-task'
-import { compute } from 'mol-geo/util/marching-cubes/algorithm'
+import { computeMarchingCubes } from 'mol-geo/util/marching-cubes/algorithm'
import { Mesh } from 'mol-geo/shape/mesh'
import { Tensor, Mat4, Vec3 } from 'mol-math/linear-algebra'
@@ -38,7 +38,7 @@ export default async function computeSurface(f: (x: number, y: number, z: number
const min = Vec3.create(-1.1, -1.1, -1.1), max = Vec3.create(1.1, 1.1, 1.1);
fillField(field, f, min, max);
- const surface = await Run(compute({
+ const surface = await Run(computeMarchingCubes({
scalarField: field,
isoLevel: 0,
oldSurface: data ? data.surface : void 0
diff --git a/src/apps/structure-info/volume.ts b/src/apps/structure-info/volume.ts
index e3b4b2e1e..bfe15e630 100644
--- a/src/apps/structure-info/volume.ts
+++ b/src/apps/structure-info/volume.ts
@@ -1,35 +1,77 @@
-
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import * as fs from 'fs'
import * as argparse from 'argparse'
-import { VolumeData, parseDensityServerData } from 'mol-model/volume'
+import * as util from 'util'
+
+import { VolumeData, parseDensityServerData, VolumeIsoValue } from 'mol-model/volume'
import { downloadCif } from './helpers'
import CIF from 'mol-io/reader/cif'
import { DensityServer_Data_Database } from 'mol-io/reader/cif/schema/density-server';
import { Run } from 'mol-task';
import { Table } from 'mol-data/db';
+import { computeVolumeMesh } from 'mol-geo/representation/volume/Mesh';
+import { StringBuilder } from 'mol-util';
+
+require('util.promisify').shim();
+const writeFileAsync = util.promisify(fs.writeFile);
type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
async function getVolume(url: string): Promise<Volume> {
- const cif = await downloadCif(url, false);
+ const cif = await downloadCif(url, true);
const data = CIF.schema.densityServer(cif.blocks[1]);
return { source: data, volume: await Run(parseDensityServerData(data)) };
}
-function print(volume: Volume) {
- const { volume_data_3d_info } = volume.source;
+function print(data: Volume) {
+ const { volume_data_3d_info } = data.source;
const row = Table.getRow(volume_data_3d_info, 0);
console.log(row);
+ console.log(data.volume.cell);
+ console.log(data.volume.dataStats);
+ console.log(data.volume.fractionalBox);
+}
+
+async function doMesh(data: Volume, filename: string) {
+ const mesh = await Run(computeVolumeMesh(data.volume, VolumeIsoValue.relative(data.volume.dataStats, 1.5)));
+ console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
+
+ // Export the mesh in OBJ format.
+ const { vertexCount, triangleCount } = mesh;
+
+ const vs = mesh.vertexBuffer.ref.value;
+ const ts = mesh.indexBuffer.ref.value;
+
+ const obj = StringBuilder.create();
+ for (let i = 0; i < vertexCount; i++) {
+ StringBuilder.write(obj, 'v ');
+ StringBuilder.writeFloat(obj, vs[3 * i + 0], 100);
+ StringBuilder.whitespace1(obj);
+ StringBuilder.writeFloat(obj, vs[3 * i + 1], 100);
+ StringBuilder.whitespace1(obj);
+ StringBuilder.writeFloat(obj, vs[3 * i + 2], 100);
+ StringBuilder.newline(obj);
+ }
+ for (let i = 0; i < triangleCount; i++) {
+ StringBuilder.write(obj, 'f ');
+ StringBuilder.writeIntegerAndSpace(obj, ts[3 * i + 0] + 1);
+ StringBuilder.writeIntegerAndSpace(obj, ts[3 * i + 1] + 1);
+ StringBuilder.writeInteger(obj, ts[3 * i + 2] + 1);
+ StringBuilder.newline(obj);
+ }
+
+ await writeFileAsync(filename, StringBuilder.getString(obj));
}
-async function run(url: string) {
+async function run(url: string, meshFilename: string) {
const volume = await getVolume(url);
print(volume);
+ await doMesh(volume, meshFilename);
}
const parser = new argparse.ArgumentParser({
@@ -39,9 +81,14 @@ description: 'Info about VolumeData from mol-model module'
parser.addArgument([ '--emdb', '-e' ], {
help: 'EMDB id, for example 8116',
});
+parser.addArgument([ '--mesh' ], {
+ help: 'Mesh filename',
+ required: true
+});
interface Args {
- emdb?: string
+ emdb?: string,
+ mesh: string
}
const args: Args = parser.parseArgs();
-run(`https://webchem.ncbr.muni.cz/DensityServer/em/emd-${args.emdb}/cell?detail=1&encoding=cif`);
\ No newline at end of file
+run(`https://webchem.ncbr.muni.cz/DensityServer/em/emd-${args.emdb}/cell?detail=4`, args.mesh);
\ No newline at end of file
diff --git a/src/mol-geo/representation/volume/Mesh.ts b/src/mol-geo/representation/volume/Mesh.ts
new file mode 100644
index 000000000..317b51b3e
--- /dev/null
+++ b/src/mol-geo/representation/volume/Mesh.ts
@@ -0,0 +1,29 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { VolumeData, VolumeIsoValue } from 'mol-model/volume'
+import { Task } from 'mol-task'
+import { Mesh } from '../../shape/mesh';
+import { computeMarchingCubes } from '../../util/marching-cubes/algorithm';
+
+function computeVolumeMesh(volume: VolumeData, isoValue: VolumeIsoValue) {
+ return Task.create<Mesh>('Volume Surface', async ctx => {
+ ctx.update({ message: 'Marching cubes...' });
+
+ const mesh = await ctx.runChild(computeMarchingCubes({
+ isoLevel: VolumeIsoValue.toAbsolute(isoValue).absoluteValue,
+ scalarField: volume.data
+ }));
+
+ const transform = VolumeData.getGridToCartesianTransform(volume);
+ ctx.update({ message: 'Transforming mesh...' });
+ Mesh.transformImmediate(mesh, transform);
+
+ return mesh;
+ });
+}
+
+export { computeVolumeMesh }
\ No newline at end of file
diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
index 25b266773..974864858 100644
--- a/src/mol-geo/util/marching-cubes/algorithm.ts
+++ b/src/mol-geo/util/marching-cubes/algorithm.ts
@@ -26,7 +26,7 @@ export interface MarchingCubesParameters {
oldSurface?: Mesh
}
-export function compute(parameters: MarchingCubesParameters) {
+export function computeMarchingCubes(parameters: MarchingCubesParameters) {
return Task.create('Marching Cubes', async ctx => {
let comp = new MarchingCubesComputation(parameters, ctx);
return await comp.run();
diff --git a/src/mol-math/geometry/primitives/box3d.ts b/src/mol-math/geometry/primitives/box3d.ts
index efceedb4f..6d0b5bd5f 100644
--- a/src/mol-math/geometry/primitives/box3d.ts
+++ b/src/mol-math/geometry/primitives/box3d.ts
@@ -12,7 +12,7 @@ interface Box3D { min: Vec3, max: Vec3 }
namespace Box3D {
export function create(min: Vec3, max: Vec3): Box3D { return { min, max }; }
-
+
export function computeBounding(data: PositionData): Box3D {
const min = [Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE];
const max = [-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE];
diff --git a/src/mol-math/geometry/spacegroup/construction.ts b/src/mol-math/geometry/spacegroup/construction.ts
index 626782b73..65aa22e84 100644
--- a/src/mol-math/geometry/spacegroup/construction.ts
+++ b/src/mol-math/geometry/spacegroup/construction.ts
@@ -15,8 +15,7 @@ interface SpacegroupCell {
/** Transfrom cartesian -> fractional coordinates within the cell */
readonly toFractional: Mat4,
/** Transfrom fractional coordinates within the cell -> cartesian */
- readonly fromFractional: Mat4,
- readonly fractionalBasis: Vec3[]
+ readonly fromFractional: Mat4
}
interface Spacegroup {
@@ -59,14 +58,8 @@ namespace SpacegroupCell {
]);
const toFractional = Mat4.invert(Mat4.zero(), fromFractional)!;
- const fractionalBasis = [
- Vec3.transformMat4(Vec3.zero(), Vec3.create(1, 0, 0), toFractional),
- Vec3.transformMat4(Vec3.zero(), Vec3.create(0, 1, 0), toFractional),
- Vec3.transformMat4(Vec3.zero(), Vec3.create(0, 0, 1), toFractional)
- ];
-
const num = typeof nameOrNumber === 'number' ? nameOrNumber : SpacegroupNumbers[nameOrNumber];
- return { number: num, size, anglesInRadians, toFractional, fromFractional, fractionalBasis };
+ return { number: num, size, anglesInRadians, toFractional, fromFractional };
}
}
diff --git a/src/mol-model/volume/_spec/data.spec.ts b/src/mol-model/volume/_spec/data.spec.ts
deleted file mode 100644
index 879b4fb84..000000000
--- a/src/mol-model/volume/_spec/data.spec.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index 19826278b..e0313d893 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -30,4 +30,36 @@ namespace VolumeData {
}
}
-export { VolumeData }
\ No newline at end of file
+type VolumeIsoValue = VolumeIsoValue.Absolute | VolumeIsoValue.Relative
+
+namespace VolumeIsoValue {
+ export type Relative = Readonly<{ kind: 'relative', stats: VolumeData['dataStats'], relativeValue: number }>
+ export type Absolute = Readonly<{ kind: 'absolute', stats: VolumeData['dataStats'], absoluteValue: number }>
+
+ export function absolute(stats: VolumeData['dataStats'], value: number): Absolute { return { kind: 'absolute', stats, absoluteValue: value }; }
+ export function relative(stats: VolumeData['dataStats'], value: number): Relative { return { kind: 'relative', stats, relativeValue: value }; }
+
+ export function toAbsolute(value: VolumeIsoValue): Absolute {
+ if (value.kind === 'absolute') return value;
+
+ const { mean, sigma } = value.stats
+ return {
+ kind: 'absolute',
+ stats: value.stats,
+ absoluteValue: value.relativeValue * sigma + mean
+ }
+ }
+
+ export function toRelative(value: VolumeIsoValue): Relative {
+ if (value.kind === 'relative') return value;
+
+ const { mean, sigma } = value.stats
+ return {
+ kind: 'relative',
+ stats: value.stats,
+ relativeValue: (mean - value.absoluteValue) / sigma
+ }
+ }
+}
+
+export { VolumeData, VolumeIsoValue }
\ No newline at end of file
diff --git a/src/mol-model/volume/formats/density-server.ts b/src/mol-model/volume/formats/density-server.ts
index c7972e690..300d7039c 100644
--- a/src/mol-model/volume/formats/density-server.ts
+++ b/src/mol-model/volume/formats/density-server.ts
@@ -13,7 +13,9 @@ import { Tensor, Vec3 } from 'mol-math/linear-algebra';
function parseDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
return Task.create<VolumeData>('Parse Volume Data', async ctx => {
const { volume_data_3d_info: info, volume_data_3d: values } = source;
- const cell = SpacegroupCell.create(info.spacegroup_number.value(0), Vec3.ofArray(info.spacegroup_cell_size.value(0)), Vec3.ofArray(info.spacegroup_cell_angles.value(0)));
+ const cell = SpacegroupCell.create(info.spacegroup_number.value(0),
+ Vec3.ofArray(info.spacegroup_cell_size.value(0)),
+ Vec3.scale(Vec3.zero(), Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180));
const tensorSpace = Tensor.Space(info.sample_count.value(0), info.axis_order.value(0), Float32Array);
const data = Tensor.create(tensorSpace, Tensor.Data1(values.values.toArray()));
--
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