From 1a04125463d305b46ed07b9298aa62a6c3812566 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 24 Oct 2018 15:14:21 +0200
Subject: [PATCH] Fixed parsing density server data
---
src/mol-math/linear-algebra/tensor.ts | 21 +++++++++++++++++++
.../volume/formats/density-server.ts | 20 ++++++++++++++----
2 files changed, 37 insertions(+), 4 deletions(-)
diff --git a/src/mol-math/linear-algebra/tensor.ts b/src/mol-math/linear-algebra/tensor.ts
index 0909730c5..f1936a505 100644
--- a/src/mol-math/linear-algebra/tensor.ts
+++ b/src/mol-math/linear-algebra/tensor.ts
@@ -202,4 +202,25 @@ export namespace Tensor {
}
return o;
}
+
+ // Convers "slow to fast" axis order to "fast to slow" and vice versa.
+ export function invertAxisOrder(v: number[]) {
+ const ret: number[] = [];
+ for (let i = 0; i < v.length; i++) {
+ ret[i] = v[v.length - i - 1];
+ }
+ return ret;
+ }
+
+ export function getCanonicalAxisIndicesFastToSlow(order: number[]) {
+ const indices = new Int32Array(order.length) as any as number[];
+ for (let i = 0; i < order.length; i++) indices[order[i]] = i;
+ return indices;
+ }
+
+ export function getCanonicalAxisIndicesSlowToFast(order: number[]) {
+ const indices = new Int32Array(order.length) as any as number[];
+ for (let i = 0; i < order.length; i++) indices[order[order.length - i - 1]] = i;
+ return indices;
+ }
}
\ 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 0b1cb234d..10f3609bc 100644
--- a/src/mol-model/volume/formats/density-server.ts
+++ b/src/mol-model/volume/formats/density-server.ts
@@ -10,6 +10,10 @@ import { Task } from 'mol-task';
import { SpacegroupCell, Box3D } from 'mol-math/geometry';
import { Tensor, Vec3 } from 'mol-math/linear-algebra';
+function normalizeOrder(v: number[], indices: number[]) {
+ return Vec3.create(v[indices[0]], v[indices[1]], v[indices[2]])
+}
+
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;
@@ -19,11 +23,19 @@ function parseDensityServerData(source: DensityServer_Data_Database): Task<Volum
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()));
+ const axis_order_fast_to_slow = info.axis_order.value(0);
+
+ const indices = Tensor.getCanonicalAxisIndicesFastToSlow(axis_order_fast_to_slow);
+
+ // sample count is in "axis order" and needs to be reordered
+ const sample_count = normalizeOrder(info.sample_count.value(0), indices);
+ const tensorSpace = Tensor.Space(sample_count, Tensor.invertAxisOrder(axis_order_fast_to_slow), Float32Array);
+
+ const data = Tensor.create(tensorSpace, Tensor.Data1(values.values.toArray({ array: Float32Array })));
- const origin = Vec3.ofArray(info.origin.value(0))
- const dimensions = Vec3.ofArray(info.dimensions.value(0));
+ // origin and dimensions are in "axis order" and need to be reordered
+ const origin = normalizeOrder(info.origin.value(0), indices)
+ const dimensions = normalizeOrder(info.dimensions.value(0), indices);
return {
cell,
--
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