From de67dbacba150aa13a9204b9bc79b573e2299b7e Mon Sep 17 00:00:00 2001
From: dsehnal <david.sehnal@gmail.com>
Date: Wed, 26 Jan 2022 17:47:23 +0100
Subject: [PATCH] iso-value adjustment for VolumeServer data in default Viewer
---
CHANGELOG.md | 1 +
src/apps/viewer/app.ts | 7 +++++--
src/mol-model/volume/volume.ts | 18 ++++++++++++++++++
src/mol-plugin-state/formats/volume.ts | 13 +------------
4 files changed, 25 insertions(+), 14 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 283c8880f..954678f09 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
- Fix VolumeServer/query CLI
+- Support automatic iso-value adjustment for VolumeServer data in ``Viewer.loadVolumeFromUrl``
## [v3.0.0] - 2022-01-23
diff --git a/src/apps/viewer/app.ts b/src/apps/viewer/app.ts
index b399d04bc..af6afd97b 100644
--- a/src/apps/viewer/app.ts
+++ b/src/apps/viewer/app.ts
@@ -17,6 +17,7 @@ import { ModelExport } from '../../extensions/model-export';
import { Mp4Export } from '../../extensions/mp4-export';
import { PDBeStructureQualityReport } from '../../extensions/pdbe';
import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { Volume } from '../../mol-model/volume';
import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
@@ -366,11 +367,13 @@ export class Viewer {
const repr = plugin.build();
for (const iso of isovalues) {
+ const volume: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume;
+ const volumeData = volume.cell!.obj!.data;
repr
- .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
+ .to(volume)
.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
type: 'isosurface',
- typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+ typeParams: { alpha: iso.alpha ?? 1, isoValue: Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
color: 'uniform',
colorParams: { value: iso.color }
}));
diff --git a/src/mol-model/volume/volume.ts b/src/mol-model/volume/volume.ts
index 280a32d7e..8a322563a 100644
--- a/src/mol-model/volume/volume.ts
+++ b/src/mol-model/volume/volume.ts
@@ -15,6 +15,7 @@ import { ModelFormat } from '../../mol-model-formats/format';
import { CustomProperties } from '../custom-property';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { toPrecision } from '../../mol-util/number';
+import { DscifFormat } from '../../mol-model-formats/volume/density-server';
export interface Volume {
readonly label?: string
@@ -84,6 +85,23 @@ export namespace Volume {
}
}
+ // Converts iso value to relative if using downsample VolumeServer data
+ export function adjustedIsoValue(volume: Volume, value: number, kind: 'absolute' | 'relative') {
+ if (kind === 'relative') return IsoValue.relative(value);
+
+ const absolute = IsoValue.absolute(value);
+ if (DscifFormat.is(volume.sourceData)) {
+ const stats = {
+ min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
+ max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
+ mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
+ sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
+ };
+ return Volume.IsoValue.toRelative(absolute, stats);
+ }
+ return absolute;
+ }
+
const defaultStats: Grid['stats'] = { min: -1, max: 1, mean: 0, sigma: 0.1 };
export function createIsoValueParam(defaultValue: Volume.IsoValue, stats?: Grid['stats']) {
const sts = stats || defaultStats;
diff --git a/src/mol-plugin-state/formats/volume.ts b/src/mol-plugin-state/formats/volume.ts
index d3701364f..f2c527738 100644
--- a/src/mol-plugin-state/formats/volume.ts
+++ b/src/mol-plugin-state/formats/volume.ts
@@ -18,7 +18,6 @@ import { objectForEach } from '../../mol-util/object';
import { RecommendedIsoValue } from '../../mol-model-formats/volume/property';
import { getContourLevelEmdb } from '../../mol-plugin/behavior/dynamic/volume-streaming/util';
import { Task } from '../../mol-task';
-import { DscifFormat } from '../../mol-model-formats/volume/density-server';
export const VolumeFormatCategory = 'Volume';
type Params = { entryId?: string };
@@ -42,19 +41,9 @@ async function tryObtainRecommendedIsoValue(plugin: PluginContext, volume?: Volu
function tryGetRecomendedIsoValue(volume: Volume) {
const recommendedIsoValue = RecommendedIsoValue.Provider.get(volume);
if (!recommendedIsoValue) return;
-
if (recommendedIsoValue.kind === 'relative') return recommendedIsoValue;
- let stats = volume.grid.stats;
- if (DscifFormat.is(volume.sourceData)) {
- stats = {
- min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
- max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
- mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
- sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
- };
- }
- return Volume.IsoValue.toRelative(recommendedIsoValue, stats);
+ return Volume.adjustedIsoValue(volume, recommendedIsoValue.absoluteValue, 'absolute');
}
async function defaultVisuals(plugin: PluginContext, data: { volume: StateObjectSelector<PluginStateObject.Volume.Data> }) {
--
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