From ab7dd9eaf35e5ab3256080a7812b68c3301a7acf Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 11 Feb 2019 14:26:10 -0800
Subject: [PATCH] volume param tweaks, handle 0 sigma
---
src/mol-geo/geometry/direct-volume/direct-volume.ts | 6 +++---
src/mol-model/volume/data.ts | 2 +-
src/mol-plugin/ui/controls/parameters.tsx | 2 +-
src/mol-repr/structure/visual/gaussian-density-volume.ts | 2 +-
src/mol-repr/volume/direct-volume.ts | 1 -
src/mol-repr/volume/isosurface.ts | 4 ++--
6 files changed, 8 insertions(+), 9 deletions(-)
diff --git a/src/mol-geo/geometry/direct-volume/direct-volume.ts b/src/mol-geo/geometry/direct-volume/direct-volume.ts
index 47d89aad9..d97903561 100644
--- a/src/mol-geo/geometry/direct-volume/direct-volume.ts
+++ b/src/mol-geo/geometry/direct-volume/direct-volume.ts
@@ -73,7 +73,7 @@ export namespace DirectVolume {
export const Params = {
...BaseGeometry.Params,
- isoValue: PD.Numeric(0.22, { min: -1, max: 1, step: 0.01 }),
+ isoValueNorm: PD.Numeric(0.22, { min: 0, max: 1, step: 0.01 }, { description: 'Normalized Isolevel Value' }),
renderMode: PD.Select('volume', RenderModeOptions),
controlPoints: PD.LineGraph([
Vec2.create(0.19, 0.0), Vec2.create(0.2, 0.05), Vec2.create(0.25, 0.05), Vec2.create(0.26, 0.0),
@@ -122,7 +122,7 @@ export namespace DirectVolume {
boundingSphere: ValueCell.create(boundingSphere),
invariantBoundingSphere: ValueCell.create(invariantBoundingSphere),
- uIsoValue: ValueCell.create(props.isoValue),
+ uIsoValue: ValueCell.create(props.isoValueNorm),
uBboxMin: bboxMin,
uBboxMax: bboxMax,
uBboxSize: bboxSize,
@@ -145,7 +145,7 @@ export namespace DirectVolume {
}
function updateValues(values: DirectVolumeValues, props: PD.Values<Params>) {
- ValueCell.updateIfChanged(values.uIsoValue, props.isoValue)
+ ValueCell.updateIfChanged(values.uIsoValue, props.isoValueNorm)
ValueCell.updateIfChanged(values.uAlpha, props.alpha)
ValueCell.updateIfChanged(values.dUseFog, props.useFog)
ValueCell.updateIfChanged(values.dRenderMode, props.renderMode)
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index 2805e7e70..6e9ab3173 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -55,7 +55,7 @@ namespace VolumeIsoValue {
}
export function calcRelative(stats: VolumeData['dataStats'], absoluteValue: number): number {
- return (absoluteValue - stats.mean) / stats.sigma
+ return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma)
}
export function toAbsolute(value: VolumeIsoValue): Absolute {
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index ed890ef13..a6bff120b 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
diff --git a/src/mol-repr/structure/visual/gaussian-density-volume.ts b/src/mol-repr/structure/visual/gaussian-density-volume.ts
index e5a8a9683..3c928cdb6 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -95,7 +95,7 @@ export function GaussianDensityVolumeVisual(): ComplexVisual<GaussianDensityVolu
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) {
state.createGeometry = true
- newProps.isoValue = Math.exp(-newProps.smoothness)
+ newProps.isoValueNorm = Math.exp(-newProps.smoothness)
}
}
})
diff --git a/src/mol-repr/volume/direct-volume.ts b/src/mol-repr/volume/direct-volume.ts
index 07f1e322e..5957435a2 100644
--- a/src/mol-repr/volume/direct-volume.ts
+++ b/src/mol-repr/volume/direct-volume.ts
@@ -152,7 +152,6 @@ export async function createDirectVolume(ctx: VisualContext, volume: VolumeData,
await createDirectVolume2d(runtime, webgl, volume, directVolume)
}
-
//
export const DirectVolumeParams = {
diff --git a/src/mol-repr/volume/isosurface.ts b/src/mol-repr/volume/isosurface.ts
index 778b82946..4504d8766 100644
--- a/src/mol-repr/volume/isosurface.ts
+++ b/src/mol-repr/volume/isosurface.ts
@@ -25,12 +25,12 @@ const IsoValueParam = PD.Conditioned(
'absolute': PD.Converted(
(v: VolumeIsoValue) => VolumeIsoValue.toAbsolute(v).absoluteValue,
(v: number) => VolumeIsoValue.absolute(VolumeData.Empty.dataStats, v),
- PD.Numeric(0, { min: -1, max: 1, step: 0.01 })
+ PD.Numeric(0.5, { min: -1, max: 1, step: 0.01 })
),
'relative': PD.Converted(
(v: VolumeIsoValue) => VolumeIsoValue.toRelative(v).relativeValue,
(v: number) => VolumeIsoValue.relative(VolumeData.Empty.dataStats, v),
- PD.Numeric(0, { min: -1, max: 1, step: 0.01 })
+ PD.Numeric(2, { min: -10, max: 10, step: 0.01 })
)
},
(v: VolumeIsoValue) => v.kind === 'absolute' ? 'absolute' : 'relative',
--
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