From c9518d437a97166292822f945f100d200a92f72d Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 19 Feb 2019 13:49:24 -0800
Subject: [PATCH] moved stats out of VolumeIsoValue
---
src/apps/structure-info/volume.ts | 2 +-
src/mol-model/volume/data.ts | 26 ++++++++------------------
src/mol-repr/volume/isosurface.ts | 31 ++++++++++++++++---------------
3 files changed, 25 insertions(+), 34 deletions(-)
diff --git a/src/apps/structure-info/volume.ts b/src/apps/structure-info/volume.ts
index 59029e155..4b3e54895 100644
--- a/src/apps/structure-info/volume.ts
+++ b/src/apps/structure-info/volume.ts
@@ -40,7 +40,7 @@ function print(data: Volume) {
}
async function doMesh(data: Volume, filename: string) {
- const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, data.volume, createEmptyTheme(), { isoValue: VolumeIsoValue.absolute(data.volume.dataStats, 1.5) } )).run();
+ const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, data.volume, createEmptyTheme(), { isoValue: VolumeIsoValue.absolute(1.5) } )).run();
console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
// Export the mesh in OBJ format.
diff --git a/src/mol-model/volume/data.ts b/src/mol-model/volume/data.ts
index 6e9ab3173..18d06c52d 100644
--- a/src/mol-model/volume/data.ts
+++ b/src/mol-model/volume/data.ts
@@ -44,11 +44,11 @@ namespace VolumeData {
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 type Relative = Readonly<{ kind: 'relative', relativeValue: number }>
+ export type Absolute = Readonly<{ kind: 'absolute', 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 absolute(value: number): Absolute { return { kind: 'absolute', absoluteValue: value }; }
+ export function relative(value: number): Relative { return { kind: 'relative', relativeValue: value }; }
export function calcAbsolute(stats: VolumeData['dataStats'], relativeValue: number): number {
return relativeValue * stats.sigma + stats.mean
@@ -58,22 +58,12 @@ namespace VolumeIsoValue {
return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma)
}
- export function toAbsolute(value: VolumeIsoValue): Absolute {
- if (value.kind === 'absolute') return value;
- return {
- kind: 'absolute',
- stats: value.stats,
- absoluteValue: calcAbsolute(value.stats, value.relativeValue)
- }
+ export function toAbsolute(value: VolumeIsoValue, stats: VolumeData['dataStats']): Absolute {
+ return value.kind === 'absolute' ? value : { kind: 'absolute', absoluteValue: VolumeIsoValue.calcAbsolute(stats, value.relativeValue) }
}
- export function toRelative(value: VolumeIsoValue): Relative {
- if (value.kind === 'relative') return value;
- return {
- kind: 'relative',
- stats: value.stats,
- relativeValue: calcRelative(value.stats, value.absoluteValue)
- }
+ export function toRelative(value: VolumeIsoValue, stats: VolumeData['dataStats']): Relative {
+ return value.kind === 'relative' ? value : { kind: 'relative', relativeValue: VolumeIsoValue.calcRelative(stats, value.absoluteValue) }
}
}
diff --git a/src/mol-repr/volume/isosurface.ts b/src/mol-repr/volume/isosurface.ts
index 4504d8766..ec560fbba 100644
--- a/src/mol-repr/volume/isosurface.ts
+++ b/src/mol-repr/volume/isosurface.ts
@@ -20,21 +20,21 @@ import { NullLocation } from 'mol-model/location';
import { Lines } from 'mol-geo/geometry/lines/lines';
const IsoValueParam = PD.Conditioned(
- VolumeIsoValue.relative(VolumeData.Empty.dataStats, 2),
+ VolumeIsoValue.relative(2),
{
'absolute': PD.Converted(
- (v: VolumeIsoValue) => VolumeIsoValue.toAbsolute(v).absoluteValue,
- (v: number) => VolumeIsoValue.absolute(VolumeData.Empty.dataStats, v),
+ (v: VolumeIsoValue) => VolumeIsoValue.toAbsolute(v, VolumeData.Empty.dataStats).absoluteValue,
+ (v: number) => VolumeIsoValue.absolute(v),
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),
+ (v: VolumeIsoValue) => VolumeIsoValue.toRelative(v, VolumeData.Empty.dataStats).relativeValue,
+ (v: number) => VolumeIsoValue.relative(v),
PD.Numeric(2, { min: -10, max: 10, step: 0.01 })
)
},
(v: VolumeIsoValue) => v.kind === 'absolute' ? 'absolute' : 'relative',
- (v: VolumeIsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? VolumeIsoValue.toAbsolute(v) : VolumeIsoValue.toRelative(v)
+ (v: VolumeIsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? VolumeIsoValue.toAbsolute(v, VolumeData.Empty.dataStats) : VolumeIsoValue.toRelative(v, VolumeData.Empty.dataStats)
)
type IsoValueParam = typeof IsoValueParam
@@ -50,7 +50,7 @@ export async function createVolumeIsosurfaceMesh(ctx: VisualContext, volume: Vol
ctx.runtime.update({ message: 'Marching cubes...' });
const surface = await computeMarchingCubesMesh({
- isoLevel: VolumeIsoValue.toAbsolute(props.isoValue).absoluteValue,
+ isoLevel: VolumeIsoValue.toAbsolute(props.isoValue, volume.dataStats).absoluteValue,
scalarField: volume.data
}, mesh).runAsChild(ctx.runtime);
@@ -88,7 +88,7 @@ export async function createVolumeIsosurfaceWireframe(ctx: VisualContext, volume
ctx.runtime.update({ message: 'Marching cubes...' });
const wireframe = await computeMarchingCubesLines({
- isoLevel: VolumeIsoValue.toAbsolute(props.isoValue).absoluteValue,
+ isoLevel: VolumeIsoValue.toAbsolute(props.isoValue, volume.dataStats).absoluteValue,
scalarField: volume.data
}, lines).runAsChild(ctx.runtime)
@@ -135,23 +135,24 @@ export const IsosurfaceParams = {
export type IsosurfaceParams = typeof IsosurfaceParams
export function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: VolumeData) {
const p = PD.clone(IsosurfaceParams)
- const { min, max, mean, sigma } = volume.dataStats
+ const stats = volume.dataStats
+ const { min, max, mean, sigma } = stats
p.isoValue = PD.Conditioned(
- VolumeIsoValue.relative(volume.dataStats, 2),
+ VolumeIsoValue.relative(2),
{
'absolute': PD.Converted(
- (v: VolumeIsoValue) => VolumeIsoValue.toAbsolute(v).absoluteValue,
- (v: number) => VolumeIsoValue.absolute(volume.dataStats, v),
+ (v: VolumeIsoValue) => VolumeIsoValue.toAbsolute(v, stats).absoluteValue,
+ (v: number) => VolumeIsoValue.absolute(v),
PD.Numeric(mean, { min, max, step: sigma / 100 })
),
'relative': PD.Converted(
- (v: VolumeIsoValue) => VolumeIsoValue.toRelative(v).relativeValue,
- (v: number) => VolumeIsoValue.relative(volume.dataStats, v),
+ (v: VolumeIsoValue) => VolumeIsoValue.toRelative(v, stats).relativeValue,
+ (v: number) => VolumeIsoValue.relative(v),
PD.Numeric(2, { min: -10, max: 10, step: 0.001 })
)
},
(v: VolumeIsoValue) => v.kind === 'absolute' ? 'absolute' : 'relative',
- (v: VolumeIsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? VolumeIsoValue.toAbsolute(v) : VolumeIsoValue.toRelative(v)
+ (v: VolumeIsoValue, c: 'absolute' | 'relative') => c === 'absolute' ? VolumeIsoValue.toAbsolute(v, stats) : VolumeIsoValue.toRelative(v, stats)
)
return p
}
--
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