From 9d87ae427c51e1139183aafeba319df5eb1b8b20 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 14 Nov 2018 15:48:02 -0800
Subject: [PATCH] iso value simplification
---
src/apps/structure-info/volume.ts | 2 +-
.../geometry/direct-volume/direct-volume.ts | 7 +++----
.../structure/visual/gaussian-density-volume.ts | 2 +-
src/mol-repr/volume/isosurface-mesh.ts | 9 ++++-----
src/mol-repr/volume/representation.ts | 15 ++-------------
5 files changed, 11 insertions(+), 24 deletions(-)
diff --git a/src/apps/structure-info/volume.ts b/src/apps/structure-info/volume.ts
index d9921d7a4..2faaf7086 100644
--- a/src/apps/structure-info/volume.ts
+++ b/src/apps/structure-info/volume.ts
@@ -38,7 +38,7 @@ function print(data: Volume) {
}
async function doMesh(data: Volume, filename: string) {
- const mesh = await Task.create('', runtime => createVolumeIsosurface({ runtime }, data.volume, { isoValueAbsolute: VolumeIsoValue.calcAbsolute(data.volume.dataStats, 1.5) } )).run();
+ const mesh = await Task.create('', runtime => createVolumeIsosurface({ runtime }, data.volume, { isoValue: VolumeIsoValue.calcAbsolute(data.volume.dataStats, 1.5) } )).run();
console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
// Export the mesh in OBJ format.
diff --git a/src/mol-geo/geometry/direct-volume/direct-volume.ts b/src/mol-geo/geometry/direct-volume/direct-volume.ts
index 919699272..47527c3d2 100644
--- a/src/mol-geo/geometry/direct-volume/direct-volume.ts
+++ b/src/mol-geo/geometry/direct-volume/direct-volume.ts
@@ -70,8 +70,7 @@ export namespace DirectVolume {
export const Params = {
...Geometry.Params,
- isoValueAbsolute: PD.Range('Iso Value Absolute', '', 0.22, -1, 1, 0.01),
- isoValueRelative: PD.Range('Iso Value Relative', '', 2, -10, 10, 0.1),
+ isoValue: PD.Range('Iso Value', '', 0.22, -1, 1, 0.01),
renderMode: PD.Select('Render Mode', '', 'isosurface', RenderModeOptions),
controlPoints: PD.Text('Control Points', '', '0.19:0.1, 0.2:0.5, 0.21:0.1, 0.4:0.3'),
}
@@ -109,7 +108,7 @@ export namespace DirectVolume {
elements: ValueCell.create(VolumeBox.indices as Uint32Array),
boundingSphere: ValueCell.create(boundingSphere),
- uIsoValue: ValueCell.create(props.isoValueAbsolute),
+ uIsoValue: ValueCell.create(props.isoValue),
uBboxMin: bboxMin,
uBboxMax: bboxMax,
uBboxSize: bboxSize,
@@ -136,7 +135,7 @@ export namespace DirectVolume {
ValueCell.update(values.boundingSphere, boundingSphere)
}
- ValueCell.updateIfChanged(values.uIsoValue, props.isoValueAbsolute)
+ ValueCell.updateIfChanged(values.uIsoValue, props.isoValue)
ValueCell.updateIfChanged(values.uAlpha, props.alpha)
ValueCell.updateIfChanged(values.dUseFog, props.useFog)
ValueCell.updateIfChanged(values.dRenderMode, props.renderMode)
diff --git a/src/mol-repr/structure/visual/gaussian-density-volume.ts b/src/mol-repr/structure/visual/gaussian-density-volume.ts
index 5a9f0a681..6e94b12ee 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -45,7 +45,7 @@ export function GaussianDensityVolumeVisual(): UnitsVisual<GaussianDensityVolume
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) {
state.createGeometry = true
- newProps.isoValueAbsolute = Math.exp(-newProps.smoothness)
+ newProps.isoValue = Math.exp(-newProps.smoothness)
}
if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
diff --git a/src/mol-repr/volume/isosurface-mesh.ts b/src/mol-repr/volume/isosurface-mesh.ts
index f7d77406d..c7d6e015f 100644
--- a/src/mol-repr/volume/isosurface-mesh.ts
+++ b/src/mol-repr/volume/isosurface-mesh.ts
@@ -20,14 +20,14 @@ import { VisualContext } from 'mol-repr/representation';
import { Theme, ThemeRegistryContext } from 'mol-theme/theme';
interface VolumeIsosurfaceProps {
- isoValueAbsolute: number
+ isoValue: number
}
export async function createVolumeIsosurface(ctx: VisualContext, volume: VolumeData, props: VolumeIsosurfaceProps, mesh?: Mesh) {
ctx.runtime.update({ message: 'Marching cubes...' });
const surface = await computeMarchingCubesMesh({
- isoLevel: props.isoValueAbsolute,
+ isoLevel: props.isoValue,
scalarField: volume.data
}, mesh).runAsChild(ctx.runtime);
@@ -41,8 +41,7 @@ export async function createVolumeIsosurface(ctx: VisualContext, volume: VolumeD
export const IsosurfaceParams = {
...Mesh.Params,
- isoValueAbsolute: PD.Range('Iso Value Absolute', '', 0.22, -1, 1, 0.01),
- isoValueRelative: PD.Range('Iso Value Relative', '', 2, -10, 10, 0.1),
+ isoValue: PD.Range('Iso Value', '', 0.22, -1, 1, 0.01),
}
export type IsosurfaceParams = typeof IsosurfaceParams
export function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: VolumeData) {
@@ -56,7 +55,7 @@ export function IsosurfaceVisual(): VolumeVisual<IsosurfaceParams> {
getLoci: () => EmptyLoci,
mark: () => false,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IsosurfaceParams>, currentProps: PD.Values<IsosurfaceParams>) => {
- if (newProps.isoValueAbsolute !== currentProps.isoValueAbsolute) state.createGeometry = true
+ if (newProps.isoValue !== currentProps.isoValue) state.createGeometry = true
},
createRenderObject: async (ctx: VisualContext, geometry: Mesh, locationIt: LocationIterator, theme: Theme, props: PD.Values<IsosurfaceParams>) => {
const transform = createIdentityTransform()
diff --git a/src/mol-repr/volume/representation.ts b/src/mol-repr/volume/representation.ts
index d974b4e49..907d7cfbd 100644
--- a/src/mol-repr/volume/representation.ts
+++ b/src/mol-repr/volume/representation.ts
@@ -6,7 +6,7 @@
import { Task } from 'mol-task'
import { Representation, Visual, RepresentationContext, VisualContext, RepresentationProvider, RepresentationParamsGetter } from '../representation';
-import { VolumeData, VolumeIsoValue } from 'mol-model/volume';
+import { VolumeData } from 'mol-model/volume';
import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
import { Geometry, updateRenderableState } from 'mol-geo/geometry/geometry';
import { ParamDefinition as PD } from 'mol-util/param-definition';
@@ -52,11 +52,6 @@ export function VolumeVisual<P extends VolumeParams>(builder: VolumeVisualGeomet
async function create(ctx: VisualContext, volume: VolumeData, theme: Theme, props: Partial<PD.Values<P>> = {}) {
currentProps = Object.assign({}, defaultProps, props)
- if (props.isoValueRelative) {
- currentProps.isoValueAbsolute = VolumeIsoValue.calcAbsolute(currentVolume.dataStats, props.isoValueRelative)
- // console.log('create props.isoValueRelative', props.isoValueRelative, currentProps.isoValueAbsolute, currentVolume.dataStats)
- }
-
geometry = await createGeometry(ctx, volume, currentProps, geometry)
locationIt = LocationIterator(1, 1, () => NullLocation)
renderObject = await createRenderObject(ctx, geometry, locationIt, theme, currentProps)
@@ -66,11 +61,6 @@ export function VolumeVisual<P extends VolumeParams>(builder: VolumeVisualGeomet
if (!renderObject) return
const newProps = Object.assign({}, currentProps, props)
- if (props.isoValueRelative) {
- newProps.isoValueAbsolute = VolumeIsoValue.calcAbsolute(currentVolume.dataStats, props.isoValueRelative)
- // console.log('update props.isoValueRelative', props.isoValueRelative, newProps.isoValueAbsolute, currentVolume.dataStats)
- }
-
VisualUpdateState.reset(updateState)
setUpdateState(updateState, newProps, currentProps)
@@ -145,8 +135,7 @@ export type VolumeRepresentationProvider<P extends VolumeParams> = Representatio
export const VolumeParams = {
...Geometry.Params,
- isoValueAbsolute: PD.Range('Iso Value Absolute', '', 0.22, -1, 1, 0.01),
- isoValueRelative: PD.Range('Iso Value Relative', '', 2, -10, 10, 0.1),
+ isoValue: PD.Range('Iso Value', '', 0.22, -1, 1, 0.01),
}
export type VolumeParams = typeof VolumeParams
--
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