From 1b382653f23854dafda33565b897c7de9adc7e57 Mon Sep 17 00:00:00 2001
From: dsehnal <david.sehnal@gmail.com>
Date: Mon, 19 Dec 2022 16:49:30 +0100
Subject: [PATCH] add volume controls to Volseg extension
---
CHANGELOG.md | 2 +-
.../volumes-and-segmentations/entry-root.ts | 13 ++++++++-
.../volumes-and-segmentations/entry-volume.ts | 2 +-
.../volumes-and-segmentations/ui.tsx | 28 +++++++++++++------
4 files changed, 33 insertions(+), 12 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 82f75dd10..fb0728b21 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Show histogram in direct volume control point settings
- Add `solidInterior` parameter to sphere/cylinder impostors
-- Add `meshes` and `volseg` extensions
+- Add `meshes` and `volumes-and-segmentations` extensions
## [v3.27.0] - 2022-12-15
diff --git a/src/extensions/volumes-and-segmentations/entry-root.ts b/src/extensions/volumes-and-segmentations/entry-root.ts
index 76971ac66..0918145b1 100644
--- a/src/extensions/volumes-and-segmentations/entry-root.ts
+++ b/src/extensions/volumes-and-segmentations/entry-root.ts
@@ -27,11 +27,12 @@ import { VolsegMeshSegmentationData } from './entry-meshes';
import { VolsegModelData } from './entry-models';
import { VolsegLatticeSegmentationData } from './entry-segmentation';
import { VolsegState, VolsegStateData, VolsegStateParams } from './entry-state';
-import { VolsegVolumeData, SimpleVolumeParamValues } from './entry-volume';
+import { VolsegVolumeData, SimpleVolumeParamValues, VOLUME_VISUAL_TAG } from './entry-volume';
import * as ExternalAPIs from './external-api';
import { VolsegGlobalStateData } from './global-state';
import { applyEllipsis, Choice, isDefined, lazyGetter, splitEntryId } from './helpers';
import { type VolsegStateFromEntry } from './transformers';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
export const MAX_VOXELS = 10 ** 7;
@@ -90,6 +91,7 @@ export namespace VolsegEntryParamValues {
export class VolsegEntry extends PluginStateObject.CreateBehavior<VolsegEntryData>({ name: 'Vol & Seg Entry' }) { }
+type VolRepr3DT = typeof StateTransforms.Representation.VolumeRepresentation3D
export class VolsegEntryData extends PluginBehavior.WithSubscribers<VolsegEntryParamValues> {
plugin: PluginContext;
@@ -111,6 +113,7 @@ export class VolsegEntryData extends PluginBehavior.WithSubscribers<VolsegEntryP
private getStateNode = lazyGetter(() => this.plugin.state.data.selectQ(q => q.byRef(this.ref).subtree().ofType(VolsegState))[0] as StateObjectCell<VolsegState, StateTransform<typeof VolsegStateFromEntry>>, 'Missing VolsegState node. Must first create VolsegState for this VolsegEntry.');
public currentState = new BehaviorSubject(ParamDefinition.getDefaultValues(VolsegStateParams));
+ public currentVolume = new BehaviorSubject<StateTransform<VolRepr3DT> | undefined>(undefined);
private constructor(plugin: PluginContext, params: VolsegEntryParamValues) {
@@ -158,6 +161,14 @@ export class VolsegEntryData extends PluginBehavior.WithSubscribers<VolsegEntryP
}
});
+ this.subscribeObservable(this.plugin.state.data.events.cell.stateUpdated, e => {
+ // TODO: subscribe cell.removed event as well to set the current volume to undefined
+ if (e.cell.transform.tags?.includes(VOLUME_VISUAL_TAG)) {
+ // TODO: make sure this belongs to the "current entry subtree"
+ this.currentVolume.next(e.cell.transform);
+ }
+ });
+
this.subscribeObservable(this.plugin.behaviors.interaction.click, async e => {
const loci = e.current.loci;
const clickedSegment = this.getSegmentIdFromLoci(loci);
diff --git a/src/extensions/volumes-and-segmentations/entry-volume.ts b/src/extensions/volumes-and-segmentations/entry-volume.ts
index 1ba4184ac..930edc5cc 100644
--- a/src/extensions/volumes-and-segmentations/entry-volume.ts
+++ b/src/extensions/volumes-and-segmentations/entry-volume.ts
@@ -24,7 +24,7 @@ import { VolsegGlobalStateData } from './global-state';
const GROUP_TAG = 'volume-group';
-const VOLUME_VISUAL_TAG = 'volume-visual';
+export const VOLUME_VISUAL_TAG = 'volume-visual';
const DIRECT_VOLUME_RELATIVE_PEAK_HALFWIDTH = 0.5;
diff --git a/src/extensions/volumes-and-segmentations/ui.tsx b/src/extensions/volumes-and-segmentations/ui.tsx
index 65df31a57..0d8a24cb0 100644
--- a/src/extensions/volumes-and-segmentations/ui.tsx
+++ b/src/extensions/volumes-and-segmentations/ui.tsx
@@ -12,6 +12,7 @@ import * as Icons from '../../mol-plugin-ui/controls/icons';
import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
import { Slider } from '../../mol-plugin-ui/controls/slider';
import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
+import { UpdateTransformControl } from '../../mol-plugin-ui/state/update-transform';
import { PluginContext } from '../../mol-plugin/context';
import { shallowEqualArrays } from '../../mol-util';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
@@ -117,11 +118,6 @@ function VolsegEntryControls({ entryData }: { entryData: VolsegEntryData }) {
const visibleModels = state.visibleModels.map(model => model.pdbId);
const allPdbs = entryData.pdbs;
- const volumeValues: SimpleVolumeParamValues = {
- volumeType: state.volumeType,
- opacity: state.volumeOpacity,
- };
-
return <>
{/* Title */}
<div style={{ fontWeight: 'bold', padding: 8, paddingTop: 6, paddingBottom: 4, overflow: 'hidden' }}>
@@ -139,10 +135,7 @@ function VolsegEntryControls({ entryData }: { entryData: VolsegEntryData }) {
</ExpandGroup>}
{/* Volume */}
- <ExpandGroup header='Volume data' initiallyExpanded>
- <WaitingParameterControls params={SimpleVolumeParams} values={volumeValues} onChangeValues={async next => { await sleep(20); await entryData.actionUpdateVolumeVisual(next); }} />
- </ExpandGroup>
-
+ <VolumeControls entryData={entryData} />
<ExpandGroup header='Segmentation data' initiallyExpanded>
{/* Segment opacity slider */}
<ControlRow label='Opacity' control={
@@ -189,6 +182,23 @@ function VolsegEntryControls({ entryData }: { entryData: VolsegEntryData }) {
</>;
}
+function VolumeControls({ entryData }: { entryData: VolsegEntryData }) {
+ const vol = useBehavior(entryData.currentVolume);
+ if (!vol) return null;
+
+ const volumeValues: SimpleVolumeParamValues = {
+ volumeType: vol.state.isHidden ? 'off' : vol.params?.type.name as any,
+ opacity: vol.params?.type.params.alpha,
+ };
+
+ return <ExpandGroup header='Volume data' initiallyExpanded>
+ <WaitingParameterControls params={SimpleVolumeParams} values={volumeValues} onChangeValues={async next => { await sleep(20); await entryData.actionUpdateVolumeVisual(next); }} />
+ <ExpandGroup header='Detailed Volume Params' headerStyle={{ marginTop: 1 }}>
+ <UpdateTransformControl state={entryData.plugin.state.data} transform={vol} customHeader='none' />
+ </ExpandGroup>
+ </ExpandGroup>;
+}
+
type ComponentParams<T extends React.Component<any, any, any> | ((props: any) => JSX.Element)> =
T extends React.Component<infer P, any, any> ? P : T extends (props: infer P) => JSX.Element ? P : never;
--
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