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quick fix for tags breaking precomputed annotations
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added "Swap visible segments when moving to annotation"
move to annotation now selects the first vertex rather than the centerpoint
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@chrisj
chrisj committed Oct 10, 2024
1 parent 8b8a9ea commit 2fd0d32
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Showing 5 changed files with 91 additions and 10 deletions.
1 change: 1 addition & 0 deletions src/annotation/annotation_layer_state.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -159,6 +159,7 @@ export class AnnotationDisplayState extends RefCounted {
new WatchableAnnotationRelationshipStates(),
);
ignoreNullSegmentFilter = new TrackableBoolean(true);
swapVisibleSegmentsOnMove = new TrackableBoolean(true);
disablePicking = new WatchableValue(false);
displayUnfiltered = makeCachedLazyDerivedWatchableValue(
(map, ignoreNullSegmentFilter) => {
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4 changes: 2 additions & 2 deletions src/annotation/frontend_source.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ import {
SliceViewChunkSource,
} from "#src/sliceview/frontend.js";
import { StatusMessage } from "#src/status.js";
import type { WatchableValue } from "#src/trackable_value.js";
import { WatchableValue } from "#src/trackable_value.js";
import type { Borrowed, Owned } from "#src/util/disposable.js";
import { ENDIANNESS, Endianness } from "#src/util/endian.js";
import * as matrix from "#src/util/matrix.js";
Expand Down Expand Up @@ -532,7 +532,7 @@ export class MultiscaleAnnotationSource
) {
super();
this.rank = options.rank;
this.properties.value = options.properties;
this.properties = new WatchableValue(options.properties);
this.annotationPropertySerializers = makeAnnotationPropertySerializers(
this.rank,
this.properties.value,
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16 changes: 11 additions & 5 deletions src/datasource/graphene/frontend.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -1329,6 +1329,7 @@ export class GraphConnection extends SegmentationGraphSourceConnection {
) {
super(graph, layer.displayState.segmentationGroupState.value);
const segmentsState = layer.displayState.segmentationGroupState.value;
this.previousVisibleSegmentCount = segmentsState.visibleSegments.size;
this.registerDisposer(
segmentsState.selectedSegments.changed.add(
(segmentIds: Uint64[] | Uint64 | null, add: boolean) => {
Expand Down Expand Up @@ -1571,6 +1572,8 @@ export class GraphConnection extends SegmentationGraphSourceConnection {
private lastDeselectionMessage: StatusMessage | undefined;
private lastDeselectionMessageExists = false;

private previousVisibleSegmentCount: number;

private visibleSegmentsChanged(segments: Uint64[] | null, added: boolean) {
const { segmentsState } = this;
const {
Expand All @@ -1597,16 +1600,18 @@ export class GraphConnection extends SegmentationGraphSourceConnection {
}
}
if (segments === null) {
const leafSegmentCount = this.segmentsState.selectedSegments.size;
this.segmentsState.segmentEquivalences.clear();
StatusMessage.showTemporaryMessage(
`Hid all ${leafSegmentCount} segments.`,
`Hid all ${this.previousVisibleSegmentCount} segment(s).`,
3000,
);
return;
}
for (const segmentId of segments) {
if (!added) {
if (
!added &&
!isBaseSegmentId(segmentId, this.graph.info.graph.nBitsForLayerId)
) {
const segmentCount = [
...segmentsState.segmentEquivalences.setElements(segmentId),
].length; // Approximation
Expand All @@ -1616,7 +1621,7 @@ export class GraphConnection extends SegmentationGraphSourceConnection {
this.lastDeselectionMessageExists = false;
}
this.lastDeselectionMessage = StatusMessage.showMessage(
`Hid ${segmentCount} segments.`,
`Hid ${segmentCount} segment(s).`,
);
this.lastDeselectionMessageExists = true;
setTimeout(() => {
Expand All @@ -1627,14 +1632,15 @@ export class GraphConnection extends SegmentationGraphSourceConnection {
}, 2000);
}
}
this.previousVisibleSegmentCount = segmentsState.visibleSegments.size;
}

private selectedSegmentsChanged(segments: Uint64[] | null, added: boolean) {
const { segmentsState } = this;
if (segments === null) {
const leafSegmentCount = this.segmentsState.selectedSegments.size;
StatusMessage.showTemporaryMessage(
`Deselected all ${leafSegmentCount} segments.`,
`Deselected all ${leafSegmentCount} segment(s).`,
3000,
);
return;
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32 changes: 30 additions & 2 deletions src/layer/annotation/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@ import type { SegmentationDisplayState } from "#src/segmentation_display_state/f
import type { TrackableBoolean } from "#src/trackable_boolean.js";
import { TrackableBooleanCheckbox } from "#src/trackable_boolean.js";
import {
ComputedWatchableValue,
makeCachedLazyDerivedWatchableValue,
WatchableValue,
} from "#src/trackable_value.js";
Expand Down Expand Up @@ -159,6 +160,7 @@ interface LinkedSegmentationLayer {
const LINKED_SEGMENTATION_LAYER_JSON_KEY = "linkedSegmentationLayer";
const FILTER_BY_SEGMENTATION_JSON_KEY = "filterBySegmentation";
const IGNORE_NULL_SEGMENT_FILTER_JSON_KEY = "ignoreNullSegmentFilter";
const SWAP_VISIBLE_SEGMENTS_ON_MOVE_JSON_KEY = "swapVisbleSegmentsOnMove";

class LinkedSegmentationLayers extends RefCounted {
changed = new NullarySignal();
Expand Down Expand Up @@ -705,7 +707,6 @@ export class AnnotationUserLayer extends Base {
this.annotationProjectionRenderScaleTarget.changed.add(
this.specificationChanged.dispatch,
);

this.registerDisposer(
this.localAnnotationProperties.changed.add(() => {
const { localAnnotations } = this;
Expand All @@ -722,12 +723,18 @@ export class AnnotationUserLayer extends Base {
order: -100,
getter: () => new RenderingOptionsTab(this),
});
this.tabs.default = "annotations";
const hideTagsTab = this.registerDisposer(
new ComputedWatchableValue(() => {
return this.localAnnotations === undefined;
}, this.dataSourcesChanged),
);
this.tabs.add("tags", {
label: "Tags",
order: 10,
getter: () => new TagsTab(this),
hidden: hideTagsTab,
});
this.tabs.default = "annotations";
}

syncTagTools = (tagIdentifiers: string[]) => {
Expand Down Expand Up @@ -798,6 +805,9 @@ export class AnnotationUserLayer extends Base {
this.annotationDisplayState.ignoreNullSegmentFilter.restoreState(
specification[IGNORE_NULL_SEGMENT_FILTER_JSON_KEY],
);
this.annotationDisplayState.swapVisibleSegmentsOnMove.restoreState(
specification[SWAP_VISIBLE_SEGMENTS_ON_MOVE_JSON_KEY],
);
this.annotationDisplayState.shader.restoreState(
specification[SHADER_JSON_KEY],
);
Expand Down Expand Up @@ -1043,6 +1053,22 @@ export class AnnotationUserLayer extends Base {
label.appendChild(checkbox.element);
tab.element.appendChild(label);
}
{
const checkbox = tab.registerDisposer(
new TrackableBooleanCheckbox(
this.annotationDisplayState.swapVisibleSegmentsOnMove,
),
);
const label = document.createElement("label");
label.appendChild(
document.createTextNode(
"Swap visible segments when moving to annotation",
),
);
label.title = "Swap visible segments when moving to annotation";
label.appendChild(checkbox.element);
tab.element.appendChild(label);
}
tab.element.appendChild(
tab.registerDisposer(
new LinkedSegmentationLayersWidget(this.linkedSegmentationLayers),
Expand Down Expand Up @@ -1072,6 +1098,8 @@ export class AnnotationUserLayer extends Base {
: localAnnotationRelationships;
x[IGNORE_NULL_SEGMENT_FILTER_JSON_KEY] =
this.annotationDisplayState.ignoreNullSegmentFilter.toJSON();
x[SWAP_VISIBLE_SEGMENTS_ON_MOVE_JSON_KEY] =
this.annotationDisplayState.swapVisibleSegmentsOnMove.toJSON();
x[SHADER_JSON_KEY] = this.annotationDisplayState.shader.toJSON();
x[SHADER_CONTROLS_JSON_KEY] =
this.annotationDisplayState.shaderControls.toJSON();
Expand Down
48 changes: 47 additions & 1 deletion src/ui/annotations.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,21 @@ export class MergedAnnotationStates
}
}

function getFirstVertexPosition(pos: Float32Array, annotation: Annotation) {
switch (annotation.type) {
case AnnotationType.AXIS_ALIGNED_BOUNDING_BOX:
case AnnotationType.LINE:
pos.set(annotation.pointA);
break;
case AnnotationType.POINT:
pos.set(annotation.point);
break;
case AnnotationType.ELLIPSOID:
pos.set(annotation.center);
break;
}
}

function getCenterPosition(center: Float32Array, annotation: Annotation) {
switch (annotation.type) {
case AnnotationType.AXIS_ALIGNED_BOUNDING_BOX:
Expand All @@ -187,6 +202,7 @@ function getCenterPosition(center: Float32Array, annotation: Annotation) {
break;
}
}
getCenterPosition;

function setLayerPosition(
layer: UserLayer,
Expand Down Expand Up @@ -240,7 +256,7 @@ const moveToAnnotation = (
const { layerRank } = chunkTransform;
const chunkPosition = new Float32Array(layerRank);
const layerPosition = new Float32Array(layerRank);
getCenterPosition(chunkPosition, annotation);
getFirstVertexPosition(chunkPosition, annotation);
matrix.transformPoint(
layerPosition,
chunkTransform.chunkToLayerTransform,
Expand All @@ -249,6 +265,36 @@ const moveToAnnotation = (
layerRank,
);
setLayerPosition(layer, chunkTransform, layerPosition);
if (state.displayState.swapVisibleSegmentsOnMove.value) {
showAnnotationSegments(annotation, state, true);
}
};

const showAnnotationSegments = (
annotation: Annotation,
state: AnnotationLayerState,
onlyVisible = false,
) => {
const { relatedSegments } = annotation;
if (relatedSegments) {
const { source, displayState } = state;
const { relationships } = source;
const { relationshipStates } = displayState;
for (let i = 0, count = relationships.length; i < count; ++i) {
const segmentationState = relationshipStates.get(relationships[i])
.segmentationState.value;
if (segmentationState) {
if (onlyVisible) {
segmentationState.segmentationGroupState.value.visibleSegments.clear();
}
for (const segmentList of relatedSegments) {
segmentationState.segmentationGroupState.value.visibleSegments.add(
segmentList,
);
}
}
}
}
};

export class AnnotationLayerView extends Tab {
Expand Down

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