@jax-data-science/sci-image-visualizer 0.8.3 → 0.10.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (579) hide show
  1. package/README.md +201 -460
  2. package/esm2022/index.mjs +34 -15
  3. package/esm2022/lib/channel-histogram/channel-histogram.component.mjs +163 -91
  4. package/esm2022/lib/contracts/capabilities.contract.mjs +4 -3
  5. package/esm2022/lib/contracts/cell-segmenter.contract.mjs +1 -1
  6. package/esm2022/lib/contracts/channel-histogram-api.contract.mjs +5 -1
  7. package/esm2022/lib/contracts/color.mjs +60 -0
  8. package/esm2022/lib/contracts/colormap-lut.mjs +213 -57
  9. package/esm2022/lib/contracts/coordinate-transform.contract.mjs +1 -1
  10. package/esm2022/lib/contracts/display-types.mjs +11 -1
  11. package/esm2022/lib/contracts/image.contract.mjs +1 -1
  12. package/esm2022/lib/contracts/instance-segmenter.contract.mjs +1 -1
  13. package/esm2022/lib/contracts/intensity.mjs +48 -5
  14. package/esm2022/lib/contracts/plot-type-contribution.contract.mjs +1 -1
  15. package/esm2022/lib/contracts/plot-type.mjs +134 -17
  16. package/esm2022/lib/contracts/ports/image-state.port.mjs +4 -1
  17. package/esm2022/lib/contracts/ports/preferences.port.mjs +5 -1
  18. package/esm2022/lib/contracts/ports/region-io.port.mjs +2 -1
  19. package/esm2022/lib/contracts/ports/spatial-data.port.mjs +5 -1
  20. package/esm2022/lib/contracts/ports/tile-access.port.mjs +2 -1
  21. package/esm2022/lib/contracts/region-editor-api.contract.mjs +1 -1
  22. package/esm2022/lib/contracts/region-overlay.contract.mjs +1 -1
  23. package/esm2022/lib/contracts/region-store.contract.mjs +1 -1
  24. package/esm2022/lib/contracts/sam.contract.mjs +1 -1
  25. package/esm2022/lib/contracts/section-view.contract.mjs +2 -0
  26. package/esm2022/lib/contracts/semantic-segmenter.contract.mjs +1 -1
  27. package/esm2022/lib/contracts/spatial-dataset.contract.mjs +3 -1
  28. package/esm2022/lib/contracts/toolbar-tool.contract.mjs +6 -4
  29. package/esm2022/lib/contracts/visualizer.contract.mjs +1 -1
  30. package/esm2022/lib/contracts/viz-config.mjs +2 -1
  31. package/esm2022/lib/geometry/contour.mjs +63 -0
  32. package/esm2022/lib/geometry/loft.mjs +128 -0
  33. package/esm2022/lib/geometry/polylabel.mjs +156 -0
  34. package/esm2022/lib/geometry/raster.mjs +98 -0
  35. package/esm2022/lib/geometry/reconstruct.mjs +315 -0
  36. package/esm2022/lib/geometry/reslice-image.mjs +57 -0
  37. package/esm2022/lib/geometry/ring.mjs +201 -0
  38. package/esm2022/lib/geometry/section.mjs +215 -0
  39. package/esm2022/lib/hex-color-picker/hex-color-picker.component.mjs +202 -102
  40. package/esm2022/lib/implementations/base-store-visualizer.mjs +201 -48
  41. package/esm2022/lib/implementations/napari-js/napari-axes-gizmo.mjs +65 -0
  42. package/esm2022/lib/implementations/napari-js/napari-display-state.mjs +136 -0
  43. package/esm2022/lib/implementations/napari-js/napari-helpers.mjs +199 -0
  44. package/esm2022/lib/implementations/napari-js/napari-image-2d-scene.mjs +602 -0
  45. package/esm2022/lib/implementations/napari-js/napari-loading-badge.mjs +12 -9
  46. package/esm2022/lib/implementations/napari-js/napari-loading-state.mjs +83 -0
  47. package/esm2022/lib/implementations/napari-js/napari-region-mesh-pointer.mjs +100 -0
  48. package/esm2022/lib/implementations/napari-js/napari-region-overlay.mjs +180 -591
  49. package/esm2022/lib/implementations/napari-js/napari-scene.mjs +2 -0
  50. package/esm2022/lib/implementations/napari-js/napari-spatial-2d-scene.mjs +614 -0
  51. package/esm2022/lib/implementations/napari-js/napari-spatial-3d-scene.mjs +769 -0
  52. package/esm2022/lib/implementations/napari-js/napari-spatial-encoding.mjs +199 -0
  53. package/esm2022/lib/implementations/napari-js/napari-spatial-hover.mjs +270 -0
  54. package/esm2022/lib/implementations/napari-js/napari-spatial-scene.mjs +159 -0
  55. package/esm2022/lib/implementations/napari-js/napari-spatial-tiles.mjs +106 -1408
  56. package/esm2022/lib/implementations/napari-js/napari-spatial-tooltip.mjs +2 -2
  57. package/esm2022/lib/implementations/napari-js/napari-surface-scene.mjs +271 -0
  58. package/esm2022/lib/implementations/napari-js/napari-tile-client.mjs +562 -0
  59. package/esm2022/lib/implementations/napari-js/napari-tool-bridge.mjs +347 -0
  60. package/esm2022/lib/implementations/napari-js/napari-visualizer.service.mjs +427 -4207
  61. package/esm2022/lib/implementations/napari-js/napari-volume-region-meshes.mjs +129 -0
  62. package/esm2022/lib/implementations/napari-js/napari-volume-scene.mjs +550 -0
  63. package/esm2022/lib/implementations/napari-js/napari-volume-slice-planes.mjs +103 -0
  64. package/esm2022/lib/implementations/napari-js/napari-volume-z-handle.mjs +6 -6
  65. package/esm2022/lib/implementations/napari-js/region-overlay/overlay-projection.mjs +96 -0
  66. package/esm2022/lib/implementations/napari-js/region-overlay/region-edit.mjs +35 -0
  67. package/esm2022/lib/implementations/napari-js/region-overlay/region-svg-renderer.mjs +194 -0
  68. package/esm2022/lib/implementations/napari-js/spatial-tiles/categorical-lookup.mjs +30 -0
  69. package/esm2022/lib/implementations/napari-js/spatial-tiles/cell-layers.mjs +274 -0
  70. package/esm2022/lib/implementations/napari-js/spatial-tiles/density-layer.mjs +144 -0
  71. package/esm2022/lib/implementations/napari-js/spatial-tiles/layer-groups.mjs +165 -0
  72. package/esm2022/lib/implementations/napari-js/spatial-tiles/plan-context.mjs +78 -0
  73. package/esm2022/lib/implementations/napari-js/spatial-tiles/transcript-hover.mjs +182 -0
  74. package/esm2022/lib/implementations/napari-js/spatial-tiles/transcript-jobs.mjs +369 -0
  75. package/esm2022/lib/implementations/napari-js/spatial-tiles/transcript-layers.mjs +306 -0
  76. package/esm2022/lib/implementations/osd/display-pipeline.mjs +102 -40
  77. package/esm2022/lib/implementations/osd/histogram-sampler.mjs +56 -31
  78. package/esm2022/lib/implementations/osd/openseadragon-viewer-options.mjs +128 -0
  79. package/esm2022/lib/implementations/osd/openseadragon-visualizer.service.mjs +333 -1685
  80. package/esm2022/lib/implementations/osd/osd-coordinate-transform.mjs +1 -1
  81. package/esm2022/lib/implementations/osd/osd-coords.mjs +5 -6
  82. package/esm2022/lib/implementations/osd/osd-export.mjs +122 -0
  83. package/esm2022/lib/implementations/osd/osd-lib.mjs +15 -1
  84. package/esm2022/lib/implementations/osd/osd-navigator-chrome.mjs +205 -0
  85. package/esm2022/lib/implementations/osd/osd-pixel-readback.mjs +68 -0
  86. package/esm2022/lib/implementations/osd/osd-region-overlay-draw.mjs +164 -0
  87. package/esm2022/lib/implementations/osd/osd-region-overlay.mjs +213 -716
  88. package/esm2022/lib/implementations/osd/osd-scale-bar.mjs +52 -60
  89. package/esm2022/lib/implementations/osd/osd-tile-source.mjs +105 -0
  90. package/esm2022/lib/implementations/osd/osd-viewer-like.mjs +2 -0
  91. package/esm2022/lib/implementations/osd/osd-viewer-mount.mjs +44 -0
  92. package/esm2022/lib/implementations/osd/osd-viewport.mjs +184 -0
  93. package/esm2022/lib/implementations/osd/osd-zoom.mjs +7 -1
  94. package/esm2022/lib/implementations/osd/simple-source.mjs +395 -0
  95. package/esm2022/lib/implementations/osd/slice-cache.mjs +53 -48
  96. package/esm2022/lib/implementations/osd/tile-client.mjs +32 -11
  97. package/esm2022/lib/implementations/osd/tile-recolor.mjs +330 -0
  98. package/esm2022/lib/implementations/plotly/omics-trace-builders.mjs +161 -73
  99. package/esm2022/lib/implementations/plotly/plotly-coordinate-transform.mjs +1 -1
  100. package/esm2022/lib/implementations/plotly/plotly-image-loader.mjs +112 -0
  101. package/esm2022/lib/implementations/plotly/plotly-image-recolor.mjs +178 -0
  102. package/esm2022/lib/implementations/plotly/plotly-intensity-inset.mjs +33 -0
  103. package/esm2022/lib/implementations/plotly/plotly-isosurface-controls.mjs +83 -0
  104. package/esm2022/lib/implementations/plotly/plotly-layouts.mjs +121 -0
  105. package/esm2022/lib/implementations/plotly/plotly-readback.mjs +117 -0
  106. package/esm2022/lib/implementations/plotly/plotly-region-overlay.mjs +19 -10
  107. package/esm2022/lib/implementations/plotly/plotly-shape-projection.mjs +223 -0
  108. package/esm2022/lib/implementations/plotly/plotly-trace-builders.mjs +79 -19
  109. package/esm2022/lib/implementations/plotly/plotly-zoom-controller.mjs +223 -0
  110. package/esm2022/lib/implementations/plotly/plotly.service.mjs +439 -1655
  111. package/esm2022/lib/implementations/region-centroids.mjs +47 -0
  112. package/esm2022/lib/implementations/simple-slice-access.service.mjs +22 -12
  113. package/esm2022/lib/implementations/spatial-data-http/spatial-data-http.service.mjs +172 -92
  114. package/esm2022/lib/implementations/spatial-data-http/spatial-wire.mjs +103 -22
  115. package/esm2022/lib/implementations/tile-server/index.mjs +6 -0
  116. package/esm2022/lib/implementations/tile-server/native-histogram.mjs +30 -0
  117. package/esm2022/lib/implementations/tile-server/poll-descriptor.mjs +65 -0
  118. package/esm2022/lib/implementations/tile-server/tile-protocol.mjs +42 -0
  119. package/esm2022/lib/implementations/tile-server/transport.mjs +135 -0
  120. package/esm2022/lib/intensity/intensity-profile.mjs +107 -0
  121. package/esm2022/lib/intensity/intensity-profile.service.mjs +223 -0
  122. package/esm2022/lib/intensity-inset/intensity-inset.component.mjs +133 -0
  123. package/esm2022/lib/models/bezier.mjs +1 -11
  124. package/esm2022/lib/models/class-preset.mjs +41 -3
  125. package/esm2022/lib/models/geometry.mjs +27 -164
  126. package/esm2022/lib/models/polygon-edit.mjs +254 -0
  127. package/esm2022/lib/models/polygon-factory.mjs +134 -0
  128. package/esm2022/lib/models/region-clone.mjs +68 -0
  129. package/esm2022/lib/models/region-geojson.mjs +411 -0
  130. package/esm2022/lib/models/region.mjs +34 -33
  131. package/esm2022/lib/models/shape.mjs +18 -16
  132. package/esm2022/lib/plot-mode/contribution-host.mjs +297 -0
  133. package/esm2022/lib/plot-mode/plot-mode-controller.mjs +9 -6
  134. package/esm2022/lib/plot-mode/plot-type-menu.mjs +85 -0
  135. package/esm2022/lib/plot-mode/tool-params-model.mjs +87 -0
  136. package/esm2022/lib/plot.utilities.mjs +296 -473
  137. package/esm2022/lib/processing/image-crop.mjs +1 -1
  138. package/esm2022/lib/processing/processing-image.mjs +28 -15
  139. package/esm2022/lib/provide-visualization.mjs +40 -14
  140. package/esm2022/lib/region-editor/class-tree/class-tree.component.mjs +156 -0
  141. package/esm2022/lib/region-editor/class-tree/class-tree.mjs +108 -0
  142. package/esm2022/lib/region-editor/classes-panel/classes-panel.component.mjs +163 -0
  143. package/esm2022/lib/region-editor/file-stem.mjs +13 -0
  144. package/esm2022/lib/region-editor/manage-classes-dialog/manage-classes-dialog.component.mjs +118 -0
  145. package/esm2022/lib/region-editor/mask-export.service.mjs +98 -0
  146. package/esm2022/lib/region-editor/mask-raster.mjs +11 -5
  147. package/esm2022/lib/region-editor/region-color-dialog/region-color-dialog.component.mjs +56 -0
  148. package/esm2022/lib/region-editor/region-editor-help/region-editor-help.component.mjs +28 -0
  149. package/esm2022/lib/region-editor/region-editor.component.mjs +896 -660
  150. package/esm2022/lib/region-editor/region-metrics.mjs +86 -0
  151. package/esm2022/lib/region-editor/region-persistence.service.mjs +160 -0
  152. package/esm2022/lib/region-editor/region-table/region-table.component.mjs +169 -0
  153. package/esm2022/lib/region-editor/save-mask-dialog/save-mask-dialog.component.mjs +91 -0
  154. package/esm2022/lib/region-editor/save-regions-dialog/save-regions-dialog.component.mjs +92 -0
  155. package/esm2022/lib/region-ops.service.mjs +28 -70
  156. package/esm2022/lib/region-overlay/region-geometry.mjs +360 -0
  157. package/esm2022/lib/region-overlay/region-hit-test.mjs +103 -0
  158. package/esm2022/lib/region-overlay/region-source-layer.mjs +378 -0
  159. package/esm2022/lib/region-overlay/region-style.mjs +97 -0
  160. package/esm2022/lib/region-overlay/svg-region-renderer.mjs +228 -0
  161. package/esm2022/lib/region-source/http-region-source.mjs +104 -0
  162. package/esm2022/lib/region-source/region-source-ops.mjs +53 -0
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  166. package/esm2022/lib/region-source/worker-region-source.mjs +229 -0
  167. package/esm2022/lib/render-orchestrator.mjs +14 -11
  168. package/esm2022/lib/render-session.mjs +207 -0
  169. package/esm2022/lib/routing-visualizer.service.mjs +858 -414
  170. package/esm2022/lib/section-pane/section-pane.component.mjs +299 -0
  171. package/esm2022/lib/spatial/density-raster.mjs +14 -0
  172. package/esm2022/lib/spatial/embedding-compute-coordinator.mjs +239 -0
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  189. package/esm2022/lib/spatial/spatial-volume-image.mjs +2 -4
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  191. package/esm2022/lib/spatial/transcript-grouping.mjs +307 -0
  192. package/esm2022/lib/spatial-controls/spatial-cells-panel/spatial-cells-panel.component.mjs +150 -0
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  201. package/esm2022/lib/spatial-controls/spatial-gene-picker.mjs +153 -0
  202. package/esm2022/lib/spatial-controls/spatial-gene-tree/spatial-gene-tree.component.mjs +241 -0
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  208. package/esm2022/lib/spatial-controls/spatial-transcripts-panel/spatial-transcripts-panel.component.mjs +370 -0
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  540. package/lib/visualizer/viewer-shortcuts.d.ts +71 -0
  541. package/lib/visualizer/visualizer-context-menu.d.ts +55 -0
  542. package/lib/visualizer/volume-sections.d.ts +64 -0
  543. package/lib/visualizer.component.d.ts +232 -447
  544. package/lib/workers/spatial-math-ops.d.ts +65 -0
  545. package/lib/workers/spatial-math-worker.d.ts +7 -0
  546. package/lib/workers/spatial-math.d.ts +74 -0
  547. package/package.json +12 -3
  548. package/src/lib/assets/slice.svg +23 -0
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  551. package/esm2022/lib/implementations/napari-js/napari-axes-labels.mjs +0 -97
  552. package/esm2022/lib/implementations/napari-js/napari-navigator.mjs +0 -195
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  555. package/fesm2022/jax-data-science-sci-image-visualizer-onnx-sam-session-BwP-A11m.mjs.map +0 -1
  556. package/lib/implementations/napari-js/napari-axes-labels.d.ts +0 -49
  557. package/lib/implementations/napari-js/napari-navigator.d.ts +0 -72
  558. package/lib/implementations/napari-js/napari-scale-bar.d.ts +0 -35
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  561. package/src/lib/assets/colormap-luts.json +0 -1
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  563. package/src/lib/assets/icons/colormap-earth.png +0 -0
  564. package/src/lib/assets/icons/colormap-placeholder.png +0 -0
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  566. package/src/lib/assets/interactive-segmentation-cursor.svg +0 -1
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@@ -0,0 +1,54 @@
1
+ import { Observable } from 'rxjs';
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+ import { Region } from '../models/region';
3
+ import * as i0 from "@angular/core";
4
+ /** Mask type: one foreground value, or a distinct id per region. */
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+ export type MaskMode = 'binary' | 'multiclass';
6
+ /** What to rasterize, at the full image size. */
7
+ export interface MaskExportRequest {
8
+ regions: Region[];
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+ imageSize: {
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+ width: number;
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+ height: number;
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+ };
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+ mode: MaskMode;
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+ /** Recorded in the PNG metadata. */
15
+ sourceName?: string;
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+ }
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+ /** Progress of one mask export, in order: planned → progress* → encoding → done. */
18
+ export type MaskExportEvent =
19
+ /** The mask size; `scale` < 1 when the image exceeds the pixel budget. */
20
+ {
21
+ type: 'planned';
22
+ width: number;
23
+ height: number;
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+ scale: number;
25
+ }
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+ /** 0–100 rasterization progress. */
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+ | {
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+ type: 'progress';
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+ percent: number;
30
+ }
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+ /** Rasterizing finished; the PNG is being encoded. */
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+ | {
33
+ type: 'encoding';
34
+ } | {
35
+ type: 'done';
36
+ blob: Blob;
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+ };
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+ /**
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+ * Rasterizes regions to a label-mask PNG in a Web Worker (jit-ui#95), so the
40
+ * full-resolution rasterize and PNG encode never freeze the UI and the job can
41
+ * be cancelled. Component-agnostic: {@link export} returns a cold Observable —
42
+ * subscribing starts a worker, unsubscribing terminates it (cancel), and a
43
+ * worker failure is an error carrying a user-facing message. Whole-slide
44
+ * images are capped to a safe pixel budget (the geometry is scaled to match).
45
+ */
46
+ export declare class MaskExportService {
47
+ export(request: MaskExportRequest): Observable<MaskExportEvent>;
48
+ /** Worker factory: a dynamic import, so the worker module (and its
49
+ * `import.meta.url`, which the CommonJS test compile rejects) loads lazily.
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+ * Overridable in tests. */
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+ protected createWorker(): Promise<Worker>;
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+ static ɵfac: i0.ɵɵFactoryDeclaration<MaskExportService, never>;
53
+ static ɵprov: i0.ɵɵInjectableDeclaration<MaskExportService>;
54
+ }
@@ -1,4 +1,6 @@
1
1
  import { Region } from '../models/region';
2
+ import type { BBoxMask } from '../geometry/raster';
3
+ export type { BBoxMask };
2
4
  /** A single closed ring (+ optional holes) in image-pixel coordinates. A region
3
5
  * rasterizes as the union of its parts. Plain data so it survives a
4
6
  * `postMessage` structured clone into the mask worker. */
@@ -7,14 +9,6 @@ export interface MaskPart {
7
9
  ypoints: number[];
8
10
  holes?: number[][][];
9
11
  }
10
- /** A bbox-relative binary mask, as returned by `WandService.rasterizePolygon`. */
11
- export interface BBoxMask {
12
- bx: number;
13
- by: number;
14
- bw: number;
15
- bh: number;
16
- mask: Uint8Array;
17
- }
18
12
  /** Polygon-fill function (the wand's scanline rasterizer), injected so this
19
13
  * module stays free of Angular/DOM and can run inside a worker. */
20
14
  export type RasterizeFn = (xpoints: number[], ypoints: number[], imageWidth: number, imageHeight: number, holes?: number[][][]) => BBoxMask | null;
@@ -0,0 +1,29 @@
1
+ import { EventEmitter } from '@angular/core';
2
+ import * as i0 from "@angular/core";
3
+ /** One class's colour in the dialog; `label` '' groups unclassified regions. */
4
+ export interface ClassColorEdit {
5
+ label: string;
6
+ color: string;
7
+ }
8
+ /**
9
+ * "Edit colour of selected regions": one picker per class among the selection.
10
+ * Edits a private copy of `edits` and reports the result on Apply; the editor
11
+ * applies it to the regions (copy-on-write) and commits.
12
+ */
13
+ export declare class RegionColorDialogComponent {
14
+ /** The dialog is open. */
15
+ visible: boolean;
16
+ /** The dialog was closed (`false`); two-way with {@link visible}. */
17
+ visibleChange: EventEmitter<boolean>;
18
+ /** Number of selected regions, for the caption. */
19
+ selectedCount: number;
20
+ /** The seeded colours; the dialog edits a copy. */
21
+ set edits(value: ClassColorEdit[] | null | undefined);
22
+ /** Apply clicked: the edited colours per class. */
23
+ apply: EventEmitter<ClassColorEdit[]>;
24
+ protected draft: ClassColorEdit[];
25
+ protected setColor(i: number, color: string): void;
26
+ protected close(): void;
27
+ static ɵfac: i0.ɵɵFactoryDeclaration<RegionColorDialogComponent, never>;
28
+ static ɵcmp: i0.ɵɵComponentDeclaration<RegionColorDialogComponent, "region-color-dialog", never, { "visible": { "alias": "visible"; "required": false; }; "selectedCount": { "alias": "selectedCount"; "required": false; }; "edits": { "alias": "edits"; "required": false; }; }, { "visibleChange": "visibleChange"; "apply": "apply"; }, never, never, true, never>;
29
+ }
@@ -0,0 +1,11 @@
1
+ import { EventEmitter } from '@angular/core';
2
+ import * as i0 from "@angular/core";
3
+ /** The Region Editor's help dialog (static content). */
4
+ export declare class RegionEditorHelpComponent {
5
+ /** The dialog is open. */
6
+ visible: boolean;
7
+ /** The dialog was closed (`false`); two-way with {@link visible}. */
8
+ visibleChange: EventEmitter<boolean>;
9
+ static ɵfac: i0.ɵɵFactoryDeclaration<RegionEditorHelpComponent, never>;
10
+ static ɵcmp: i0.ɵɵComponentDeclaration<RegionEditorHelpComponent, "region-editor-help", never, { "visible": { "alias": "visible"; "required": false; }; }, { "visibleChange": "visibleChange"; }, never, never, true, never>;
11
+ }