@jax-data-science/sci-image-visualizer 0.3.1 → 0.3.2

package/fesm2022/jax-data-science-sci-image-visualizer.mjs

@@ -1002,6 +1002,62 @@ class MultiPolygon {
         this.polygons = [];
     }
 }
+/**
+ * Rebuild a plain-object `bounds` as the class instance the renderers expect
+ * (jit-ui#124).
+ *
+ * Regions that arrive as JSON — a host's server response, a `structuredClone`,
+ * anything that has been through `JSON.parse` — carry a `bounds` that has the
+ * right *fields* but not the right *prototype*. The renderers disagree about
+ * whether that is acceptable: `Region.getShape()` (Plotly) and the napari
+ * overlay duck-type the bounds, while the OpenSeadragon overlay discriminates
+ * with `bounds instanceof Rectangle`. So a JSON region drew in Heatmap mode and
+ * silently vanished in Image mode. `instanceof` also gates the store's own
+ * geometry de-duplication, `moveRegion`, and the GeoJSON export — a JSON region
+ * is undraggable and absent from a save in *every* mode.
+ *
+ * Rather than duck-type ~20 call sites, the store normalizes here on the way in,
+ * so everything downstream can keep relying on `instanceof`. Values that are
+ * already instances are returned **by reference**, untouched: overlays and tools
+ * hold onto the bounds they created and mutate them in place during a drag.
+ */
+function hydrateBounds(bounds) {
+    if (!bounds ||
+        bounds instanceof Rectangle ||
+        bounds instanceof Polygon ||
+        bounds instanceof MultiPolygon) {
+        return bounds;
+    }
+    if (Array.isArray(bounds.polygons)) {
+        const multi = new MultiPolygon();
+        multi.polygons = bounds.polygons.map((part) => hydratePolygon(part));
+        return multi;
+    }
+    if ('npoints' in bounds || 'xpoints' in bounds) {
+        return hydratePolygon(bounds);
+    }
+    if ('width' in bounds && 'height' in bounds) {
+        return Object.assign(new Rectangle(), bounds);
+    }
+    // Nothing recognisable — hand it back rather than coerce it into the wrong
+    // geometry. It renders nowhere either way, but a caller can still inspect it.
+    return bounds;
+}
+/** {@link hydrateBounds} for one polygon, deriving the fields a lean serializer
+ *  omits: JIT's Java `PolygonSerializer` writes only `npoints`/`xpoints`/
+ *  `ypoints`, while the GeoJSON export reads `coordinates` and the overlays read
+ *  `closed`. */
+function hydratePolygon(raw) {
+    if (raw instanceof Polygon)
+        return raw;
+    const polygon = Object.assign(new Polygon(), raw);
+    polygon.xpoints = [...(raw.xpoints ?? [])];
+    polygon.ypoints = [...(raw.ypoints ?? [])];
+    polygon.npoints = raw.npoints ?? polygon.xpoints.length;
+    polygon.coordinates = raw.coordinates ?? polygon.xpoints.map((x, i) => [x, polygon.ypoints[i]]);
+    polygon.closed = raw.closed ?? true;
+    return polygon;
+}
 
 /**
  * Preset annotation classes (jit-ui#70).
@@ -10359,6 +10415,10 @@ class RegionStore {
                 region.id = this.nextId++;
             if (region.name == null)
                 region.name = `shape${region.id}`;
+            // JSON in, class instances out — everything downstream (the overlays'
+            // rendering, geometry de-dup, moveRegion, GeoJSON export) discriminates
+            // the bounds with `instanceof` (jit-ui#124).
+            region.bounds = hydrateBounds(region.bounds);
         }
         this.applyClassificationColors(regions);
         this.isRegionSavedOn = isRegionSaveOn;
@@ -10511,6 +10571,7 @@ class RegionStore {
             if (region.name == null)
                 region.name = `shape${region.id}`;
             region.z = z;
+            region.bounds = hydrateBounds(region.bounds); // jit-ui#124
         }
         this.applyClassificationColors(regions);
         return regions.slice();
@@ -10762,6 +10823,7 @@ class RegionStore {
             region.id = this.nextId++;
         if (region.name == null)
             region.name = `shape${region.id}`;
+        region.bounds = hydrateBounds(region.bounds); // jit-ui#124
         // A region drawn on a stack belongs to the slice currently displayed, so
         // it saves/reloads on that slice (jit-ui#93). No-op for single-plane images
         // (currentSliceZ stays 0).
@@ -22098,5 +22160,5 @@ function provideVisualization() {
  * Generated bundle index. Do not edit.
  */
 
-export { ALL_TOOLBAR_TOOLS, CELL_SEGMENTER, CHANNEL_HISTOGRAM_API, CellposeSegmenterService, ChannelHistogramComponent, DEFAULT_FALLBACK_PALETTE, DEFAULT_SAM_MODEL_ID, HexColorPickerComponent, IMAGE_STATE_PORT, INSTANCE_SEGMENTER, ImageConverterService, LUT_COLORS, MultiPolygon, NAPARI_DECIMATE_OPTIONS, NAPARI_DEFAULT_DECIMATE, PLOT_TYPE_DESCRIPTORS, PREFERENCES_PORT, PlotType, Polygon, ProcessingImage, REGION_EDITOR_API, REGION_IO_PORT, Rectangle, Region, RegionEditorComponent, RoutingVisualizerService, SAM_MODELS, SEMANTIC_SEGMENTER, ShapeSelection, TILE_ACCESS_PORT, TOOLBAR_TOOLS, VISUALIZER, VIZ_CONFIG, ViewerFeature, VisualizationModule, VisualizerComponent, capabilitiesOf, cropImage, defaultPresetSet, getDefaultSamModelId, getOrtWasmBase, getPlotTypeDescriptor, getSamModel, isEmptyPresetSet, isNapari3d, isNapariIsosurface, isNapariScatter, isNapariScatter3d, isNapariSurface, isNapariVolume, isSamModelReady, isThreeDimensional, provideVisualization, setDefaultSamModel, setOrtWasmBase, setSamModelUrls, sortToolContributions, visibleToolContributions };
+export { ALL_TOOLBAR_TOOLS, CELL_SEGMENTER, CHANNEL_HISTOGRAM_API, CellposeSegmenterService, ChannelHistogramComponent, DEFAULT_FALLBACK_PALETTE, DEFAULT_SAM_MODEL_ID, HexColorPickerComponent, IMAGE_STATE_PORT, INSTANCE_SEGMENTER, ImageConverterService, LUT_COLORS, MultiPolygon, NAPARI_DECIMATE_OPTIONS, NAPARI_DEFAULT_DECIMATE, PLOT_TYPE_DESCRIPTORS, PREFERENCES_PORT, PlotType, Polygon, ProcessingImage, REGION_EDITOR_API, REGION_IO_PORT, Rectangle, Region, RegionEditorComponent, RoutingVisualizerService, SAM_MODELS, SEMANTIC_SEGMENTER, ShapeSelection, TILE_ACCESS_PORT, TOOLBAR_TOOLS, VISUALIZER, VIZ_CONFIG, ViewerFeature, VisualizationModule, VisualizerComponent, capabilitiesOf, cropImage, defaultPresetSet, getDefaultSamModelId, getOrtWasmBase, getPlotTypeDescriptor, getSamModel, hydrateBounds, isEmptyPresetSet, isNapari3d, isNapariIsosurface, isNapariScatter, isNapariScatter3d, isNapariSurface, isNapariVolume, isSamModelReady, isThreeDimensional, provideVisualization, setDefaultSamModel, setOrtWasmBase, setSamModelUrls, sortToolContributions, visibleToolContributions };
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