@vitessce/scatterplot-gating 3.2.1 → 3.3.0

package/dist/{deflate-10f9d67d.js → deflate-db1c8f5b.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-743f7ba3.js";
+import { B as BaseDecoder } from "./index-ffb8adc6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-743f7ba3.js → index-ffb8adc6.js}

@@ -10927,6 +10927,7 @@ const DataType$2 = {
 const FileType$1 = {
   // Joint file types
   ANNDATA_ZARR: "anndata.zarr",
+  SPATIALDATA_ZARR: "spatialdata.zarr",
   // Atomic file types
   OBS_EMBEDDING_CSV: "obsEmbedding.csv",
   OBS_SPOTS_CSV: "obsSpots.csv",
@@ -10949,6 +10950,16 @@ const FileType$1 = {
   OBS_SEGMENTATIONS_ANNDATA_ZARR: "obsSegmentations.anndata.zarr",
   OBS_LABELS_ANNDATA_ZARR: "obsLabels.anndata.zarr",
   FEATURE_LABELS_ANNDATA_ZARR: "featureLabels.anndata.zarr",
+  // SpatialData
+  IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
+  LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
+  SHAPES_SPATIALDATA_ZARR: "shapes.spatialdata.zarr",
+  OBS_FEATURE_MATRIX_SPATIALDATA_ZARR: "obsFeatureMatrix.spatialdata.zarr",
+  OBS_SETS_SPATIALDATA_ZARR: "obsSets.spatialdata.zarr",
+  OBS_SPOTS_SPATIALDATA_ZARR: "obsSpots.spatialdata.zarr",
+  // TODO:
+  // OBS_POINTS_SPATIALDATA_ZARR: 'obsPoints.spatialdata.zarr',
+  // OBS_LOCATIONS_SPATIALDATA_ZARR: 'obsLocations.spatialdata.zarr',
   // MuData
   OBS_FEATURE_MATRIX_MUDATA_ZARR: "obsFeatureMatrix.mudata.zarr",
   OBS_SETS_MUDATA_ZARR: "obsSets.mudata.zarr",
@@ -11750,9 +11761,30 @@ z.object({
   offsetsUrl: z.string().optional(),
   coordinateTransformations: omeCoordinateTransformations.optional()
 });
-z.object({
+const imageOmeZarrSchema = z.object({
   coordinateTransformations: omeCoordinateTransformations.optional()
 });
+imageOmeZarrSchema.extend({
+  path: z.string()
+});
+z.object({
+  path: z.string()
+});
+z.object({
+  path: z.string()
+});
+z.object({
+  path: z.string(),
+  tablePath: z.string().optional().describe("The path to a table which annotates the spots. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected.")
+});
+annDataObsFeatureMatrix.extend({
+  region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional()
+});
+z.object({
+  region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional(),
+  tablePath: z.string().optional().describe("The path to a table which contains the index for the set values."),
+  obsSets: annDataObsSets
+});
 z.object({
   obsIndex: z.string(),
   obsEmbedding: z.array(z.string()).length(2)
@@ -18472,9 +18504,9 @@ const schemePlasma = [[13, 8, 135], [16, 7, 136], [19, 7, 137], [22, 7, 138], [2
 function rgbSpline(spline) {
   return (colors) => {
     const n2 = colors.length;
-    let r2 = new Array(n2);
-    let g2 = new Array(n2);
-    let b = new Array(n2);
+    const r2 = new Array(n2);
+    const g2 = new Array(n2);
+    const b = new Array(n2);
     let i2;
     let color;
     for (i2 = 0; i2 < n2; ++i2) {
@@ -18483,10 +18515,10 @@ function rgbSpline(spline) {
       g2[i2] = color[1] || 0;
       b[i2] = color[2] || 0;
     }
-    r2 = spline(r2);
-    g2 = spline(g2);
-    b = spline(b);
-    return (t2) => [r2(t2), g2(t2), b(t2)];
+    const rFunc = spline(r2);
+    const gFunc = spline(g2);
+    const bFunc = spline(b);
+    return (t2) => [rFunc(t2), gFunc(t2), bFunc(t2)];
   };
 }
 function basis(values2) {
@@ -121094,16 +121126,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-4828923d.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-8a95c676.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-d8d40fca.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-5c97cf9e.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-da2166c3.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-10f9d67d.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-3b55e8df.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-ea6f16cd.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-f3457c94.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-b7775743.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-db1c8f5b.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-3e7a20be.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-8db218c1.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-adb9e0d3.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -130003,6 +130035,67 @@ function makeBoundingBox(viewState) {
     viewport.unproject([0, viewport.height])
   ];
 }
+const TARGETS = [1, 2, 3, 4, 5, 10, 20, 25, 50, 100, 200, 250, 500, 1e3];
+const MIN_TARGET = TARGETS[0];
+const MAX_TARGET = TARGETS[TARGETS.length - 1];
+const SI_PREFIXES = [
+  { symbol: "Y", exponent: 24 },
+  { symbol: "Z", exponent: 21 },
+  { symbol: "E", exponent: 18 },
+  { symbol: "P", exponent: 15 },
+  { symbol: "T", exponent: 12 },
+  { symbol: "G", exponent: 9 },
+  { symbol: "M", exponent: 6 },
+  { symbol: "k", exponent: 3 },
+  { symbol: "h", exponent: 2 },
+  { symbol: "da", exponent: 1 },
+  { symbol: "", exponent: 0 },
+  { symbol: "d", exponent: -1 },
+  { symbol: "c", exponent: -2 },
+  { symbol: "m", exponent: -3 },
+  { symbol: "µ", exponent: -6 },
+  { symbol: "n", exponent: -9 },
+  { symbol: "p", exponent: -12 },
+  { symbol: "f", exponent: -15 },
+  { symbol: "a", exponent: -18 },
+  { symbol: "z", exponent: -21 },
+  { symbol: "y", exponent: -24 }
+];
+function sizeToMeters(size, unit) {
+  if (!unit || unit === "m") {
+    return size;
+  }
+  if (unit.length > 1) {
+    let unitPrefix = unit.substring(0, unit.length - 1);
+    if (unitPrefix === "u") {
+      unitPrefix = "µ";
+    }
+    const unitObj = SI_PREFIXES.find((p) => p.symbol === unitPrefix);
+    if (unitObj) {
+      return size * 10 ** unitObj.exponent;
+    }
+  }
+  throw new Error("Received unknown unit");
+}
+function snapValue(value) {
+  let magnitude = 0;
+  if (value < MIN_TARGET || value > MAX_TARGET) {
+    magnitude = Math.floor(Math.log10(value));
+  }
+  let snappedUnit = SI_PREFIXES.find(
+    (p) => p.exponent % 3 === 0 && p.exponent <= magnitude
+  );
+  let adjustedValue = value / 10 ** snappedUnit.exponent;
+  if (adjustedValue > 500 && adjustedValue <= 1e3) {
+    snappedUnit = SI_PREFIXES.find(
+      (p) => p.exponent % 3 === 0 && p.exponent <= magnitude + 3
+    );
+    adjustedValue = value / 10 ** snappedUnit.exponent;
+  }
+  const targetNewUnits = TARGETS.find((t2) => t2 > adjustedValue);
+  const targetOrigUnits = targetNewUnits * 10 ** snappedUnit.exponent;
+  return [targetOrigUnits, targetNewUnits, snappedUnit.symbol];
+}
 const fs$1$1 = `#define SHADER_NAME xr-layer-fragment-shader
 
 precision highp float;
@@ -130770,26 +130863,27 @@ const OverviewLayer = class extends CompositeLayer {
 OverviewLayer.layerName = "OverviewLayer";
 OverviewLayer.defaultProps = defaultProps$3;
 function getPosition$1(boundingBox, position, length2) {
-  const viewLength = boundingBox[2][0] - boundingBox[0][0];
+  const viewWidth = boundingBox[2][0] - boundingBox[0][0];
+  const viewHeight = boundingBox[2][1] - boundingBox[0][1];
   switch (position) {
     case "bottom-right": {
-      const yCoord = boundingBox[2][1] - (boundingBox[2][1] - boundingBox[0][1]) * length2;
-      const xLeftCoord = boundingBox[2][0] - viewLength * length2;
+      const yCoord = boundingBox[2][1] - viewHeight * length2;
+      const xLeftCoord = boundingBox[2][0] - viewWidth * length2;
       return [yCoord, xLeftCoord];
     }
     case "top-right": {
-      const yCoord = (boundingBox[2][1] - boundingBox[0][1]) * length2;
-      const xLeftCoord = boundingBox[2][0] - viewLength * length2;
+      const yCoord = boundingBox[0][1] + viewHeight * length2;
+      const xLeftCoord = boundingBox[2][0] - viewWidth * length2;
       return [yCoord, xLeftCoord];
     }
     case "top-left": {
-      const yCoord = (boundingBox[2][1] - boundingBox[0][1]) * length2;
-      const xLeftCoord = viewLength * length2;
+      const yCoord = boundingBox[0][1] + viewHeight * length2;
+      const xLeftCoord = boundingBox[0][0] + viewWidth * length2;
       return [yCoord, xLeftCoord];
     }
     case "bottom-left": {
-      const yCoord = boundingBox[2][1] - (boundingBox[2][1] - boundingBox[0][1]) * length2;
-      const xLeftCoord = viewLength * length2;
+      const yCoord = boundingBox[2][1] - viewHeight * length2;
+      const xLeftCoord = boundingBox[0][0] + viewWidth * length2;
       return [yCoord, xLeftCoord];
     }
     default: {
@@ -130807,11 +130901,12 @@ const defaultProps$2$1 = {
   unit: { type: "string", value: "", compare: true },
   size: { type: "number", value: 1, compare: true },
   position: { type: "string", value: "bottom-right", compare: true },
-  length: { type: "number", value: 0.085, compare: true }
+  length: { type: "number", value: 0.085, compare: true },
+  snap: { type: "boolean", value: false, compare: true }
 };
 const ScaleBarLayer = class extends CompositeLayer {
   renderLayers() {
-    const { id, unit, size, position, viewState, length: length2 } = this.props;
+    const { id, unit, size, position, viewState, length: length2, snap } = this.props;
     const boundingBox = makeBoundingBox(viewState);
     const { zoom } = viewState;
     const viewLength = boundingBox[2][0] - boundingBox[0][0];
@@ -130820,15 +130915,27 @@ const ScaleBarLayer = class extends CompositeLayer {
       2 ** (-zoom + 1.5),
       (boundingBox[2][1] - boundingBox[0][1]) * 7e-3
     );
-    const numUnits = barLength * size;
+    let adjustedBarLength = barLength;
+    let displayNumber = (barLength * size).toPrecision(5);
+    let displayUnit = unit;
+    if (snap) {
+      const meterSize = sizeToMeters(size, unit);
+      const numUnits = barLength * meterSize;
+      const [snappedOrigUnits, snappedNewUnits, snappedUnitPrefix] = snapValue(numUnits);
+      adjustedBarLength = snappedOrigUnits / meterSize;
+      displayNumber = snappedNewUnits;
+      displayUnit = `${snappedUnitPrefix}m`;
+    }
     const [yCoord, xLeftCoord] = getPosition$1(boundingBox, position, length2);
+    const xRightCoord = xLeftCoord + barLength;
+    const isLeft = position.endsWith("-left");
     const lengthBar = new LineLayer({
       id: `scale-bar-length-${id}`,
       coordinateSystem: COORDINATE_SYSTEM.CARTESIAN,
       data: [
         [
-          [xLeftCoord, yCoord],
-          [xLeftCoord + barLength, yCoord]
+          [isLeft ? xLeftCoord : xRightCoord - adjustedBarLength, yCoord],
+          [isLeft ? xLeftCoord + adjustedBarLength : xRightCoord, yCoord]
         ]
       ],
       getSourcePosition: (d) => d[0],
@@ -130841,8 +130948,14 @@ const ScaleBarLayer = class extends CompositeLayer {
       coordinateSystem: COORDINATE_SYSTEM.CARTESIAN,
       data: [
         [
-          [xLeftCoord, yCoord - barHeight],
-          [xLeftCoord, yCoord + barHeight]
+          [
+            isLeft ? xLeftCoord : xRightCoord - adjustedBarLength,
+            yCoord - barHeight
+          ],
+          [
+            isLeft ? xLeftCoord : xRightCoord - adjustedBarLength,
+            yCoord + barHeight
+          ]
         ]
       ],
       getSourcePosition: (d) => d[0],
@@ -130855,8 +130968,14 @@ const ScaleBarLayer = class extends CompositeLayer {
       coordinateSystem: COORDINATE_SYSTEM.CARTESIAN,
       data: [
         [
-          [xLeftCoord + barLength, yCoord - barHeight],
-          [xLeftCoord + barLength, yCoord + barHeight]
+          [
+            isLeft ? xLeftCoord + adjustedBarLength : xRightCoord,
+            yCoord - barHeight
+          ],
+          [
+            isLeft ? xLeftCoord + adjustedBarLength : xRightCoord,
+            yCoord + barHeight
+          ]
         ]
       ],
       getSourcePosition: (d) => d[0],
@@ -130869,8 +130988,11 @@ const ScaleBarLayer = class extends CompositeLayer {
       coordinateSystem: COORDINATE_SYSTEM.CARTESIAN,
       data: [
         {
-          text: numUnits.toPrecision(5) + unit,
-          position: [xLeftCoord + barLength * 0.5, yCoord + barHeight * 4]
+          text: `${displayNumber}${displayUnit}`,
+          position: [
+            isLeft ? xLeftCoord + barLength * 0.5 : xRightCoord - barLength * 0.5,
+            yCoord + barHeight * 4
+          ]
         }
       ],
       getColor: [220, 220, 220, 255],
@@ -130879,7 +131001,7 @@ const ScaleBarLayer = class extends CompositeLayer {
       sizeUnits: "meters",
       sizeScale: 2 ** -zoom,
       characterSet: [
-        ...unit.split(""),
+        ...displayUnit.split(""),
         ...range(10).map((i2) => String(i2)),
         ".",
         "e",

package/dist/index.js

@@ -1,4 +1,4 @@
-import { G } from "./index-743f7ba3.js";
+import { G } from "./index-ffb8adc6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-da2166c3.js → jpeg-b7775743.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-743f7ba3.js";
+import { B as BaseDecoder } from "./index-ffb8adc6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-ea6f16cd.js → lerc-8db218c1.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-743f7ba3.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-ffb8adc6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-8a95c676.js → lzw-5c97cf9e.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-743f7ba3.js";
+import { B as BaseDecoder } from "./index-ffb8adc6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-3b55e8df.js → packbits-3e7a20be.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-743f7ba3.js";
+import { B as BaseDecoder } from "./index-ffb8adc6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-4828923d.js → raw-d8d40fca.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-743f7ba3.js";
+import { B as BaseDecoder } from "./index-ffb8adc6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-f3457c94.js → webimage-adb9e0d3.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-743f7ba3.js";
+import { B as BaseDecoder } from "./index-ffb8adc6.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-gating",
-  "version": "3.2.1",
+  "version": "3.3.0",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,11 +20,11 @@
     "d3-array": "^2.4.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.2.1",
-    "@vitessce/scatterplot": "3.2.1",
-    "@vitessce/sets-utils": "3.2.1",
-    "@vitessce/utils": "3.2.1",
-    "@vitessce/vit-s": "3.2.1"
+    "@vitessce/constants-internal": "3.3.0",
+    "@vitessce/scatterplot": "3.3.0",
+    "@vitessce/sets-utils": "3.3.0",
+    "@vitessce/utils": "3.3.0",
+    "@vitessce/vit-s": "3.3.0"
   },
   "devDependencies": {
     "react": "^18.0.0",