@vitessce/vit-s 3.9.5 → 3.9.7

package/dist/index.js

@@ -17852,6 +17852,11 @@ const CloseIcon = createSvgIcon(/* @__PURE__ */ jsxRuntimeExports.jsx("path", {
 const CloudDownloadIcon = createSvgIcon(/* @__PURE__ */ jsxRuntimeExports.jsx("path", {
   d: "M19.35 10.04C18.67 6.59 15.64 4 12 4 9.11 4 6.6 5.64 5.35 8.04 2.34 8.36 0 10.91 0 14c0 3.31 2.69 6 6 6h13c2.76 0 5-2.24 5-5 0-2.64-2.05-4.78-4.65-4.96M17 13l-5 5-5-5h3V9h4v4z"
 }), "CloudDownload");
+const MenuBookIcon = createSvgIcon([/* @__PURE__ */ jsxRuntimeExports.jsx("path", {
+  d: "M21 5c-1.11-.35-2.33-.5-3.5-.5-1.95 0-4.05.4-5.5 1.5-1.45-1.1-3.55-1.5-5.5-1.5S2.45 4.9 1 6v14.65c0 .25.25.5.5.5.1 0 .15-.05.25-.05C3.1 20.45 5.05 20 6.5 20c1.95 0 4.05.4 5.5 1.5 1.35-.85 3.8-1.5 5.5-1.5 1.65 0 3.35.3 4.75 1.05.1.05.15.05.25.05.25 0 .5-.25.5-.5V6c-.6-.45-1.25-.75-2-1m0 13.5c-1.1-.35-2.3-.5-3.5-.5-1.7 0-4.15.65-5.5 1.5V8c1.35-.85 3.8-1.5 5.5-1.5 1.2 0 2.4.15 3.5.5z"
+}, "0"), /* @__PURE__ */ jsxRuntimeExports.jsx("path", {
+  d: "M17.5 10.5c.88 0 1.73.09 2.5.26V9.24c-.79-.15-1.64-.24-2.5-.24-1.7 0-3.24.29-4.5.83v1.66c1.13-.64 2.7-.99 4.5-.99M13 12.49v1.66c1.13-.64 2.7-.99 4.5-.99.88 0 1.73.09 2.5.26V11.9c-.79-.15-1.64-.24-2.5-.24-1.7 0-3.24.3-4.5.83m4.5 1.84c-1.7 0-3.24.29-4.5.83v1.66c1.13-.64 2.7-.99 4.5-.99.88 0 1.73.09 2.5.26v-1.52c-.79-.16-1.64-.24-2.5-.24"
+}, "1")], "MenuBook");
 const HelpIcon = createSvgIcon(/* @__PURE__ */ jsxRuntimeExports.jsx("path", {
   d: "M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10S17.52 2 12 2m1 17h-2v-2h2zm2.07-7.75-.9.92C13.45 12.9 13 13.5 13 15h-2v-.5c0-1.1.45-2.1 1.17-2.83l1.24-1.26c.37-.36.59-.86.59-1.41 0-1.1-.9-2-2-2s-2 .9-2 2H8c0-2.21 1.79-4 4-4s4 1.79 4 4c0 .88-.36 1.68-.93 2.25"
 }), "Help");
@@ -33975,6 +33980,7 @@ const FileType$1 = {
   // Neuroglancer
   // Precomputed (mesh) format
   OBS_SEGMENTATIONS_NG_PRECOMPUTED: "obsSegmentations.ng-precomputed",
+  OBS_POINTS_NG_ANNOTATIONS: "obsPoints.ng-annotations",
   // New file types to support old file types:
   // - cells.json
   OBS_EMBEDDING_CELLS_JSON: "obsEmbedding.cells.json",
@@ -34208,6 +34214,7 @@ const STATUS = {
   [FileType$1.FEATURE_LABELS_MUDATA_ZARR]: DataType$1.FEATURE_LABELS,
   [FileType$1.OBS_SEGMENTATIONS_GLB]: DataType$1.OBS_SEGMENTATIONS,
   [FileType$1.OBS_SEGMENTATIONS_NG_PRECOMPUTED]: DataType$1.OBS_SEGMENTATIONS,
+  [FileType$1.OBS_POINTS_NG_ANNOTATIONS]: DataType$1.OBS_POINTS,
   [FileType$1.IMAGE_SPATIALDATA_ZARR]: DataType$1.IMAGE,
   [FileType$1.LABELS_SPATIALDATA_ZARR]: DataType$1.OBS_SEGMENTATIONS,
   [FileType$1.SHAPES_SPATIALDATA_ZARR]: DataType$1.OBS_SEGMENTATIONS,
@@ -34427,6 +34434,8 @@ const AUTO_INDEPENDENT_COORDINATION_TYPES = [
 ];
 ({
   [ViewType$1.NEUROGLANCER]: [
+    CoordinationType$1.META_COORDINATION_SCOPES,
+    CoordinationType$1.META_COORDINATION_SCOPES_BY,
     CoordinationType$1.DATASET,
     CoordinationType$1.SPATIAL_TARGET_X,
     CoordinationType$1.SPATIAL_TARGET_Y,
@@ -34448,7 +34457,26 @@ const AUTO_INDEPENDENT_COORDINATION_TYPES = [
     CoordinationType$1.OBS_COLOR_ENCODING,
     CoordinationType$1.EMBEDDING_TYPE,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
-    CoordinationType$1.TOOLTIPS_VISIBLE
+    CoordinationType$1.TOOLTIPS_VISIBLE,
+    CoordinationType$1.FILE_UID,
+    CoordinationType$1.IMAGE_LAYER,
+    CoordinationType$1.SEGMENTATION_LAYER,
+    CoordinationType$1.IMAGE_CHANNEL,
+    CoordinationType$1.SEGMENTATION_CHANNEL,
+    CoordinationType$1.POINT_LAYER,
+    CoordinationType$1.FEATURE_COLOR,
+    CoordinationType$1.FEATURE_FILTER_MODE,
+    CoordinationType$1.FEATURE_HIGHLIGHT,
+    CoordinationType$1.FEATURE_SELECTION,
+    CoordinationType$1.FEATURE_VALUE_COLORMAP,
+    CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType$1.SPATIAL_LAYER_COLOR,
+    CoordinationType$1.SPATIAL_LAYER_OPACITY,
+    CoordinationType$1.SPATIAL_LAYER_VISIBLE,
+    CoordinationType$1.SPATIAL_CHANNEL_COLOR,
+    CoordinationType$1.SPATIAL_CHANNEL_OPACITY,
+    CoordinationType$1.SPATIAL_CHANNEL_VISIBLE,
+    CoordinationType$1.LEGEND_VISIBLE
   ],
   [ViewType$1.SCATTERPLOT]: [
     CoordinationType$1.DATASET,
@@ -35086,7 +35114,7 @@ const AUTO_INDEPENDENT_COORDINATION_TYPES = [
     CoordinationType$1.HIERARCHY_LEVELS
   ]
 });
-const version = "3.9.5";
+const version = "3.9.7";
 const META_VERSION = {
   version
 };
@@ -35567,14 +35595,23 @@ z.object({
 z.object({
   // TODO: Should this explicitly specify sharded vs. unsharded?
   // Or can/should that be inferred from the data?
-  dimensionX: z.number(),
-  dimensionY: z.number(),
-  dimensionZ: z.number(),
-  dimensionUnit: z.enum(["nm", "um", "µm", "mm", "cm", "m"]),
+  // Note: None of these make sense to specify at the file level, since they
+  // are global camera settings that would apply to all layers.
+  // Intead, initial values should be set via the usual coordination space mechanism,
+  // and the NeuroglancerSubscriber should handle conversion into values to pass to Neuroglancer.
+  // dimensionX: z.number(),
+  // dimensionY: z.number(),
+  // dimensionZ: z.number(),
+  // dimensionUnit: z.enum(['nm', 'um', 'µm', 'mm', 'cm', 'm']),
   // TODO: should the following be passed via coordination types instead?
-  projectionScale: z.number(),
-  position: z.array(z.number()).length(3),
-  projectionOrientation: z.array(z.number()).length(4)
+  // projectionScale: z.number(),
+  // position: z.array(z.number()).length(3),
+  // projectionOrientation: z.array(z.number()).length(4),
+}).partial().nullable();
+z.object({
+  projectionAnnotationSpacing: z.number(),
+  featureIndexProp: z.string().optional().describe("The name of the Neuroglancer AnnotationProperty containing feature IDs. For example, specify 'gene' to use prop_gene() in the Neuroglancer shader code."),
+  pointIndexProp: z.string().optional().describe("The name of the Neuroglancer AnnotationProperty containing point IDs. For example, specify 'point_id' to use prop_point_id() in the Neuroglancer shader code.")
 }).partial().nullable();
 z.object({
   obsIndex: z.string(),
@@ -46470,7 +46507,7 @@ function DownloadOptions(props) {
   ) : null;
 }
 function HelpButton(props) {
-  const { helpText } = props;
+  const { helpText, guideUrl } = props;
   const [open2, setOpen] = useState(false);
   const { classes } = useStyles$1();
   return /* @__PURE__ */ React__default.createElement(
@@ -46485,7 +46522,20 @@ function HelpButton(props) {
       "aria-label": "Open help info",
       withPaper: false
     },
-    /* @__PURE__ */ React__default.createElement("span", { className: classes.helpTextSpan }, helpText)
+    /* @__PURE__ */ React__default.createElement("span", { className: classes.helpTextSpan }, helpText, guideUrl ? /* @__PURE__ */ React__default.createElement(
+      IconButton,
+      {
+        component: "a",
+        href: guideUrl,
+        target: "_blank",
+        rel: "noopener noreferrer",
+        size: "small",
+        className: classes.iconButton,
+        title: "Open Navigation Guide",
+        "aria-label": "Open navigation guide"
+      },
+      /* @__PURE__ */ React__default.createElement(MenuBookIcon, null)
+    ) : null)
   );
 }
 function ErrorInfo(props) {
@@ -46548,7 +46598,8 @@ function TitleInfo(props) {
     downloadButtonVisible = true,
     helpText,
     withPadding = true,
-    errors: errorsProp
+    errors: errorsProp,
+    guideUrl
   } = props;
   const errors = errorsProp == null ? void 0 : errorsProp.filter(Boolean);
   const { classes } = useTitleStyles();
@@ -46573,7 +46624,8 @@ function TitleInfo(props) {
     ) : null, helpText ? /* @__PURE__ */ React__default.createElement(
       HelpButton,
       {
-        helpText
+        helpText,
+        guideUrl
       }
     ) : null, closeButtonVisible && removeGridComponent ? /* @__PURE__ */ React__default.createElement(
       ClosePaneButton,

package/dist-tsc/TitleInfo.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"TitleInfo.d.ts","sourceRoot":"","sources":["../src/TitleInfo.js"],"names":[],"mappings":"AAmNA,mDAwEC"}
+{"version":3,"file":"TitleInfo.d.ts","sourceRoot":"","sources":["../src/TitleInfo.js"],"names":[],"mappings":"AAqOA,mDAyEC"}

package/dist-tsc/TitleInfo.js

@@ -1,7 +1,7 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import React, { useState, useMemo } from 'react';
 import clsx from 'clsx';
-import { makeStyles, MenuItem, IconButton, Link, List, Alert, CloudDownload as CloudDownloadIcon, ArrowDropDown as ArrowDropDownIcon, ArrowDropUp as ArrowDropUpIcon, Settings as SettingsIcon, Close as CloseIcon, Help as HelpIcon, Warning as WarningIcon, } from '@vitessce/styles';
+import { makeStyles, MenuItem, IconButton, Link, List, Alert, CloudDownload as CloudDownloadIcon, ArrowDropDown as ArrowDropDownIcon, ArrowDropUp as ArrowDropUpIcon, Settings as SettingsIcon, Close as CloseIcon, Help as HelpIcon, Warning as WarningIcon, MenuBook as MenuBookIcon, } from '@vitessce/styles';
 import { TOOLTIP_ANCESTOR } from './classNames.js';
 import LoadingIndicator from './LoadingIndicator.js';
 import { PopperMenu } from './shared-mui/components.js';
@@ -80,10 +80,10 @@ function DownloadOptions(props) {
     return (urls && urls.length ? (_jsx(PopperMenu, { open: open, setOpen: setOpen, buttonIcon: buttonIcon, buttonClassName: classes.iconButton, placement: "bottom-end", title: "Download Options", "aria-label": "Open download options menu", children: urls.map(({ url, name }) => (_jsx(MenuItem, { dense: true, "aria-label": `Click to download ${name}`, children: _jsxs(Link, { underline: "always", href: url, target: "_blank", rel: "noopener", className: classes.downloadLink, children: ["Download ", name] }) }, `${url}_${name}`))) })) : null);
 }
 function HelpButton(props) {
-    const { helpText } = props;
+    const { helpText, guideUrl } = props;
     const [open, setOpen] = useState(false);
     const { classes } = useStyles();
-    return (_jsx(PopperMenu, { open: open, setOpen: setOpen, buttonIcon: _jsx(HelpIcon, {}), buttonClassName: classes.iconButton, placement: "bottom-end", title: "Help Info", "aria-label": "Open help info", withPaper: false, children: _jsx("span", { className: classes.helpTextSpan, children: helpText }) }));
+    return (_jsx(PopperMenu, { open: open, setOpen: setOpen, buttonIcon: _jsx(HelpIcon, {}), buttonClassName: classes.iconButton, placement: "bottom-end", title: "Help Info", "aria-label": "Open help info", withPaper: false, children: _jsxs("span", { className: classes.helpTextSpan, children: [helpText, guideUrl ? (_jsx(IconButton, { component: "a", href: guideUrl, target: "_blank", rel: "noopener noreferrer", size: "small", className: classes.iconButton, title: "Open Navigation Guide", "aria-label": "Open navigation guide", children: _jsx(MenuBookIcon, {}) })) : null] }) }));
 }
 function ErrorInfo(props) {
     const { errors } = props;
@@ -99,13 +99,13 @@ function ClosePaneButton(props) {
     return (_jsx(IconButton, { onClick: removeGridComponent, size: "small", className: classes.iconButton, title: "Close View", "aria-label": "Close panel button", children: _jsx(CloseIcon, {}) }));
 }
 export function TitleInfo(props) {
-    const { title, info, children, isScroll, isSpatial, removeGridComponent, urls, isReady, options, closeButtonVisible = true, downloadButtonVisible = true, helpText, withPadding = true, errors: errorsProp, } = props;
+    const { title, info, children, isScroll, isSpatial, removeGridComponent, urls, isReady, options, closeButtonVisible = true, downloadButtonVisible = true, helpText, withPadding = true, errors: errorsProp, guideUrl, } = props;
     const errors = errorsProp?.filter(Boolean);
     const { classes } = useTitleStyles();
     const hasInfoText = Boolean(info);
     return (
     // d-flex without wrapping div is not always full height; I don't understand the root cause.
-    _jsxs(_Fragment, { children: [_jsxs("div", { className: classes.title, role: "banner", children: [_jsx("div", { className: classes.titleLeft, role: "heading", "aria-level": "1", children: title }), _jsxs("div", { className: classes.titleButtons, role: "toolbar", "aria-label": "Plot options and controls", children: [_jsx(PlotOptions, { options: options }), downloadButtonVisible ? (_jsx(DownloadOptions, { urls: urls })) : null, Array.isArray(errors) && errors.length > 0 ? (_jsx(ErrorInfo, { errors: errors })) : null, helpText ? (_jsx(HelpButton, { helpText: helpText })) : null, closeButtonVisible && removeGridComponent ? (_jsx(ClosePaneButton, { removeGridComponent: removeGridComponent })) : null] })] }), _jsxs("div", { className: clsx(TOOLTIP_ANCESTOR, classes.card, {
+    _jsxs(_Fragment, { children: [_jsxs("div", { className: classes.title, role: "banner", children: [_jsx("div", { className: classes.titleLeft, role: "heading", "aria-level": "1", children: title }), _jsxs("div", { className: classes.titleButtons, role: "toolbar", "aria-label": "Plot options and controls", children: [_jsx(PlotOptions, { options: options }), downloadButtonVisible ? (_jsx(DownloadOptions, { urls: urls })) : null, Array.isArray(errors) && errors.length > 0 ? (_jsx(ErrorInfo, { errors: errors })) : null, helpText ? (_jsx(HelpButton, { helpText: helpText, guideUrl: guideUrl })) : null, closeButtonVisible && removeGridComponent ? (_jsx(ClosePaneButton, { removeGridComponent: removeGridComponent })) : null] })] }), _jsxs("div", { className: clsx(TOOLTIP_ANCESTOR, classes.card, {
                     [classes.scrollCard]: isScroll,
                     [classes.spatialCard]: isSpatial,
                     [classes.noScrollCard]: !isScroll && !isSpatial,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vit-s",
-  "version": "3.9.5",
+  "version": "3.9.7",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -31,17 +31,17 @@
     "react-error-boundary": "^5.0.0",
     "@placemarkio/flat-drop-files": "^1.0.2",
     "zarrita": "0.6.1",
-    "@vitessce/styles": "3.9.5",
-    "@vitessce/error": "3.9.5",
-    "@vitessce/abstract": "3.9.5",
-    "@vitessce/plugins": "3.9.5",
-    "@vitessce/constants-internal": "3.9.5",
-    "@vitessce/schemas": "3.9.5",
-    "@vitessce/sets-utils": "3.9.5",
-    "@vitessce/utils": "3.9.5",
-    "@vitessce/zarr-utils": "3.9.5",
-    "@vitessce/config": "3.9.5",
-    "@vitessce/globals": "3.9.5"
+    "@vitessce/styles": "3.9.7",
+    "@vitessce/abstract": "3.9.7",
+    "@vitessce/error": "3.9.7",
+    "@vitessce/plugins": "3.9.7",
+    "@vitessce/schemas": "3.9.7",
+    "@vitessce/utils": "3.9.7",
+    "@vitessce/constants-internal": "3.9.7",
+    "@vitessce/sets-utils": "3.9.7",
+    "@vitessce/config": "3.9.7",
+    "@vitessce/zarr-utils": "3.9.7",
+    "@vitessce/globals": "3.9.7"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^6.6.3",
@@ -50,7 +50,7 @@
     "react-dom": "18.3.1",
     "vite": "^7.0.0",
     "vitest": "^3.1.4",
-    "@vitessce/types": "3.9.5"
+    "@vitessce/types": "3.9.7"
   },
   "peerDependencies": {
     "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0"

package/src/TitleInfo.js

@@ -14,6 +14,7 @@ import {
   Close as CloseIcon,
   Help as HelpIcon,
   Warning as WarningIcon,
+  MenuBook as MenuBookIcon,
 } from '@vitessce/styles';
 
 import { TOOLTIP_ANCESTOR } from './classNames.js';
@@ -141,7 +142,7 @@ function DownloadOptions(props) {
 }
 
 function HelpButton(props) {
-  const { helpText } = props;
+  const { helpText, guideUrl } = props;
   const [open, setOpen] = useState(false);
   const { classes } = useStyles();
   return (
@@ -155,7 +156,23 @@ function HelpButton(props) {
       aria-label="Open help info"
       withPaper={false}
     >
-      <span className={classes.helpTextSpan}>{helpText}</span>
+      <span className={classes.helpTextSpan}>
+        {helpText}
+        {guideUrl ? (
+          <IconButton
+            component="a"
+            href={guideUrl}
+            target="_blank"
+            rel="noopener noreferrer"
+            size="small"
+            className={classes.iconButton}
+            title="Open Navigation Guide"
+            aria-label="Open navigation guide"
+          >
+            <MenuBookIcon />
+          </IconButton>
+        ) : null}
+      </span>
     </PopperMenu>
   );
 }
@@ -209,11 +226,12 @@ function ClosePaneButton(props) {
   );
 }
 
+
 export function TitleInfo(props) {
   const {
     title, info, children, isScroll, isSpatial, removeGridComponent, urls,
     isReady, options, closeButtonVisible = true, downloadButtonVisible = true,
-    helpText, withPadding = true, errors: errorsProp,
+    helpText, withPadding = true, errors: errorsProp, guideUrl,
   } = props;
 
   const errors = errorsProp?.filter(Boolean);
@@ -245,6 +263,7 @@ export function TitleInfo(props) {
           {helpText ? (
             <HelpButton
               helpText={helpText}
+              guideUrl={guideUrl}
             />
           ) : null}
           {closeButtonVisible && removeGridComponent ? (