feature: Loading from the landing page, viewer page routing

package.json

@@ -47,6 +47,7 @@
     "lodash": "^4.17.20",
     "nouislider-react": "^3.4.0",
     "react-color": "^2.19.3",
+    "react-router-dom": "^6.22.3",
     "styled-components": "^6.1.8"
   },
   "peerDependencies": {

public/index.tsx

@@ -1,262 +1,38 @@
 import React from "react";
 import ReactDOM from "react-dom";
+import { createBrowserRouter, RouterProvider } from "react-router-dom";
 
 import "antd/dist/antd.less";
 
 // Components
+import { RenderMode, ViewerChannelSettings, ViewMode } from "../src";
+import AppWrapper from "../src/website/components/AppWrapper";
+import LandingPage from "../src/website/components/LandingPage";
+import { AppProps, GlobalViewerSettings } from "../src/aics-image-viewer/components/App/types";
+import StyleProvider from "../src/aics-image-viewer/components/StyleProvider";
 import "../src/aics-image-viewer/assets/styles/typography.css";
 import "./App.css";
 
-import { ImageViewerApp, RenderMode, ViewerChannelSettings, ViewMode } from "../src";
-import FirebaseRequest, { DatasetMetaData } from "./firebase";
-import { AppProps, GlobalViewerSettings } from "../src/aics-image-viewer/components/App/types";
-
 // vars filled at build time using webpack DefinePlugin
 console.log(`website-3d-cell-viewer ${WEBSITE3DCELLVIEWER_BUILD_ENVIRONMENT} build`);
 console.log(`website-3d-cell-viewer Version ${WEBSITE3DCELLVIEWER_VERSION}`);
 console.log(`volume-viewer Version ${VOLUMEVIEWER_VERSION}`);
 
-export const VIEWER_3D_SETTINGS: ViewerChannelSettings = {
-  groups: [
-    {
-      name: "Observed channels",
-      channels: [
-        { name: "Membrane", match: ["(CMDRP)"], color: "E2CDB3", enabled: true, lut: ["p50", "p98"] },
-        {
-          name: "Labeled structure",
-          match: ["(EGFP)|(RFPT)"],
-          color: "6FBA11",
-          enabled: true,
-          lut: ["p50", "p98"],
-        },
-        { name: "DNA", match: ["(H3342)"], color: "8DA3C0", enabled: true, lut: ["p50", "p98"] },
-        { name: "Bright field", match: ["(100)|(Bright)"], color: "F5F1CB", enabled: false, lut: ["p50", "p98"] },
-      ],
-    },
-    {
-      name: "Segmentation channels",
-      channels: [
-        {
-          name: "Labeled structure",
-          match: ["(SEG_STRUCT)"],
-          color: "E0E3D1",
-          enabled: false,
-          lut: ["p50", "p98"],
-        },
-        { name: "Membrane", match: ["(SEG_Memb)"], color: "DD9BF5", enabled: false, lut: ["p50", "p98"] },
-        { name: "DNA", match: ["(SEG_DNA)"], color: "E3F4F5", enabled: false, lut: ["p50", "p98"] },
-      ],
-    },
-    {
-      name: "Contour channels",
-      channels: [
-        { name: "Membrane", match: ["(CON_Memb)"], color: "FF6200", enabled: false, lut: ["p50", "p98"] },
-        { name: "DNA", match: ["(CON_DNA)"], color: "F7DB78", enabled: false, lut: ["p50", "p98"] },
-      ],
-    },
-  ],
-  // must be the true channel name in the volume data
-  maskChannelName: "SEG_Memb",
-};
-
-type ParamKeys = "mask" | "ch" | "luts" | "colors" | "url" | "file" | "dataset" | "id" | "view";
-type Params = { [_ in ParamKeys]?: string };
-
-function parseQueryString(): Params {
-  const pairs = location.search.slice(1).split("&");
-  const result = {};
-  pairs.forEach((pairString) => {
-    const pair = pairString.split("=");
-    result[pair[0]] = decodeURIComponent(pair[1] || "");
-  });
-  return JSON.parse(JSON.stringify(result));
-}
-const params = parseQueryString();
-
-const decodeURL = (url: string): string => {
-  const decodedUrl = decodeURIComponent(url);
-  return decodedUrl.endsWith("/") ? decodedUrl.slice(0, -1) : decodedUrl;
-};
-
-/** Try to parse a `string` as a list of 2 or more URLs. Returns `undefined` if the string is not a valid URL list. */
-const tryDecodeURLList = (url: string, delim = ","): string[] | undefined => {
-  if (!url.includes(delim)) {
-    return undefined;
-  }
-
-  const urls = url.split(delim).map((u) => decodeURL(u));
-
-  // Verify that all urls are valid
-  for (const u of urls) {
-    try {
-      new URL(u);
-    } catch (_e) {
-      return undefined;
-    }
-  }
-
-  return urls;
-};
-
-const BASE_URL = "https://s3-us-west-2.amazonaws.com/bisque.allencell.org/v1.4.0/Cell-Viewer_Thumbnails/";
-const args: Omit<AppProps, "appHeight" | "canvasMargin"> = {
-  cellId: "2025",
-  imageUrl: BASE_URL + "AICS-22/AICS-22_8319_2025_atlas.json",
-  parentImageUrl: BASE_URL + "AICS-22/AICS-22_8319_atlas.json",
-  parentImageDownloadHref: "https://files.allencell.org/api/2.0/file/download?collection=cellviewer-1-4/?id=F8319",
-  imageDownloadHref: "https://files.allencell.org/api/2.0/file/download?collection=cellviewer-1-4/?id=C2025",
-  viewerChannelSettings: VIEWER_3D_SETTINGS,
-};
-const viewerSettings: Partial<GlobalViewerSettings> = {
-  showAxes: false,
-  showBoundingBox: false,
-  autorotate: false,
-  viewMode: ViewMode.threeD,
-  renderMode: RenderMode.volumetric,
-  maskAlpha: 50,
-  brightness: 70,
-  density: 50,
-  levels: [0, 128, 255] as [number, number, number],
-  backgroundColor: [0, 0, 0] as [number, number, number],
-  boundingBoxColor: [255, 255, 255] as [number, number, number],
-};
-
-async function loadDataset(dataset: string, id: string) {
-  const db = new FirebaseRequest();
-
-  const datasets = await db.getAvailableDatasets();
-
-  let datasetMeta: DatasetMetaData | undefined = undefined;
-  for (const d of datasets) {
-    const innerDatasets = d.datasets!;
-    const names = Object.keys(innerDatasets);
-    const matchingName = names.find((name) => name === dataset);
-    if (matchingName) {
-      datasetMeta = innerDatasets[matchingName];
-      break;
-    }
-  }
-  if (datasetMeta === undefined) {
-    console.error(`No matching dataset: ${dataset}`);
-    return;
-  }
-
-  const datasetData = await db.selectDataset(datasetMeta.manifest!);
-  const baseUrl = datasetData.volumeViewerDataRoot + "/";
-  args.imageDownloadHref = datasetData.downloadRoot + "/" + id;
-  // args.fovDownloadHref = datasetData.downloadRoot + "/" + id;
-
-  const fileInfo = await db.getFileInfoByCellId(id);
-  args.imageUrl = baseUrl + fileInfo!.volumeviewerPath;
-  args.parentImageUrl = baseUrl + fileInfo!.fovVolumeviewerPath;
-  runApp();
-
-  // only now do we have all the data needed
-}
-
-if (params) {
-  if (params.mask) {
-    viewerSettings.maskAlpha = parseInt(params.mask, 10);
-  }
-  if (params.view) {
-    const mapping = {
-      "3D": ViewMode.threeD,
-      Z: ViewMode.xy,
-      Y: ViewMode.xz,
-      X: ViewMode.yz,
-    };
-    const allowedViews = Object.keys(mapping);
-    if (!allowedViews.includes(params.view)) {
-      params.view = "3D";
-    }
-    viewerSettings.viewMode = mapping[params.view];
-  }
-  if (params.ch) {
-    // ?ch=1,2
-    // ?luts=0,255,0,255
-    // ?colors=ff0000,00ff00
-    const initialChannelSettings: ViewerChannelSettings = {
-      groups: [{ name: "Channels", channels: [] }],
-    };
-    const ch = initialChannelSettings.groups[0].channels;
-
-    const channelsOn = params.ch.split(",").map((numstr) => parseInt(numstr, 10));
-    for (let i = 0; i < channelsOn.length; ++i) {
-      ch.push({ match: channelsOn[i], enabled: true });
-    }
-    // look for luts or color
-    if (params.luts) {
-      const luts = params.luts.split(",");
-      if (luts.length !== ch.length * 2) {
-        console.log("ILL-FORMED QUERYSTRING: luts must have a min/max for each ch");
-      }
-      for (let i = 0; i < ch.length; ++i) {
-        ch[i]["lut"] = [luts[i * 2], luts[i * 2 + 1]];
-      }
-    }
-    if (params.colors) {
-      const colors = params.colors.split(",");
-      if (colors.length !== ch.length) {
-        console.log("ILL-FORMED QUERYSTRING: if colors specified, must have a color for each ch");
-      }
-      for (let i = 0; i < ch.length; ++i) {
-        ch[i]["color"] = colors[i];
-      }
-    }
-    args.viewerChannelSettings = initialChannelSettings;
-  }
-  if (params.url) {
-    const imageUrls = tryDecodeURLList(params.url) ?? decodeURL(params.url);
-    const firstUrl = Array.isArray(imageUrls) ? imageUrls[0] : imageUrls;
-
-    args.cellId = "1";
-    args.imageUrl = imageUrls;
-    // this is invalid for zarr?
-    args.imageDownloadHref = firstUrl;
-    args.parentImageUrl = "";
-    args.parentImageDownloadHref = "";
-    // if json, then use the CFE settings for now.
-    // (See VIEWER_3D_SETTINGS)
-    // otherwise turn the first 3 channels on and group them
-    if (!firstUrl.endsWith("json") && !params.ch) {
-      args.viewerChannelSettings = {
-        groups: [
-          // first 3 channels on by default!
-          {
-            name: "Channels",
-            channels: [
-              { match: [0, 1, 2], enabled: true },
-              { match: "(.+)", enabled: false },
-            ],
-          },
-        ],
-      };
-    }
-    runApp();
-  } else if (params.file) {
-    // quick way to load a atlas.json from a special directory.
-    //
-    // ?file=relative-path-to-atlas-on-isilon
-    args.cellId = "1";
-    const baseUrl = "http://dev-aics-dtp-001.corp.alleninstitute.org/dan-data/";
-    args.imageUrl = baseUrl + params.file;
-    args.parentImageUrl = baseUrl + params.file;
-    args.parentImageDownloadHref = "";
-    args.imageDownloadHref = "";
-    runApp();
-  } else if (params.dataset && params.id) {
-    // ?dataset=aics_hipsc_v2020.1&id=232265
-    loadDataset(params.dataset, params.id);
-  } else {
-    runApp();
-  }
-} else {
-  runApp();
-}
-
-function runApp() {
-  ReactDOM.render(
-    <ImageViewerApp {...args} appHeight="100vh" canvasMargin="0 0 0 0" viewerSettings={viewerSettings} />,
-    document.getElementById("cell-viewer")
-  );
-}
+const router = createBrowserRouter([
+  {
+    path: "/",
+    element: <LandingPage />,
+  },
+  {
+    path: "viewer",
+    element: <AppWrapper />,
+  },
+]);
+
+ReactDOM.render(
+  // <ImageViewerApp {...args} appHeight="100vh" canvasMargin="0 0 0 0" viewerSettings={viewerSettings} />,
+  <StyleProvider>
+    <RouterProvider router={router} />
+  </StyleProvider>,
+  document.getElementById("cell-viewer")
+);

src/aics-image-viewer/components/Toolbar/index.tsx

@@ -69,9 +69,12 @@ export default class Toolbar extends React.Component<ToolbarProps, ToolbarState>
 
   checkSize = debounce((): void => {
     const { leftRef, centerRef, rightRef, barRef } = this;
-    const leftRect = leftRef.current!.getBoundingClientRect();
-    const centerRect = centerRef.current!.getBoundingClientRect();
-    const rightRect = rightRef.current!.getBoundingClientRect();
+    if (!leftRef.current || !centerRef.current || !rightRef.current || !barRef.current) {
+      return;
+    }
+    const leftRect = leftRef.current.getBoundingClientRect();
+    const centerRect = centerRef.current.getBoundingClientRect();
+    const rightRect = rightRef.current.getBoundingClientRect();
 
     // when calculating width required to leave scroll mode, add a bit of extra width to ensure that triggers
     // for entering and leaving scroll mode never overlap (causing toolbar to rapidly switch when resizing)