Merge pull request #663 from will-moore/zarr

Zarr

Author: will-moore

omero_figure/views.py

@@ -124,6 +124,7 @@ def index(request, file_id=None, conn=None, **kwargs):
                         'const BASE_OMEROWEB_URL = "%s";' % omeroweb_index)
     html = html.replace('const APP_ROOT_URL = "";',
                         'const APP_ROOT_URL = "%s";' % figure_index)
+    # Replace various other placeholder values with OMERO data/configs
     html = html.replace('const USER_ID = 0;', 'const USER_ID = %s' % user.id)
     html = html.replace('const PING_URL = "";',
                         'const PING_URL = "%s";' % ping_url)
@@ -403,9 +404,13 @@ def save_web_figure(request, conn=None, **kwargs):
     try:
         json_data = json.loads(figure_json)
         for panel in json_data['panels']:
-            image_ids.append(panel['imageId'])
+            try:
+                image_ids.append(int(panel['imageId']))
+            except ValueError:
+                # For NGFF images, the imageId is a string
+                pass
         if len(image_ids) > 0:
-            first_img_id = int(image_ids[0])
+            first_img_id = image_ids[0]
         # remove duplicates
         image_ids = list(set(image_ids))
         # pretty-print json
@@ -442,7 +447,7 @@ def save_web_figure(request, conn=None, **kwargs):
     if file_id is None:
         # Create new file
         # Try to set Group context to the same as first image
-        curr_gid = conn.SERVICE_OPTS.getOmeroGroup()
+        curr_gid = conn.getEventContext().groupId
         i = None
         if first_img_id:
             i = conn.getObject("Image", first_img_id)

package-lock.json

@@ -39,9 +39,11 @@
     "jquery": "^3.6.0",
     "marked": "^4.2.12",
     "mousetrap": "^1.6.5",
+    "ome-zarr.js": "^0.0.17",
     "raphael": "^2.3.0",
     "sortablejs": "^1.15.2",
     "underscore": "^1.13.8",
-    "vite-plugin-html-inject": "^1.1.2"
+    "vite-plugin-html-inject": "^1.1.2",
+    "zarrita": "^0.5.4"
   }
 }

package.json

@@ -7,9 +7,10 @@
     import { recoverFigureFromStorage,
         clearFigureFromStorage,
         figureConfirmDialog,
-        getJson,
+        getJsonWithCredentials,
         saveFigureToStorage,
         normalizeZProjectionBounds} from "../views/util";
+    import { loadZarrForPanel } from "./zarr_utils";
 
     // Version of the json file we're saving.
     // This only needs to increment when we make breaking changes (not linked to release versions.)
@@ -66,7 +67,7 @@
             var load_url = BASE_WEBFIGURE_URL + "load_web_figure/" + fileId + "/",
                 self = this;
 
-            getJson(load_url).then(data => {
+            getJsonWithCredentials(load_url).then(data => {
                 data.fileId = fileId;
                 self.load_from_JSON(data);
                 self.set('unsaved', false);
@@ -310,7 +311,7 @@
                 if (iids.length > 0) {
                     var ptUrl = BASE_WEBFIGURE_URL + 'pixels_type/';
                     ptUrl += '?image=' + iids.join('&image=');
-                    getJson(ptUrl).then(data => {
+                    getJsonWithCredentials(ptUrl).then(data => {
                         // Update all panels
                         // NB: By the time that this callback runs, the panels will have been created
                         self.panels.forEach(function(p){
@@ -533,6 +534,11 @@
             // new image panels appropriately in a grid.
             var invalidIds = [];
             for (var i=0; i<iIds.length; i++) {
+                console.log("Adding image", iIds[i]);
+                if (iIds[i].includes("http")) {
+                    this.importZarrImage(iIds[i], coords, i);
+                    continue;
+                }
                 var imgId = iIds[i].replace("|", ""),
                     validId = parseInt(imgId, 10) + "",
                     imgDataUrl = BASE_WEBFIGURE_URL + 'imgData/' + validId + '/';
@@ -548,6 +554,73 @@
             }
         },
 
+        updateCoordsAndPanelCoords(panel_json, coords, index) {
+            // update panel_json and coords
+            coords.spacer = coords.spacer || panel_json.orig_width/20;
+            var full_width = (coords.colCount * (panel_json.orig_width + coords.spacer)) - coords.spacer,
+                full_height = (coords.rowCount * (panel_json.orig_height + coords.spacer)) - coords.spacer;
+            coords.scale = coords.paper_width / (full_width + (2 * coords.spacer));
+            coords.scale = Math.min(coords.scale, 1);    // only scale down
+            // For the FIRST IMAGE ONLY (coords.px etc undefined), we
+            // need to work out where to start (px,py) now that we know size of panel
+            // (assume all panels are same size)
+            coords.px = coords.px || coords.c.x - (full_width * coords.scale)/2;
+            coords.py = coords.py || coords.c.y - (full_height * coords.scale)/2;
+            // calculate panel coordinates from index...
+            var row = parseInt(index / coords.colCount, 10);
+            var col = index % coords.colCount;
+            var panelX = coords.px + ((panel_json.orig_width + coords.spacer) * coords.scale * col);
+            var panelY = coords.py + ((panel_json.orig_height + coords.spacer) * coords.scale * row);
+            
+            // update panel_json
+            panel_json.x = panelX;
+            panel_json.y = panelY;
+            panel_json.width = panel_json.orig_width * coords.scale;
+            panel_json.height = panel_json.orig_height * coords.scale;
+        },
+
+        importZarrImage: async function(zarrUrl, coords, index) {
+            if (zarrUrl.endsWith("/")) {
+                zarrUrl = zarrUrl.slice(0, -1);
+            }
+            this.set('loading_count', this.get('loading_count') + 1);
+
+            let panel_json = await loadZarrForPanel(zarrUrl);
+            if (panel_json.Error) {
+                let zarrErr = panel_json.Error;
+                for (let fmt of ["bioformats2raw.layout", "OME-Zarr Plates"]) {
+                    if (zarrErr.includes(fmt)) {
+                        zarrErr = `Error loading Zarr ${zarrUrl}:
+                        <p>${fmt} not currently supported.</p>
+                        <p>Please <a href="https://ome.github.io/ome-ngff-validator/?source=${encodeURIComponent(zarrUrl)}" target="_blank">
+                        open in the OME-NGFF Validator</a> to choose a single Image url.</p>
+                        `;
+                    }
+                }
+                if (zarrErr.includes("File not found")) {
+                    zarrErr = `Error loading Zarr from <br/>${zarrUrl}:
+                    <p>File not found (No <code>zarr.json</code> or <code>.zattrs</code>)</p>`;
+                }
+                figureConfirmDialog(
+                    "Zarr Load Error",
+                    zarrErr,
+                    ["OK"]
+                );
+                // alert(`Error loading Zarr ${zarrUrl}: ${panel_json.Error}`);
+                this.set('loading_count', this.get('loading_count') - 1);
+                return;
+            }
+
+            // coords (px, py etc) are incremented for each panel added
+            this.updateCoordsAndPanelCoords(panel_json, coords, index)
+
+            this.set('loading_count', this.get('loading_count') - 1);
+            // create Panel (and select it)
+            // We do some additional processing in Panel.parse()
+            this.panels.create(panel_json, {'parse': true}).set('selected', true);
+            this.notifySelectionChange();
+        },
+
         importImage: function(imgDataUrl, coords, baseUrl, index) {
 
             var self = this,
@@ -580,23 +653,6 @@
                         return;
                     }
 
-                    coords.spacer = coords.spacer || data.size.width/20;
-                    var full_width = (coords.colCount * (data.size.width + coords.spacer)) - coords.spacer,
-                        full_height = (coords.rowCount * (data.size.height + coords.spacer)) - coords.spacer;
-                    coords.scale = coords.paper_width / (full_width + (2 * coords.spacer));
-                    coords.scale = Math.min(coords.scale, 1);    // only scale down
-                    // For the FIRST IMAGE ONLY (coords.px etc undefined), we
-                    // need to work out where to start (px,py) now that we know size of panel
-                    // (assume all panels are same size)
-                    coords.px = coords.px || coords.c.x - (full_width * coords.scale)/2;
-                    coords.py = coords.py || coords.c.y - (full_height * coords.scale)/2;
-
-                    // calculate panel coordinates from index...
-                    var row = parseInt(index / coords.colCount, 10);
-                    var col = index % coords.colCount;
-                    var panelX = coords.px + ((data.size.width + coords.spacer) * coords.scale * col);
-                    var panelY = coords.py + ((data.size.height + coords.spacer) * coords.scale * row);
-
                     // ****** This is the Data Model ******
                     //-------------------------------------
                     // Any changes here will create a new version
@@ -617,8 +673,8 @@
                         'channels': data.channels,
                         'orig_width': data.size.width,
                         'orig_height': data.size.height,
-                        'x': panelX,
-                        'y': panelY,
+                        'x': 0,
+                        'y': 0,
                         'datasetName': data.meta.datasetName,
                         'datasetId': data.meta.datasetId,
                         'pixel_size_x': data.pixel_size.valueX,
@@ -636,6 +692,10 @@
                     if (baseUrl) {
                         n.baseUrl = baseUrl;
                     }
+
+                    // coords (px, py etc) are incremented for each panel added
+                    self.updateCoordsAndPanelCoords(n, coords, index);
+
                     // create Panel (and select it)
                     // We do some additional processing in Panel.parse()
                     self.panels.create(n, {'parse': true}).set('selected', true);

src/js/models/figure_model.js

@@ -3,6 +3,7 @@
     import _ from "underscore";
     import $ from "jquery";
     import { rotatePoint, figureConfirmDialog, normalizeZProjectionBounds } from "../views/util";
+    import {renderZarrToSrc} from "./zarr_utils";
 
     // Corresponds to css - allows us to calculate size of labels
     var LINE_HEIGHT = 1.43;
@@ -1032,7 +1033,33 @@
             return this.get('orig_width') * this.get('orig_height') > MAX_PLANE_SIZE;
         },
 
-        get_img_src: function(force_no_padding) {
+        get_zarr_img_src: async function(force_no_padding, targetSize) {
+            var rect;
+            if (this.is_big_image()) {
+                rect = this.getViewportAsRect();
+                if (!force_no_padding) {
+                    var length = Math.max(rect.width, rect.height) * 1.5;
+                    rect.x = rect.x - ((length - rect.width) / 2);
+                    rect.y = rect.y - ((length - rect.height) / 2);
+                    rect.width = length;
+                    rect.height = length;
+                }
+            } else {
+                // Since we render the whole plane every time (no 'rect' here), caching will prevent reloading on pan/zoom.
+                // as long as targetSize doesn't change. So we can afford to render at higher resolution...
+                targetSize = Math.max(targetSize, 2000);
+            }
+            return renderZarrToSrc(this.get('imageId'), this.get('zarr'), this.get('theZ'), this.get('theT'), this.get('channels'), rect, targetSize);
+        },
+
+        get_img_src: async function(force_no_padding) {
+            // async function since zarr src is the rendered image data
+            if (this.get("zarr")) {
+                // use current size to choose resolution level...
+                let targetSize = 4 * Math.max(this.get('width'), this.get('height'));
+                targetSize = Math.max(targetSize, 500);
+                return this.get_zarr_img_src(force_no_padding, targetSize);
+            }
             var chs = this.get('channels');
             var cStrings = chs.map(function(c, i){
                 return (c.active ? '' : '-') + (1+i) + "|" + c.window.start + ":" + c.window.end + "$" + c.color;
@@ -1500,7 +1527,11 @@
 
         createLabelsFromTags: function(options) {
             // Loads Tags for selected images and creates labels
-            var image_ids = this.map(function(s){return s.get('imageId')})
+            var image_ids = this.map(function(s){return s.get('imageId')});
+            image_ids = _.uniq(image_ids).filter(id => !isNaN(id));    // ignore zarr images
+            if (image_ids.length === 0) {
+                return;
+            }
             image_ids = "image=" + image_ids.join("&image=");
             // TODO: Use /api/ when annotations is supported
             var url = WEBINDEX_URL + "api/annotations/?type=tag&parents=true&limit=1000&" + image_ids;