Plate well labels

omero_figure/omeroutils.py

@@ -40,3 +40,15 @@ def get_timestamps(conn, image):
         if t in timemap:
             time_list.append(timemap[t])
     return time_list
+
+
+def get_wellsample_index(conn, wellsample_id):
+    params = ParametersI()
+    params.addId(wellsample_id)
+    query = """select index(wellSamples) from Well well
+        left outer join well.wellSamples as wellSamples
+        where wellSamples.id = :id
+        """
+    qs = conn.getQueryService()
+    rsp = qs.projection(query, params, conn.SERVICE_OPTS)
+    return rsp[0][0].val

omero_figure/urls.py

@@ -76,6 +76,10 @@
     # Use query ?image=1&image=2
     re_path(r'^timestamps/$', views.timestamps, name='figure_timestamps'),
 
+    # Get parents (e.g. Plate, Well, WellSample) for images
+    # Use query ?image=1&image=2
+    re_path(r'^parents/$', views.parents, name='figure_parents'),
+
     # Get Z scale for images
     # Use query ?image=1&image=2
     re_path(r'^z_scale/$', views.z_scale, name='figure_z_scale'),

omero_figure/views.py

@@ -26,6 +26,8 @@
 import json
 import time
 
+from omeroweb.webclient.show import paths_to_object
+
 from omeroweb.webgateway.marshal import imageMarshal
 from omeroweb.webgateway.views import _get_prepared_image
 from omeroweb.webclient.views import run_script
@@ -40,7 +42,7 @@
 from io import BytesIO
 
 from omeroweb.webclient.decorators import login_required
-from .omeroutils import get_timestamps
+from .omeroutils import get_timestamps, get_wellsample_index
 
 from . import utils
 import logging
@@ -160,6 +162,36 @@ def timestamps(request, conn=None, **kwargs):
     return JsonResponse(data)
 
 
+@login_required()
+def parents(request, conn=None, **kwargs):
+
+    image_ids = request.GET.getlist('image')
+    try:
+        image_ids = [int(iid) for iid in image_ids]
+    except ValueError:
+        return Http404("Invalid 'image' id")
+
+    parents = {}
+    for img_id in image_ids:
+        img_parents = {}
+        for img_path in paths_to_object(conn, image_id=img_id):
+            for item in img_path:
+                o_type = item["type"]
+                del item["type"]
+                img_parents[o_type] = item
+                if o_type == "wellsample":
+                    item["index"] = get_wellsample_index(conn, item["id"])
+                    continue
+                obj = conn.getObject(o_type, item["id"])
+                if o_type == "well":
+                    item["label"] = obj.getWellPos()
+                else:
+                    item["name"] = obj.getName()
+        parents[img_id] = img_parents
+
+    return JsonResponse({"parents": parents})
+
+
 @login_required()
 def z_scale(request, conn=None, **kwargs):
 

src/js/models/panel_model.js

@@ -374,6 +374,9 @@
                 } else if (format === "name") {
                     text = this.get('datasetName') ? this.get('datasetName') : "No/Many Datasets";
                 }
+            } else {
+                // screen, plate, well, (name or id)
+                text = "" + this.get(property)?.[format] ?? "Not Found";
             }
             return text;
         },
@@ -1025,6 +1028,30 @@
             }
         },
 
+        addLabelsFromPlatesWellsFields: function(label_data) {
+
+            // TODO: could ignore image IDs if Plate/Well/Field loaded already
+            var image_ids = this.map(function(s){return s.get('imageId')});
+            image_ids = "image=" + image_ids.join("&image=");
+            var url = BASE_WEBFIGURE_URL + "parents/?" + image_ids;
+            console.log('url', url);
+            $.getJSON(url, function(data){
+                console.log(data);
+                // {screen: {id:3, name:abc}, plate: {id:1, name:foo}, well:{id:2, name:A1}}
+                const parents = data.parents;
+
+                // Add parents to each panel, then add label
+                this.forEach(function(p){
+                    var iid = p.get('imageId');
+                    if (parents[iid]) {
+                        p.set(parents[iid]);
+                    }
+                    console.log("Adding label..", label_data);
+                    p.add_labels([label_data]);
+                });
+            }.bind(this));
+        },
+
         createLabelsFromTags: function(options) {
             // Loads Tags for selected images and creates labels
             var image_ids = this.map(function(s){return s.get('imageId')})

src/js/views/panel_view.js

@@ -219,11 +219,12 @@
                             format = prop_nf[1] ? prop_nf[1] : "index";
                             precision = param_dict["precision"] !== undefined ? param_dict["precision"] : 0; // decimal places default to 0
                             label_value = self.model.get_time_label_text(format, param_dict["offset"], precision);
-                        } else if (['image', 'dataset'].includes(prop_nf[0])){
+                        } else if (['image', 'dataset', 'screen', 'plate', 'well', 'wellsample'].includes(prop_nf[0])){
                             format = prop_nf[1] ? prop_nf[1] : "name";
                             label_value = self.model.get_name_label_text(prop_nf[0], format);
+                            console.log("render_label label_value", label_value, prop_nf);
                             //Escape the underscore for markdown
-                            label_value = label_value.replaceAll("_", "\\_");
+                            label_value = ("" + label_value).replaceAll("_", "\\_");
                         } else if (['x', 'y', 'z', 'width', 'height', 'w', 'h', 'rotation', 'rot'].includes(prop_nf[0])){
                             format = prop_nf[1] ? prop_nf[1] : "pixel";
                             precision = param_dict["precision"] !== undefined ? param_dict["precision"] : 2; // decimal places default to 2

src/js/views/right_panel_view.js

@@ -353,6 +353,18 @@
                 return false;
             }
 
+            // If we need SPW info and we don't have it, load...
+            if (label_text.includes('[plate.name]') || label_text.includes('well.name') || label_text.includes('field.index')) {
+                // Load Plate Name for images...
+                console.log("label_text", label_text);
+                selected.addLabelsFromPlatesWellsFields({
+                    text: label_text,
+                    position: position,
+                    size: font_size,
+                    color: color});
+                return false;
+            }
+
             if (label_text == '[tags]') {
                 // Load Tags for this image and create labels
 

src/templates/labels_form_inner_template.html

@@ -13,6 +13,8 @@
                     <li role="presentation" class="divider"></li>
                     <li><a href="#" data-label="[image.name]">Image Name</a></li>
                     <li><a href="#" data-label="[dataset.name]">Dataset Name</a></li>
+                    <li><a href="#" data-label="[well.label] Field#[field.index]">Well & Fieild</a></li>
+                    <li><a href="#" data-label="[plate.name]">Plate Name</a></li>
                     <li title="Create labels from active Channels on the selected panel">
                         <a href="#" data-label="[channels labels]">Channels (separate labels)</a>
                     </li>