Merge remote-tracking branch 'upstream/gating'

labsyspharm · Oct 6, 2023 · d4c963f · d4c963f
2 parents 184ac72 + b56b78f
commit d4c963f
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Showing 11 changed files with 777 additions and 91 deletions.
diff --git a/minerva_analysis/client/src/css/main.css b/minerva_analysis/client/src/css/main.css
@@ -464,3 +464,25 @@ label {
 
 .col-svg-wrapper {
 }
+
+.lasso_selection_toggle {
+    float: right;
+    margin-left: auto;
+    margin-top: 3px;
+    margin-right: 20px;
+    color: orange;
+}
+
+.lasso_polygon {
+    fill-opacity: 0;
+    stroke: orange;
+    stroke-width: 3px;
+    vector-effect: non-scaling-stroke;
+}
+
+.btn_lasso_delete {
+    float: right;
+    padding-top: 0;
+    padding-bottom: 0;
+    border: 1px;
+}
diff --git a/minerva_analysis/client/src/js/main.js b/minerva_analysis/client/src/js/main.js
@@ -65,7 +65,7 @@ async function init(config) {
 
     //Create image viewer
     const imageArgs = [imgMetadata, numericData, eventHandler];
-    const seaDragonViewer = new ImageViewer(config, ...imageArgs);
+    const seaDragonViewer = new ImageViewer(config, dataLayer, ...imageArgs);
     const viewerManager = new ViewerManager(seaDragonViewer, channelList);
 
     //Initialize with database description
@@ -166,12 +166,23 @@ async function init(config) {
         seaDragonViewer.forceRepaint();
     }
 
+    /**
+     * Add picked cell ids from lasso selection
+     */
+    const imageLassoSel = (d) => {
+        updateSeaDragonSelection(d);
+        csv_gatingList.updateGMM(d['picked']);
+    };
+    eventHandler.bind(ImageViewer.events.imageLassoSel, imageLassoSel);
+
     /**
      * Remove currently selected picked cell ids
      */
     function clearSeaDragonSelection() {
       updateSeaDragonSelection({ picked: [] });
+      csv_gatingList.updateGMM([]);
     }
+    eventHandler.bind(ImageViewer.events.clearImageLasso, clearSeaDragonSelection);
 
     const handler = () => updateSeaDragonSelection();
     eventHandler.bind(CSVGatingList.events.GATING_BRUSH_END, handler);

diff --git a/minerva_analysis/client/src/js/services/dataLayer.js b/minerva_analysis/client/src/js/services/dataLayer.js
@@ -90,7 +90,7 @@ class DataLayer {
         }
     }
 
-    downloadGatingCSV(channels, selections, fullCsv = false) {
+    downloadGatingCSV(channels, selections, lassos, selection_ids, fullCsv = false) {
         let form = document.createElement("form");
         form.action = "/download_gating_csv";
 
@@ -133,17 +133,29 @@ class DataLayer {
         channelsElement.name = "channels";
         form.appendChild(channelsElement);
 
+        let lassosElement = document.createElement("input");
+        lassosElement.type = "hidden";
+        lassosElement.value = JSON.stringify(lassos);
+        lassosElement.name = "lassos";
+        form.appendChild(lassosElement);
+
+        let idsElement = document.createElement("input");
+        idsElement.type = "hidden";
+        idsElement.value = JSON.stringify(selection_ids);
+        idsElement.name = "selection_ids";
+        form.appendChild(idsElement);
+
         let datasourceElement = document.createElement("input");
         datasourceElement.type = "hidden";
         datasourceElement.value = datasource;
         datasourceElement.name = "datasource";
         form.appendChild(datasourceElement);
+
         document.body.appendChild(form);
         form.submit()
-
     }
 
-    async saveGatingList(channels, selections) {
+    async saveGatingList(channels, selections, lassos) {
         const self = this;
         try {
             let response = await fetch('/save_gating_list', {
@@ -156,7 +168,8 @@ class DataLayer {
                     {
                         datasource: datasource,
                         filter: selections,
-                        channels: channels
+                        channels: channels,
+                        lassos: lassos
                     }
                 )
             });
@@ -363,12 +376,22 @@ class DataLayer {
         }
     }
 
-    async getGatingGMM(channel) {
+    async getGatingGMM(channel, selection_ids) {
         try {
-            let response = await fetch('/get_gating_gmm?' + new URLSearchParams({
-                channel: channel,
-                datasource: datasource
-            }))
+            let response = await fetch('/get_gating_gmm', {
+                method: 'POST',
+                headers: {
+                    'Accept': 'application/json',
+                    'Content-Type': 'application/json'
+                },
+                body: JSON.stringify(
+                    {
+                        channel: channel,
+                        datasource: datasource,
+                        selection_ids: selection_ids
+                    }
+                )
+            });
             let packet_gmm = await response.json();
             return packet_gmm;
         } catch (e) {
@@ -557,4 +580,48 @@ class DataLayer {
       return false;
     }
 
+     async getCellsInPolygon(points) {
+        try {
+            let response = await fetch('/get_cells_in_polygon', {
+                method: 'POST',
+                headers: {
+                    'Accept': 'application/json',
+                    'Content-Type': 'application/json'
+                },
+                body: JSON.stringify(
+                    {
+                        datasource: datasource,
+                        points: points,
+                    }
+                )
+            });
+            let cells = await response.json();
+            return cells;
+        } catch (e) {
+            console.log("Error Getting Polygon Cells", e);
+        }
+    }
+
+    async getCellsInLassos(list_lassos) {
+        try {
+            let response = await fetch('/get_cells_in_lassos', {
+                method: 'POST',
+                headers: {
+                    'Accept': 'application/json',
+                    'Content-Type': 'application/json'
+                },
+                body: JSON.stringify(
+                    {
+                        datasource: datasource,
+                        list_lassos: list_lassos,
+                    }
+                )
+            });
+            let cells = await response.json();
+            return cells;
+        } catch (e) {
+            console.log("Error Getting Cells in Lassos", e);
+        }
+    }
+
 }