Insert previous preds all at once in IDB

episphere · Aug 23, 2023 · 1bdc665 · 1bdc665
1 parent d56fcf2
commit 1bdc665
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Showing 5 changed files with 49 additions and 25 deletions.
diff --git a/scripts/miscProcessing.js b/scripts/miscProcessing.js
@@ -417,10 +417,12 @@ onmessage = async (evt) => {
       } catch (e) {
         console.log("Error saving thumbnail to Box", e)
       }
+      break
 
     case "getTMAAnnotations":
       const { folderToGetFrom, annotations, format } = data
       await retrieveTMAAnnotations(op, folderToGetFrom, annotations, format)
+      break
   }
 }
 

diff --git a/scripts/modelPrediction.js b/scripts/modelPrediction.js
@@ -470,6 +470,7 @@ onmessage = async (evt) => {
       const datasetConfig = data.body.datasetConfig
 
       clearWSIDataFromIndexedDB()
+      const predsToInsert = []
       const { previousPredictions, ...otherChanges } = await getPredsFromBox(imageId, annotationId, modelId, datasetConfig, wsiPredsFiles)
       const positiveLabel = data.body.positiveLabel || datasetConfig.annotations.find(annot => annot.annotationId === annotationId).labels[0]
       previousPredictions
@@ -481,8 +482,9 @@ onmessage = async (evt) => {
           predictedLabel,
           predictionScore
         }
-        insertWSIDataToIndexedDB(predictionForIDB, annotationId)
+        predsToInsert.push(predictionForIDB)
       })
+      insertWSIDataToIndexedDB(predsToInsert, annotationId)
 
       postMessage({
         op,

diff --git a/scripts/modelWorkerUtils.js b/scripts/modelWorkerUtils.js
@@ -330,10 +330,26 @@ const getPredsFromBox = async (imageId, annotationId, modelId, datasetConfig, ws
 }
 
 const insertWSIDataToIndexedDB = (data, annotationId) => new Promise (async resolve => {
-  if (indexedDBConfig['wsi'].objectStoreOpts.keyPath.every(key => data[key] >= 0)) {
+  let dataValidated = false
+  if (Array.isArray(data)) {
+    // Check if all relevant keys of all rows are non-negative.
+    dataValidated = data.every(row => indexedDBConfig['wsi'].objectStoreOpts.keyPath.every(key => row[key] >= 0))
+  } else if (typeof(data) === 'object') {
+    dataValidated = indexedDBConfig['wsi'].objectStoreOpts.keyPath.every(key => data[key] >= 0)
+  } else {
+    console.error("Data to be inserted into IDB out of range of possible values", data)
+  }
+  if (dataValidated) {
     wsiPredsDB = wsiPredsDB || await fetchIndexedDBInstance('wsi')
-    const objectStore = wsiPredsDB.transaction(`${indexedDBConfig['wsi'].objectStoreNamePrefix}_${annotationId}`, "readwrite").objectStore(`${indexedDBConfig['wsi'].objectStoreNamePrefix}_${annotationId}`)
-    objectStore.put(data).onsuccess = ({target}) => resolve(target.result)
+    const transaction = wsiPredsDB.transaction(`${indexedDBConfig['wsi'].objectStoreNamePrefix}_${annotationId}`, "readwrite")
+    if (Array.isArray(data)) {
+      data.forEach(row => {
+        transaction.objectStore(`${indexedDBConfig['wsi'].objectStoreNamePrefix}_${annotationId}`).put(row)
+      })
+      transaction.oncomplete = ({target}) => resolve(target.result)
+    } else {
+      transaction.objectStore(`${indexedDBConfig['wsi'].objectStoreNamePrefix}_${annotationId}`).put(row).onsuccess = ({target}) => resolve(target.result)
+    }
   }
 })
 

diff --git a/scripts/path.js b/scripts/path.js
@@ -84,6 +84,8 @@ const loadHashParams = async () => {
 
     if (hashParams.image && hashParams.image !== path.tmaImage.getAttribute("entry_id")) {
       loadImageFromBox(hashParams.image)
+    } else if (hashParams.wsiCenterX && hashParams.wsiCenterY && hashParams.wsiZoom) {
+      wsi.handlePanAndZoom(hashParams.wsiCenterX, hashParams.wsiCenterY, hashParams.wsiZoom)
     }
 
     if (hashParams.folder) {
@@ -96,9 +98,6 @@ const loadHashParams = async () => {
       path.selectFolder(boxRootFolderId)
     }
 
-    if (hashParams.wsiCenterX && hashParams.wsiCenterY && hashParams.wsiZoom) {
-      wsi.handlePanAndZoom(hashParams.wsiCenterX, hashParams.wsiCenterY, hashParams.wsiZoom)
-    }
 
     if (!hashParams.sort) {
       window.location.hash += "&sort=name"
@@ -512,7 +511,6 @@ const loadImageFromBox = async (id, url) => {
       }
 
       window.localStorage.currentThumbnailsFolder = parent.id
-      thumbnails.showThumbnailPicker(window.localStorage.currentThumbnailsOffset, DEFAULT_THUMBNAILS_LIST_LENGTH)
 
       path.isWSI = utils.isWSI(name)
       path.tmaImage.setAttribute("alt", name)
@@ -552,10 +550,10 @@ const loadImageFromBox = async (id, url) => {
                 }
               }, { resolution: 0, url: "" })
 
-              url = await box.getRepresentation(maxResolutionRep.url)
-              if (url) {
-                await loadImgFromBoxFile(null, url)
-              }
+              box.getRepresentation(maxResolutionRep.url).then(repURL => {
+                url = repURL
+                loadImgFromBoxFile(null, url)
+              })
 
               if (!path.datasetConfig.jpegRepresentationsFolderId || path.datasetConfig.jpegRepresentationsFolderId === -1) {
                 const jpegRepresentationsFolderEntry = await box.createFolder("jpegRepresentations", path.datasetConfig.datasetConfigFolderId)
@@ -567,7 +565,7 @@ const loadImageFromBox = async (id, url) => {
 
               if (typeof OffscreenCanvas === "function") {
                 const op = "tiffConvert"
-                path.miscProcessWorker.postMessage({
+                path.miscProcessingWorker.postMessage({
                   op,
                   'data': {
                     'imageId': id,
@@ -577,7 +575,7 @@ const loadImageFromBox = async (id, url) => {
                   }
                 })
 
-                path.miscProcessWorker.onmessage = (evt) => {
+                path.miscProcessingWorker.onmessage = (evt) => {
                   if (evt.data.op === op) {
                     const { originalImageId, metadataWithRepresentation: newMetadata, representationFileId } = evt.data
                     if (originalImageId === hashParams.image) {
@@ -588,24 +586,25 @@ const loadImageFromBox = async (id, url) => {
                   }
                 }
 
-                path.miscProcessWorker.onerror = (err) => {
+                path.miscProcessingWorker.onerror = (err) => {
                   console.log("Error converting TIFF from worker", err)
                 }
               }
 
             } else { // Just use the representation created before.
               const { representationFileId } = JSON.parse(fileMetadata["jpegRepresentation"])
               console.log("Using the JPEG representation created already", new Date())
-              await loadImgFromBoxFile(representationFileId)
+              loadImgFromBoxFile(representationFileId)
             }
 
           } else {
-            await loadImgFromBoxFile(id)
+            loadImgFromBoxFile(id)
           }
         }
       }
 
       addImageHeader(filePathInBox, id, name)
+      thumbnails.showThumbnailPicker(window.localStorage.currentThumbnailsOffset, DEFAULT_THUMBNAILS_LIST_LENGTH)
 
       if (!hashParams.folder) {
         path.selectFolder(parent.id)

diff --git a/scripts/wsi.js b/scripts/wsi.js
@@ -100,7 +100,6 @@ wsi.loadImage = async (id, name, fileMetadata={}) => {
     }
   }
 
-
   if (!path.wsiViewer.canvas) {
     path.tmaCanvas.parentElement.style.backgroundColor = "black"
     path.wsiViewer = OpenSeadragon({
@@ -352,7 +351,7 @@ wsi.loadImage = async (id, name, fileMetadata={}) => {
           } 
           if (!wsiPredsFileId)  {
             wsi.getPreviousPredsFromBox(fileMetadata)
-            document.addEventListener("previousPredsReady", (e) => {
+            path.wsiViewer.addEventListener("previousPredsReady", (e) => {
               e.preventDefault()
               wsiPredsFileId = e.detail.wsiPredsFileId
               wsi.startPrediction(annotationId, imageId, name, width, height, predictionBounds, wsiPredsFileId)
@@ -797,11 +796,12 @@ wsi.loadImage = async (id, name, fileMetadata={}) => {
         fileMetadata = await box.updateMetadata(id, "/wsiInfo", JSON.stringify(imageInfoForMetadata))
         window.localStorage.fileMetadata = JSON.stringify(fileMetadata)
       }
-      wsi.getPreviousPredsFromBox(fileMetadata)
     }
-
+    
     path.wsiViewer.world.getItemAt(0).addOnceHandler('fully-loaded-change', fullyLoadedChangeHandler)
 
+    wsi.getPreviousPredsFromBox(fileMetadata)
+
     // Handle cases where the image loads but an error (typically "SOI not found") causes the fully-loaded-change event to not fire.
     let failedTiles = 0
     path.wsiViewer.addHandler('tile-load-failed', (e) => failedTiles += 1)
@@ -1254,7 +1254,7 @@ wsi.handleMessage = (data, op) => {
           'wsiPredsFileId': JSON.parse(data.newFileMetadata.wsiPredsFiles).find(file => file.annotationId === data.annotationId && file.modelId === data.modelId).fileId
         }
       })
-      document.dispatchEvent(previousPredsReadyEvent)
+      path.wsiViewer.dispatchEvent(previousPredsReadyEvent)
     }
     wsi.overlayPreviousPredictions()
     annotations.populateWSIAnnotations(true, true)
@@ -1416,18 +1416,21 @@ wsi.getFromIndexedDB = (objectStore, queryOpts={}) => new Promise((resolve, reje
       reject("Malformed query")
     }
     const queryResult = []
-    let offset = typeof(queryOpts.offset) === "number" && queryOpts.offset >= 0 ? queryOpts.offset : 0 
+    queryOpts.offset = typeof(queryOpts.offset) === "number" && queryOpts.offset >= 0 ? queryOpts.offset : 0 
     queryOpts.limit = typeof(queryOpts.limit) === "number" && queryOpts.limit > 0 ? queryOpts.limit : 25
     // let numRecords = 0
     // objectStoreTransaction.count(queryOpts.query).onsuccess = (e) => {
-      // numRecords = e.target.result
+    //   numRecords = e.target.result
+    //   console.log(numRecords)
+    // }
 
     let cursorSource = objectStoreTransaction
     if (queryOpts.index) {
       cursorSource = objectStoreTransaction.index(queryOpts.index)
     }
 
     let pagesSkippedFlag = queryOpts.pageNum && queryOpts.pageNum > 0
+
     const cursorRequest = cursorSource.openCursor(queryOpts.query, queryOpts.direction)
     cursorRequest.onsuccess = (e) => {
       const cursor = e.target.result
@@ -1528,6 +1531,7 @@ wsi.overlayPreviousPredictions = async (labelsToDisplay=wsi.defaultSelectedLabel
   })
   handleLabelSelectionChanged()
 
+
   for (const objectStore of Object.values(wsi.predsDB.objectStoreNames)) {
     const annotation = path.datasetConfig.annotations.find(annot => annot.annotationId === parseInt(objectStore.split(`${indexedDBConfig['wsi'].objectStoreNamePrefix}_`)[1]))
     if (annotation && annotation.labels.some(annotationLabel => labelsToDisplay.find(displayLabel => displayLabel.label === annotationLabel.label))) {
@@ -1593,10 +1597,11 @@ wsi.overlayPreviousPredictions = async (labelsToDisplay=wsi.defaultSelectedLabel
         } else {
           offset += limit
         }
-
+        
       }
     }
   }
+
   for (const i in allOverlays) {
     if (interruptFlag) {
       break