Merge pull request #6 from neurolabusc/main

Bump dependencies
niivue · May 3, 2024 · 85a8ffe · 85a8ffe
2 parents 506ed5b + ff733f6
commit 85a8ffe
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Showing 7 changed files with 52 additions and 47 deletions.
diff --git a/brainchop-mainthread.js b/brainchop-mainthread.js
@@ -2010,7 +2010,7 @@ async function enableProductionMode(textureF16Flag = true) {
 
 async function runInference(opts, modelEntry, niftiHeader, niftiImage, callbackImg, callbackUI) {
   const statData = []
-  statData.startTime = performance.now()
+  statData.startTime = Date.now() // for common webworker/mainthread do not use performance.now()
   callbackUI('Segmentation started', 0)
   const startTime = performance.now()
   const batchSize = opts.batchSize

diff --git a/brainchop-telemetry.js b/brainchop-telemetry.js
@@ -149,7 +149,6 @@ async function isChrome() {
 }
 
 async function localSystemDetails(statData, gl = null) {
-    const Preprocess_t = ((performance.now() - statData.startTime) / 1000).toFixed(4)
     // -- Timing data to collect
     const today = new Date()
     if (statData.isModelFullVol) {
@@ -168,9 +167,9 @@ async function localSystemDetails(statData, gl = null) {
           statData["State"] = ""
           statData["City"] = ""
     } */
-
+    statData.Total_t = (Date.now() - statData.startTime) / 1000.0
+    delete statData.startTime
     statData.Date = parseInt(today.getMonth() + 1) + '/' + today.getDate() + '/' + today.getFullYear()
-    statData.Time_Elapsed = Preprocess_t
     statData.Browser = await detectBrowser()
     statData.Browser_Ver = await detectBrowserVersion()
     statData.OS = await detectOperatingSys()

diff --git a/brainchop-webworker.js b/brainchop-webworker.js
@@ -2013,7 +2013,7 @@ async function enableProductionMode(textureF16Flag = true) {
 
 async function runInferenceWW(opts, modelEntry, niftiHeader, niftiImage, callbackImg, callbackUI) {
   const statData = []
-  statData.startTime = performance.now()
+  statData.startTime = Date.now() // for common webworker/mainthread do not use performance.now()
   callbackUI('Segmentation started', 0)
   const batchSize = opts.batchSize
   const numOfChan = opts.numOfChan

diff --git a/index.html b/index.html
@@ -10,6 +10,8 @@
 
 <body>
   <header>
+    <label for="smoothCheck">Interpolate</label>
+    <input type="checkbox" id="smoothCheck" unchecked />
     &nbsp;
     <label for="clipCheck">Clip Plane</label>
     <input type="checkbox" id="clipCheck" unchecked />

diff --git a/main.js b/main.js
@@ -5,6 +5,9 @@ import { isChrome, localSystemDetails } from "./brainchop-telemetry.js"
 import MyWorker from "./brainchop-webworker.js?worker"
 
 async function main() {
+  smoothCheck.onchange = function () {
+    nv1.setInterpolation(!smoothCheck.checked)
+  }
   aboutBtn.onclick = function () {
     window.alert("BrainChop models https://github.com/neuroneural/brainchop")
   }
@@ -99,8 +102,6 @@ async function main() {
       nv1.setClipPlane([2, 0, 90])
     }
   }
-
-
   async function fetchJSON(fnm) {
     const response = await fetch(fnm)
     const js = await response.json()
@@ -116,6 +117,8 @@ async function main() {
     if (modelEntry.colormapPath) {
       let cmap = await fetchJSON(modelEntry.colormapPath)
       overlayVolume.setColormapLabel(cmap)
+      // n.b. most models create indexed labels, but those without colormap mask scalar input
+      overlayVolume.hdr.intent_code = 1002 // NIFTI_INTENT_LABEL
     } else {
       let colormap = opts.atlasSelectedColorTable.toLowerCase()
       const cmaps = nv1.colormaps()
@@ -179,6 +182,7 @@ async function main() {
   nv1.opts.multiplanarForceRender = true
   nv1.opts.yoke3Dto2DZoom = true
   nv1.opts.crosshairGap = 11
+  smoothCheck.onchange()
   await nv1.loadVolumes([{ url: "./t1_crop.nii.gz" }])
   for (let i = 0; i < inferenceModelsList.length; i++) {
     var option = document.createElement("option")

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -9,8 +9,8 @@
     "preview": "vite preview"
   },
   "dependencies": {
-    "@niivue/niivue":"^0.42.0",
-    "@tensorflow/tfjs": "^4.18.0",
+    "@niivue/niivue":"^0.43.0",
+    "@tensorflow/tfjs": "^4.19.0",
     "gl-matrix": "^3.4.3"
   },
   "devDependencies": {