Hollow meshes only for faster mode

Author: neurolabusc

brainchop-webworker.js

@@ -624,7 +624,11 @@ async function inferenceFullVolumePhase2(
           const argMaxTime = performance.now()
           console.log(' Try tf.argMax for fullVolume ..')
           if (isScalar) {
-            const input = tf.softmax(curTensor[i], -1) // shape: [..., C], with C >= 2
+            // const input = tf.softmax(curTensor[i], -1) // shape: [..., C], with C >= 2
+            
+            const temperature = 1.2 // >1 softens, <1 sharpens
+            const input = tf.softmax(curTensor[i].div(temperature), -1)
+
             const shape = input.shape
             const lastDim = shape.length - 1
             // Slice the last dimension to keep only channels 1 and onward (ignore channel 0)
@@ -743,7 +747,7 @@ async function inferenceFullVolumePhase2(
         console.log(' outLabelVolume final shape after resizing :  ', outLabelVolume.shape)
 
         if (isScalar) {
-          const thresh  = tf.scalar(0.04);   // threshold
+          const thresh  = tf.scalar(0.10);   // threshold
           const scale255 = tf.scalar(255.0); // if you still need the scaling step
           const mask = outLabelVolume.greaterEqual(thresh).toFloat();
           outLabelVolume = outLabelVolume.mul(mask);

index.html

@@ -65,19 +65,6 @@
   </footer>
   <dialog id="remeshDialog">
     <form method="dialog">
-      <p>
-        <label>
-          Hollow:
-          <select id="hollowSelect" title="hollow meshes require less material but may be fragile">
-            <option value="0" selected>False: solid</option>
-            <option value="-2">2mm</option>
-            <option value="-3">3mm</option>
-            <option value="-4">4mm</option>
-            <option value="-8">8mm</option>
-            <option value="-16">16mm</option>
-          </select>
-        </label>
-      </p>
       <p>
         <label>
           Quality:
@@ -90,6 +77,19 @@
       <p id="largestClusterGroup">
         <label>&nbsp;Largest cluster only</label><input type="checkbox" id="largestCheck" unchecked/>
       </p>
+      <p id="hollowGroup">
+        <label>
+          &nbsp;Hollow:
+          <select id="hollowSelect" title="hollow meshes require less material but may be fragile">
+            <option value="0" selected>False: solid</option>
+            <option value="-2">2mm</option>
+            <option value="-3">3mm</option>
+            <option value="-4">4mm</option>
+            <option value="-8">8mm</option>
+            <option value="-16">16mm</option>
+          </select>
+        </label>
+      </p>
       <p id="bubbleGroup">
         <label>&nbsp;Fill bubbles</label><input type="checkbox" id="bubbleCheck" unchecked/>
       </p>

main.js

@@ -4,7 +4,7 @@ import { isChrome, localSystemDetails } from "./brainchop-telemetry.js"
 import MyWorker from "./brainchop-webworker.js?worker"
 import { Niimath } from "@niivue/niimath"
 import {
-  antiAliasCuberille,
+  antiAliasCuberille, cuberille,
   setPipelinesBaseUrl as setCuberillePipelinesUrl
 } from "@itk-wasm/cuberille"
 import {
@@ -240,6 +240,8 @@ async function main() {
     const opacity = 1.0 - (0.5 * Number(isBetterQuality))
     largestCheck.disabled = isBetterQuality
     largestClusterGroup.style.opacity = opacity
+    hollowGroup.style.opacity = opacity
+    hollowSelect.disabled = isBetterQuality
     bubbleCheck.disabled = isBetterQuality
     bubbleGroup.style.opacity = opacity
     closeMM.disabled = isBetterQuality
@@ -262,7 +264,7 @@ async function main() {
     //mesh with specified isosurface
     let isoValue = 0.5
     if (nv1.volumes[nv1.volumes.length - 1].hdr.intent_code === 0) {
-      isoValue = 222 //isScalar
+      isoValue = 240 //isScalar
     }
     //const largestCheckValue = largestCheck.checked
     let reduce = Math.min(Math.max(Number(shrinkPct.value) / 100, 0.01), 1)
@@ -299,10 +301,10 @@ async function main() {
     const volIdx = nv1.volumes.length - 1
     let hdr = nv1.volumes[volIdx].hdr
     let img = nv1.volumes[volIdx].img
-    let hollowInt = Number(hollowSelect.value )
+    /*let hollowInt = Number(hollowSelect.value )
     if (hollowInt < 0){
       const vol = nv1.volumes[volIdx]
-      const niiBuffer = await nv1.saveImage({volumeByIndex: nv1.volumes.length - 1}).buffer
+      const niiBuffer = await nv1.saveImage({volumeByIndex: nv1.volumes.length - 1})
       const niiBlob = new Blob([niiBuffer], { type: 'application/octet-stream' })
       const niiFile = new File([niiBlob], 'input.nii')
       niimath.setOutputDataType('input') // call before setting image since this is passed to the image constructor
@@ -318,13 +320,19 @@ async function main() {
       })
       hdr = outVol.hdr
       img = outVol.img
-    }
+    }*/
     loadingCircle.classList.remove("hidden")
     meshProcessingMsg.classList.remove("hidden")
     meshProcessingMsg.textContent = "Generating mesh from segmentation"
     const itkImage = nii2iwi(hdr, img, false)
     itkImage.size = itkImage.size.map(Number)
-    const { mesh } = await antiAliasCuberille(itkImage, { noClosing: true })
+    let mesh
+    if (nv1.volumes[nv1.volumes.length - 1].hdr.intent_code === 0) {
+      ({ mesh } = await cuberille(itkImage, { isoSurfaceValue: 240 }))
+    } else {
+      ({ mesh } = await antiAliasCuberille(itkImage, { noClosing: true }))
+    }
+
     meshProcessingMsg.textContent = "Generating manifold"
     const { outputMesh: repairedMesh } = await repair(mesh, { maximumHoleArea: 50.0 })
     meshProcessingMsg.textContent = "Keep largest mesh component"