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reintroduce faster nii2mesh option
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@neurolabusc
neurolabusc committed Dec 27, 2024
1 parent 78fe6c2 commit 59f437d
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Showing 2 changed files with 89 additions and 15 deletions.
23 changes: 21 additions & 2 deletions index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,25 @@
</select>
</label>
</p>
<p>
<label>
Quality:
<select id="qualitySelect" title="choose better or faster meshing">
<option value="0">faster (can create defects)</option>
<option value="1" selected>better</option>
</select>
</label>
</p>
<p id="largestClusterGroup">
<label>&nbsp;Largest cluster only</label><input type="checkbox" id="largestCheck" unchecked/>
</p>
<p id="bubbleGroup">
<label>&nbsp;Fill bubbles</label><input type="checkbox" id="bubbleCheck" unchecked/>
</p>
<p id="closeGroup">
<label>Closing (mm)</label>
<input id="closeMM" type="number" min="0" value="4" max="100">
</p>
<p>
<label for="smoothSlide">Smoothing</label>
<input
Expand All @@ -91,8 +110,8 @@
/>
</p>
<p>
<label>Simplify Percent (10..150)</label>
<input title="triangle reduction reduces the file size and computation time but can reduce mesh quality, smaller values result in a smaller mesh" id="shrinkPct" type="number" min="10" value="25" max="150">
<label>Simplify Percent (10..100)</label>
<input title="triangle reduction reduces the file size and computation time but can reduce mesh quality, smaller values result in a smaller mesh" id="shrinkPct" type="number" min="10" value="25" max="100">
</p>
<button id="cancelBtn" formmethod="dialog">Cancel</button>
<button autofocus id="applyBtn" value="default">Apply</button>
Expand Down
81 changes: 68 additions & 13 deletions main.js
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ setMeshFiltersPipelinesUrl(pipelinesBaseUrl)
async function main() {
const niimath = new Niimath()
await niimath.init()
niimath.setOutputDataType('input') // call before setting image since this is passed to the image constructor
aboutBtn.onclick = function () {
const url = "https://github.com/niivue/brain2print"
window.open(url, "_blank")
Expand Down Expand Up @@ -153,7 +154,7 @@ async function main() {
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
overlayVolume.hdr.intent_code = 1002 // NIFTI_INTENT_LABEL
} else {
let colormap = opts.atlasSelectedColorTable.toLowerCase()
const cmaps = nv1.colormaps()
Expand Down Expand Up @@ -204,7 +205,64 @@ async function main() {
remeshDialog.show()
}
}
qualitySelect.onchange = function () {
const isBetterQuality = Boolean(Number(qualitySelect.value))
const opacity = 1.0 - (0.5 * Number(isBetterQuality))
largestCheck.disabled = isBetterQuality
largestClusterGroup.style.opacity = opacity
bubbleCheck.disabled = isBetterQuality
bubbleGroup.style.opacity = opacity
closeMM.disabled = isBetterQuality
closeGroup.style.opacity = opacity
}
applyBtn.onclick = async function () {
const isBetterQuality = Boolean(Number(qualitySelect.value))
const startTime = performance.now()
if (isBetterQuality)
await applyQuality()
else
await applyFaster()
console.log(`Execution time: ${Math.round(performance.now() - startTime)} ms`)
}
async function applyFaster() {
const niiBuffer = await nv1.saveImage({volumeByIndex: nv1.volumes.length - 1}).buffer
const niiFile = new File([niiBuffer], 'image.nii')
let processor = niimath.image(niiFile)
loadingCircle.classList.remove('hidden')
//mesh with specified isosurface
const isoValue = 0.5
//const largestCheckValue = largestCheck.checked
let reduce = Math.min(Math.max(Number(shrinkPct.value) / 100, 0.01), 1)
let hollowSz = Number(hollowSelect.value )
let closeSz = Number(closeMM.value)
const pixDim = Math.min(Math.min(nv1.volumes[0].hdr.pixDims[1],nv1.volumes[0].hdr.pixDims[2]), nv1.volumes[0].hdr.pixDims[3])
if ((pixDim < 0.2) && ((hollowSz !== 0) || (closeSz !== 0))) {
hollowSz *= pixDim
closeSz *= pixDim
console.log('Very small pixels, scaling hollow and close values by ', pixDim)
}
if (hollowSz < 0) {
processor = processor.hollow(0.5, hollowSz)
}
if ((isFinite(closeSz)) && (closeSz > 0)){
processor = processor.close(isoValue, closeSz, 2 * closeSz)
}
processor = processor.mesh({
i: isoValue,
l: largestCheck.checked ? 1 : 0,
r: reduce,
b: bubbleCheck.checked ? 1 : 0
})
console.log('niimath operation', processor.commands)
const retBlob = await processor.run('test.mz3')
const arrayBuffer = await retBlob.arrayBuffer()
loadingCircle.classList.add('hidden')
if (nv1.meshes.length > 0)
nv1.removeMesh(nv1.meshes[0])
await nv1.loadFromArrayBuffer(arrayBuffer, 'test.mz3')
nv1.reverseFaces(0)
}
async function applyQuality() {
const volIdx = nv1.volumes.length - 1
let hdr = nv1.volumes[volIdx].hdr
let img = nv1.volumes[volIdx].img
Expand All @@ -214,17 +272,13 @@ async function main() {
const niiBuffer = await nv1.saveImage({volumeByIndex: nv1.volumes.length - 1}).buffer
const niiBlob = new Blob([niiBuffer], { type: 'application/octet-stream' })
const niiFile = new File([niiBlob], 'input.nii')
// with niimath wasm ZLIB builds, isGz seems to be the default output type:
// see: https://github.com/rordenlab/niimath/blob/9f3a301be72c331b90ef5baecb7a0232e9b47ba4/src/core.c#L201
// also added new option to set outputDataType in niimath in version 0.3.0 (published 20 Dec 2024)
niimath.setOutputDataType('input') // call before setting image since this is passed to the image constructor
let image = niimath.image(niiFile)
image = image.gz(0)
image = image.ras()
image = image.hollow(0.5, hollowInt)
// must use .gz extension because niimath will create .nii.gz by default, so
// wasm file system commands will look for this, not .nii.
// Error 44 will happen otherwise (file not found error)
const outBlob = await image.run('output.nii.gz')
let outFile = new File([outBlob], 'hollow.nii.gz')
const outBlob = await image.run('output.nii')
let outFile = new File([outBlob], 'hollow.nii')
const outVol = await NVImage.loadFromFile({
file: outFile,
name: outFile.name
Expand All @@ -236,7 +290,6 @@ async function main() {
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 })
Expand All @@ -254,6 +307,7 @@ async function main() {
meshProcessingMsg.textContent = "Smoothing and remeshing"
const smooth = parseInt(smoothSlide.value)
const shrink = parseFloat(shrinkPct.value)
console.log(`smoothing iterations ${smooth} shrink percent ${shrink}`)
const { outputMesh: smoothedMesh } = await smoothRemesh(largestOnly, { newtonIterations: smooth, numberPoints: shrink })
const { outputMesh: smoothedRepairedMesh } = await repair(smoothedMesh, { maximumHoleArea: 50.0 })
const niiMesh = iwm2meshCore(smoothedRepairedMesh)
Expand Down Expand Up @@ -302,13 +356,14 @@ async function main() {
option.value = inferenceModelsList[i].id.toString()
modelSelect.appendChild(option)
}
qualitySelect.onchange()
nv1.onImageLoaded = doLoadImage
modelSelect.selectedIndex = -1
workerCheck.checked = await isChrome(); //TODO: Safari does not yet support WebGL TFJS webworkers, test FireFox
workerCheck.checked = await isChrome() //TODO: Safari does not yet support WebGL TFJS webworkers, test FireFox
console.log('brain2print 20241218')
// uncomment next two lines to automatically run segmentation when web page is loaded
// modelSelect.selectedIndex = 11
// modelSelect.onchange()
// modelSelect.selectedIndex = 11
// modelSelect.onchange()
}

main()

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