zincjs 1.19.0 → 1.19.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "zincjs",
-  "version": "1.19.0",
+  "version": "1.19.2",
   "description": "ZincJS (Web-based-Zinc-Visualisation)",
   "main": "build/zinc.js",
   "directories": {

package/src/loaders/niftiReader.js

@@ -121,6 +121,89 @@ function readNIFTI(data) {
   return {niftiHeader: undefined, niftiImage: undefined};
 }
 
+
+function createSources(niftiHeader, niftiImage, maskHeader, maskImage, options) {
+  if (niftiHeader?.dims && niftiHeader.dims[0] === 3) {
+    const width = niftiHeader.dims[1];
+    const height = niftiHeader.dims[2];
+    const depth = niftiHeader.dims[3];
+    const { typedData, dataType } = getTypedData(niftiHeader, niftiImage);
+    const sliceSize = width * height;
+    const length = sliceSize * depth * 4;
+    const fullArray = new Uint8Array(length);
+    let maskData = undefined;
+    if (maskHeader && maskImage) {
+      const maskWidth = maskHeader.dims[1];
+      const maskHeight = maskHeader.dims[2];
+      const maskDepth = maskHeader.dims[3];
+      if (maskWidth === width && maskHeight === height && maskDepth === depth) {
+        const maskedTypedData = getTypedData(maskHeader, maskImage);
+        maskData = maskedTypedData.typedData;
+      }
+    }
+    let slope = niftiHeader.scl_slope || 1;
+    let intercept = niftiHeader.scl_inter || 0;
+
+    let min = Infinity;
+    let max = -Infinity;
+
+    const dataLength = typedData.length;
+    for (let i = 0; i < dataLength; i++) {
+      let val = (typedData[i] * slope) + intercept;
+      if (val < min) min = val;
+      if (val > max) max = val;
+    }
+    let range = max - min;
+
+    for (let slice = 0; slice < depth; slice++) {
+      const sliceOffset = sliceSize * slice;
+      for (let row = 0; row < height; row++) {
+        const rowOffset = row * width;
+        for (let col = 0; col < width; col++) {
+          const offset = sliceOffset + rowOffset + col;
+          let trueVal = typedData[offset] * slope + intercept;
+          let value = 0;
+          if (range !== 0) {
+            // Map [min, max] to [0, 255]
+            value = ((trueVal - min) / range) * 255;
+          }
+          fullArray[offset * 4] = value;
+          fullArray[offset * 4 + 1] = value;
+          fullArray[offset * 4 + 2] = value;
+          fullArray[offset * 4 + 3] = 255;
+          if (maskData) {
+            const maskedValue = maskData[offset];
+            if (options.hideBlackPixel) {
+              //if (maskedValue === 0 && 20 > value) {
+              if (maskedValue === 0) {
+                fullArray[offset * 4 + 3] = 0;
+              }
+            }
+          } else if (options.filterByValue) {
+            if (options.hideWhitePixel && value === 255) {
+              fullArray[offset * 4 + 3] = 0;
+            }
+            if (options.hideBlackPixel && 2 >= value) {
+              fullArray[offset * 4] = 240;
+              fullArray[offset * 4 + 1] = 240;
+              fullArray[offset * 4 + 2] = 240;
+              fullArray[offset * 4 + 3] = 1.0;
+            }
+          }
+        }
+      }
+    }
+
+    return {
+      data: fullArray,
+      width,
+      height,
+      depth,
+    };
+  }
+  return undefined;
+}
+/*
 function createSources(niftiHeader, niftiImage, maskHeader, maskImage, options) {
   if (niftiHeader?.dims && niftiHeader.dims[0] === 3) {
     const width = niftiHeader.dims[1];
@@ -206,6 +289,8 @@ function createSources(niftiHeader, niftiImage, maskHeader, maskImage, options)
   return undefined;
 }
 
+*/
+
 function getTypedData(niftiHeader, niftiImage) {
   if (niftiHeader.datatypeCode === nifti.NIFTI1.TYPE_UINT8) {
     return { typedData: new Uint8Array(niftiImage), dataType: "uint" };
@@ -360,9 +445,7 @@ async function createPrimitivesFromNIFTI(url, useHeaderInfo, maskURL, textureSet
   }
   if (timeEnabled && textureP) {
     for (let i = 1; i < url.length; i++) {
-      console.log(i, url[i])
       const tArray = await createTextureFromNIFTI(url[i], maskURL, optionsIn);
-      console.log(tArray)
       textureP.addTextureArray(tArray);
     }
     textureP.timeEnabled = true;

package/src/primitives/texturePrimitive.js

@@ -47,7 +47,6 @@ const TexturePrimitive = function (textureIn) {
     if (this.textureList.length === 0 && this.texture) {
       this.textureList.push(this.texture);
     }
-    console.log("addTextureArray", tArray)
     if (tArray && tArray.isTextureArray) {
       this.textureList.push(tArray);
     }

package/src/primitives/textureSlides.js

@@ -415,7 +415,6 @@ const TextureSlides = function (textureIn) {
       const t0 = Math.floor(iTime);
       const t1 = Math.ceil(iTime);
       const ratio = iTime - t0;
-      console.log("update", t0, t1, ratio)
       this.morph.children.forEach((mesh) => {
         const material = mesh.material;
         if (material.type === "ShaderMaterial") {