zincjs 1.19.0 → 1.19.1

package/build/zinc.js

@@ -32,7 +32,7 @@ module.exports = require("url-polyfill");
 /***/ ((module) => {
 
 "use strict";
-module.exports = /*#__PURE__*/JSON.parse('{"name":"zincjs","version":"1.19.0","description":"ZincJS (Web-based-Zinc-Visualisation)","main":"build/zinc.js","directories":{"doc":"docs"},"files":["package.json","LICENSE","README.md","src/*","build/zinc.js","build/zinc.frontend.js","build/zinc.js.map","webpack.config.js"],"scripts":{"build-bundle":"webpack --config webpack.frontend.js; webpack --config webpack.backend.js","build-backend":"webpack --config webpack.backend.js","test":"npm --prefix ./test install && npm --prefix ./test run test-ci","changelog":"auto-changelog -p --output CHANGELOG.md --template keepachangelog","jsdoc":"jsdoc -c jsdoc_conf.json","version":"npm run build-bundle;npm run jsdoc;npm run changelog; git add CHANGELOG.md docs","release:beta":"npm version prerelease --preid=beta; npm publish --tag beta","release:minor":"npm version minor; npm publish","release:patch":"npm version patch;  npm publish"},"repository":{"type":"git","url":"git+https://github.com/alan-wu/ZincJS.git"},"keywords":["library","webgl","3d","zincjs"],"author":"Alan Wu <alan.wu@auckland.ac.nz>","license":"MIT","bugs":{"url":"https://github.com/alan-wu/ZincJS/issues"},"homepage":"http://alan-wu.github.io/ZincJS/","devDependencies":{"@babel/core":"^7.23.9","@babel/preset-env":"^7.23.9","auto-changelog":"^2.4.0","babel-loader":"^9.1.3","babel-preset-minify":"^0.5.1","file-loader":"^6.2.0","jsdoc":"^4.0.2","raw-loader":"^4.0.2","webpack":"^5.90.3","webpack-cli":"^5.1.4","webpack-node-externals":"^3.0.0"},"dependencies":{"css-element-queries":"^1.2.2","lodash":"^4.17.19","nifti-reader-js":"^0.8.0","promise-polyfill":"^8.1.3","three":"^0.130.1","three-spritetext":"1.6.2","url-loader":"^4.1.1","url-polyfill":"^1.1.7","webworkify-webpack":"^2.1.5"}}');
+module.exports = /*#__PURE__*/JSON.parse('{"name":"zincjs","version":"1.19.1","description":"ZincJS (Web-based-Zinc-Visualisation)","main":"build/zinc.js","directories":{"doc":"docs"},"files":["package.json","LICENSE","README.md","src/*","build/zinc.js","build/zinc.frontend.js","build/zinc.js.map","webpack.config.js"],"scripts":{"build-bundle":"webpack --config webpack.frontend.js; webpack --config webpack.backend.js","build-backend":"webpack --config webpack.backend.js","test":"npm --prefix ./test install && npm --prefix ./test run test-ci","changelog":"auto-changelog -p --output CHANGELOG.md --template keepachangelog","jsdoc":"jsdoc -c jsdoc_conf.json","version":"npm run build-bundle;npm run jsdoc;npm run changelog; git add CHANGELOG.md docs","release:beta":"npm version prerelease --preid=beta; npm publish --tag beta","release:minor":"npm version minor; npm publish","release:patch":"npm version patch;  npm publish"},"repository":{"type":"git","url":"git+https://github.com/alan-wu/ZincJS.git"},"keywords":["library","webgl","3d","zincjs"],"author":"Alan Wu <alan.wu@auckland.ac.nz>","license":"MIT","bugs":{"url":"https://github.com/alan-wu/ZincJS/issues"},"homepage":"http://alan-wu.github.io/ZincJS/","devDependencies":{"@babel/core":"^7.23.9","@babel/preset-env":"^7.23.9","auto-changelog":"^2.4.0","babel-loader":"^9.1.3","babel-preset-minify":"^0.5.1","file-loader":"^6.2.0","jsdoc":"^4.0.2","raw-loader":"^4.0.2","webpack":"^5.90.3","webpack-cli":"^5.1.4","webpack-node-externals":"^3.0.0"},"dependencies":{"css-element-queries":"^1.2.2","lodash":"^4.17.19","nifti-reader-js":"^0.8.0","promise-polyfill":"^8.1.3","three":"^0.130.1","three-spritetext":"1.6.2","url-loader":"^4.1.1","url-polyfill":"^1.1.7","webworkify-webpack":"^2.1.5"}}');
 
 /***/ }),
 /* 3 */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "zincjs",
-  "version": "1.19.0",
+  "version": "1.19.1",
   "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" };