three-stdlib 2.22.9 → 2.22.10

package/dist/misc/Volume.mjs

@@ -1,118 +1,119 @@
-import { Matrix3, Matrix4, Vector3 } from "three";
+import { Matrix3, Vector3, Matrix4 } from "three";
 import { VolumeSlice } from "./VolumeSlice.mjs";
-var Volume = function(xLength, yLength, zLength, type, arrayBuffer) {
-  if (arguments.length > 0) {
-    this.xLength = Number(xLength) || 1;
-    this.yLength = Number(yLength) || 1;
-    this.zLength = Number(zLength) || 1;
-    switch (type) {
-      case "Uint8":
-      case "uint8":
-      case "uchar":
-      case "unsigned char":
-      case "uint8_t":
-        this.data = new Uint8Array(arrayBuffer);
-        break;
-      case "Int8":
-      case "int8":
-      case "signed char":
-      case "int8_t":
-        this.data = new Int8Array(arrayBuffer);
-        break;
-      case "Int16":
-      case "int16":
-      case "short":
-      case "short int":
-      case "signed short":
-      case "signed short int":
-      case "int16_t":
-        this.data = new Int16Array(arrayBuffer);
-        break;
-      case "Uint16":
-      case "uint16":
-      case "ushort":
-      case "unsigned short":
-      case "unsigned short int":
-      case "uint16_t":
-        this.data = new Uint16Array(arrayBuffer);
-        break;
-      case "Int32":
-      case "int32":
-      case "int":
-      case "signed int":
-      case "int32_t":
-        this.data = new Int32Array(arrayBuffer);
-        break;
-      case "Uint32":
-      case "uint32":
-      case "uint":
-      case "unsigned int":
-      case "uint32_t":
-        this.data = new Uint32Array(arrayBuffer);
-        break;
-      case "longlong":
-      case "long long":
-      case "long long int":
-      case "signed long long":
-      case "signed long long int":
-      case "int64":
-      case "int64_t":
-      case "ulonglong":
-      case "unsigned long long":
-      case "unsigned long long int":
-      case "uint64":
-      case "uint64_t":
-        throw "Error in Volume constructor : this type is not supported in JavaScript";
-        break;
-      case "Float32":
-      case "float32":
-      case "float":
-        this.data = new Float32Array(arrayBuffer);
-        break;
-      case "Float64":
-      case "float64":
-      case "double":
-        this.data = new Float64Array(arrayBuffer);
-        break;
-      default:
-        this.data = new Uint8Array(arrayBuffer);
-    }
-    if (this.data.length !== this.xLength * this.yLength * this.zLength) {
-      throw "Error in Volume constructor, lengths are not matching arrayBuffer size";
+class Volume {
+  constructor(xLength, yLength, zLength, type, arrayBuffer) {
+    if (xLength !== void 0) {
+      this.xLength = Number(xLength) || 1;
+      this.yLength = Number(yLength) || 1;
+      this.zLength = Number(zLength) || 1;
+      this.axisOrder = ["x", "y", "z"];
+      switch (type) {
+        case "Uint8":
+        case "uint8":
+        case "uchar":
+        case "unsigned char":
+        case "uint8_t":
+          this.data = new Uint8Array(arrayBuffer);
+          break;
+        case "Int8":
+        case "int8":
+        case "signed char":
+        case "int8_t":
+          this.data = new Int8Array(arrayBuffer);
+          break;
+        case "Int16":
+        case "int16":
+        case "short":
+        case "short int":
+        case "signed short":
+        case "signed short int":
+        case "int16_t":
+          this.data = new Int16Array(arrayBuffer);
+          break;
+        case "Uint16":
+        case "uint16":
+        case "ushort":
+        case "unsigned short":
+        case "unsigned short int":
+        case "uint16_t":
+          this.data = new Uint16Array(arrayBuffer);
+          break;
+        case "Int32":
+        case "int32":
+        case "int":
+        case "signed int":
+        case "int32_t":
+          this.data = new Int32Array(arrayBuffer);
+          break;
+        case "Uint32":
+        case "uint32":
+        case "uint":
+        case "unsigned int":
+        case "uint32_t":
+          this.data = new Uint32Array(arrayBuffer);
+          break;
+        case "longlong":
+        case "long long":
+        case "long long int":
+        case "signed long long":
+        case "signed long long int":
+        case "int64":
+        case "int64_t":
+        case "ulonglong":
+        case "unsigned long long":
+        case "unsigned long long int":
+        case "uint64":
+        case "uint64_t":
+          throw new Error("Error in Volume constructor : this type is not supported in JavaScript");
+          break;
+        case "Float32":
+        case "float32":
+        case "float":
+          this.data = new Float32Array(arrayBuffer);
+          break;
+        case "Float64":
+        case "float64":
+        case "double":
+          this.data = new Float64Array(arrayBuffer);
+          break;
+        default:
+          this.data = new Uint8Array(arrayBuffer);
+      }
+      if (this.data.length !== this.xLength * this.yLength * this.zLength) {
+        throw new Error("Error in Volume constructor, lengths are not matching arrayBuffer size");
+      }
     }
+    this.spacing = [1, 1, 1];
+    this.offset = [0, 0, 0];
+    this.matrix = new Matrix3();
+    this.matrix.identity();
+    let lowerThreshold = -Infinity;
+    Object.defineProperty(this, "lowerThreshold", {
+      get: function() {
+        return lowerThreshold;
+      },
+      set: function(value) {
+        lowerThreshold = value;
+        this.sliceList.forEach(function(slice) {
+          slice.geometryNeedsUpdate = true;
+        });
+      }
+    });
+    let upperThreshold = Infinity;
+    Object.defineProperty(this, "upperThreshold", {
+      get: function() {
+        return upperThreshold;
+      },
+      set: function(value) {
+        upperThreshold = value;
+        this.sliceList.forEach(function(slice) {
+          slice.geometryNeedsUpdate = true;
+        });
+      }
+    });
+    this.sliceList = [];
+    this.segmentation = false;
   }
-  this.spacing = [1, 1, 1];
-  this.offset = [0, 0, 0];
-  this.matrix = new Matrix3();
-  this.matrix.identity();
-  var lowerThreshold = -Infinity;
-  Object.defineProperty(this, "lowerThreshold", {
-    get: function() {
-      return lowerThreshold;
-    },
-    set: function(value) {
-      lowerThreshold = value;
-      this.sliceList.forEach(function(slice) {
-        slice.geometryNeedsUpdate = true;
-      });
-    }
-  });
-  var upperThreshold = Infinity;
-  Object.defineProperty(this, "upperThreshold", {
-    get: function() {
-      return upperThreshold;
-    },
-    set: function(value) {
-      upperThreshold = value;
-      this.sliceList.forEach(function(slice) {
-        slice.geometryNeedsUpdate = true;
-      });
-    }
-  });
-  this.sliceList = [];
-};
-Volume.prototype = {
-  constructor: Volume,
   /**
    * @member {Function} getData Shortcut for data[access(i,j,k)]
    * @memberof Volume
@@ -121,9 +122,9 @@ Volume.prototype = {
    * @param {number} k    Third coordinate
    * @returns {number}  value in the data array
    */
-  getData: function(i, j, k) {
+  getData(i, j, k) {
     return this.data[k * this.xLength * this.yLength + j * this.xLength + i];
-  },
+  }
   /**
    * @member {Function} access compute the index in the data array corresponding to the given coordinates in IJK system
    * @memberof Volume
@@ -132,21 +133,21 @@ Volume.prototype = {
    * @param {number} k    Third coordinate
    * @returns {number}  index
    */
-  access: function(i, j, k) {
+  access(i, j, k) {
     return k * this.xLength * this.yLength + j * this.xLength + i;
-  },
+  }
   /**
    * @member {Function} reverseAccess Retrieve the IJK coordinates of the voxel corresponding of the given index in the data
    * @memberof Volume
    * @param {number} index index of the voxel
    * @returns {Array}  [x,y,z]
    */
-  reverseAccess: function(index) {
-    var z = Math.floor(index / (this.yLength * this.xLength));
-    var y = Math.floor((index - z * this.yLength * this.xLength) / this.xLength);
-    var x = index - z * this.yLength * this.xLength - y * this.xLength;
+  reverseAccess(index) {
+    const z = Math.floor(index / (this.yLength * this.xLength));
+    const y = Math.floor((index - z * this.yLength * this.xLength) / this.xLength);
+    const x = index - z * this.yLength * this.xLength - y * this.xLength;
     return [x, y, z];
-  },
+  }
   /**
    * @member {Function} map Apply a function to all the voxels, be careful, the value will be replaced
    * @memberof Volume
@@ -157,14 +158,14 @@ Volume.prototype = {
    * @param {Object}   context    You can specify a context in which call the function, default if this Volume
    * @returns {Volume}   this
    */
-  map: function(functionToMap, context) {
-    var length = this.data.length;
+  map(functionToMap, context) {
+    const length = this.data.length;
     context = context || this;
     for (let i = 0; i < length; i++) {
       this.data[i] = functionToMap.call(context, this.data[i], i, this.data);
     }
     return this;
-  },
+  }
   /**
    * @member {Function} extractPerpendicularPlane Compute the orientation of the slice and returns all the information relative to the geometry such as sliceAccess, the plane matrix (orientation and position in RAS coordinate) and the dimensions of the plane in both coordinate system.
    * @memberof Volume
@@ -172,17 +173,17 @@ Volume.prototype = {
    * @param {number}            index the index of the slice
    * @returns {Object} an object containing all the usefull information on the geometry of the slice
    */
-  extractPerpendicularPlane: function(axis, RASIndex) {
-    var iLength, jLength, sliceAccess, planeMatrix = new Matrix4().identity(), volume = this, planeWidth, planeHeight, firstSpacing, secondSpacing, positionOffset, IJKIndex;
-    var axisInIJK = new Vector3(), firstDirection = new Vector3(), secondDirection = new Vector3();
-    var dimensions = new Vector3(this.xLength, this.yLength, this.zLength);
+  extractPerpendicularPlane(axis, RASIndex) {
+    let firstSpacing, secondSpacing, positionOffset, IJKIndex;
+    const axisInIJK = new Vector3(), firstDirection = new Vector3(), secondDirection = new Vector3(), planeMatrix = new Matrix4().identity(), volume = this;
+    const dimensions = new Vector3(this.xLength, this.yLength, this.zLength);
     switch (axis) {
       case "x":
         axisInIJK.set(1, 0, 0);
         firstDirection.set(0, 0, -1);
         secondDirection.set(0, -1, 0);
-        firstSpacing = this.spacing[2];
-        secondSpacing = this.spacing[1];
+        firstSpacing = this.spacing[this.axisOrder.indexOf("z")];
+        secondSpacing = this.spacing[this.axisOrder.indexOf("y")];
         IJKIndex = new Vector3(RASIndex, 0, 0);
         planeMatrix.multiply(new Matrix4().makeRotationY(Math.PI / 2));
         positionOffset = (volume.RASDimensions[0] - 1) / 2;
@@ -192,8 +193,8 @@ Volume.prototype = {
         axisInIJK.set(0, 1, 0);
         firstDirection.set(1, 0, 0);
         secondDirection.set(0, 0, 1);
-        firstSpacing = this.spacing[0];
-        secondSpacing = this.spacing[2];
+        firstSpacing = this.spacing[this.axisOrder.indexOf("x")];
+        secondSpacing = this.spacing[this.axisOrder.indexOf("z")];
         IJKIndex = new Vector3(0, RASIndex, 0);
         planeMatrix.multiply(new Matrix4().makeRotationX(-Math.PI / 2));
         positionOffset = (volume.RASDimensions[1] - 1) / 2;
@@ -204,43 +205,45 @@ Volume.prototype = {
         axisInIJK.set(0, 0, 1);
         firstDirection.set(1, 0, 0);
         secondDirection.set(0, -1, 0);
-        firstSpacing = this.spacing[0];
-        secondSpacing = this.spacing[1];
+        firstSpacing = this.spacing[this.axisOrder.indexOf("x")];
+        secondSpacing = this.spacing[this.axisOrder.indexOf("y")];
         IJKIndex = new Vector3(0, 0, RASIndex);
         positionOffset = (volume.RASDimensions[2] - 1) / 2;
         planeMatrix.setPosition(new Vector3(0, 0, RASIndex - positionOffset));
         break;
     }
-    firstDirection.applyMatrix4(volume.inverseMatrix).normalize();
-    firstDirection.argVar = "i";
-    secondDirection.applyMatrix4(volume.inverseMatrix).normalize();
-    secondDirection.argVar = "j";
-    axisInIJK.applyMatrix4(volume.inverseMatrix).normalize();
+    let iLength, jLength;
+    if (!this.segmentation) {
+      firstDirection.applyMatrix4(volume.inverseMatrix).normalize();
+      secondDirection.applyMatrix4(volume.inverseMatrix).normalize();
+      axisInIJK.applyMatrix4(volume.inverseMatrix).normalize();
+    }
+    firstDirection.arglet = "i";
+    secondDirection.arglet = "j";
     iLength = Math.floor(Math.abs(firstDirection.dot(dimensions)));
     jLength = Math.floor(Math.abs(secondDirection.dot(dimensions)));
-    planeWidth = Math.abs(iLength * firstSpacing);
-    planeHeight = Math.abs(jLength * secondSpacing);
+    const planeWidth = Math.abs(iLength * firstSpacing);
+    const planeHeight = Math.abs(jLength * secondSpacing);
     IJKIndex = Math.abs(Math.round(IJKIndex.applyMatrix4(volume.inverseMatrix).dot(axisInIJK)));
-    var base = [new Vector3(1, 0, 0), new Vector3(0, 1, 0), new Vector3(0, 0, 1)];
-    var iDirection = [firstDirection, secondDirection, axisInIJK].find(function(x) {
+    const base = [new Vector3(1, 0, 0), new Vector3(0, 1, 0), new Vector3(0, 0, 1)];
+    const iDirection = [firstDirection, secondDirection, axisInIJK].find(function(x) {
       return Math.abs(x.dot(base[0])) > 0.9;
     });
-    var jDirection = [firstDirection, secondDirection, axisInIJK].find(function(x) {
+    const jDirection = [firstDirection, secondDirection, axisInIJK].find(function(x) {
       return Math.abs(x.dot(base[1])) > 0.9;
     });
-    var kDirection = [firstDirection, secondDirection, axisInIJK].find(function(x) {
+    const kDirection = [firstDirection, secondDirection, axisInIJK].find(function(x) {
       return Math.abs(x.dot(base[2])) > 0.9;
     });
-    sliceAccess = function(i, j) {
-      var accessI, accessJ, accessK;
-      var si = iDirection === axisInIJK ? IJKIndex : iDirection.argVar === "i" ? i : j;
-      var sj = jDirection === axisInIJK ? IJKIndex : jDirection.argVar === "i" ? i : j;
-      var sk = kDirection === axisInIJK ? IJKIndex : kDirection.argVar === "i" ? i : j;
-      var accessI = iDirection.dot(base[0]) > 0 ? si : volume.xLength - 1 - si;
-      var accessJ = jDirection.dot(base[1]) > 0 ? sj : volume.yLength - 1 - sj;
-      var accessK = kDirection.dot(base[2]) > 0 ? sk : volume.zLength - 1 - sk;
+    function sliceAccess(i, j) {
+      const si = iDirection === axisInIJK ? IJKIndex : iDirection.arglet === "i" ? i : j;
+      const sj = jDirection === axisInIJK ? IJKIndex : jDirection.arglet === "i" ? i : j;
+      const sk = kDirection === axisInIJK ? IJKIndex : kDirection.arglet === "i" ? i : j;
+      const accessI = iDirection.dot(base[0]) > 0 ? si : volume.xLength - 1 - si;
+      const accessJ = jDirection.dot(base[1]) > 0 ? sj : volume.yLength - 1 - sj;
+      const accessK = kDirection.dot(base[2]) > 0 ? sk : volume.zLength - 1 - sk;
       return volume.access(accessI, accessJ, accessK);
-    };
+    }
     return {
       iLength,
       jLength,
@@ -249,7 +252,7 @@ Volume.prototype = {
       planeWidth,
       planeHeight
     };
-  },
+  }
   /**
    * @member {Function} extractSlice Returns a slice corresponding to the given axis and index
    *                        The coordinate are given in the Right Anterior Superior coordinate format
@@ -258,36 +261,36 @@ Volume.prototype = {
    * @param {number}            index the index of the slice
    * @returns {VolumeSlice} the extracted slice
    */
-  extractSlice: function(axis, index) {
-    var slice = new VolumeSlice(this, index, axis);
+  extractSlice(axis, index) {
+    const slice = new VolumeSlice(this, index, axis);
     this.sliceList.push(slice);
     return slice;
-  },
+  }
   /**
    * @member {Function} repaintAllSlices Call repaint on all the slices extracted from this volume
    * @see VolumeSlice.repaint
    * @memberof Volume
    * @returns {Volume} this
    */
-  repaintAllSlices: function() {
+  repaintAllSlices() {
     this.sliceList.forEach(function(slice) {
       slice.repaint();
     });
     return this;
-  },
+  }
   /**
    * @member {Function} computeMinMax Compute the minimum and the maximum of the data in the volume
    * @memberof Volume
    * @returns {Array} [min,max]
    */
-  computeMinMax: function() {
-    var min = Infinity;
-    var max = -Infinity;
-    var datasize = this.data.length;
-    var i = 0;
+  computeMinMax() {
+    let min = Infinity;
+    let max = -Infinity;
+    const datasize = this.data.length;
+    let i = 0;
     for (i = 0; i < datasize; i++) {
       if (!isNaN(this.data[i])) {
-        var value = this.data[i];
+        const value = this.data[i];
         min = Math.min(min, value);
         max = Math.max(max, value);
       }
@@ -296,7 +299,7 @@ Volume.prototype = {
     this.max = max;
     return [min, max];
   }
-};
+}
 export {
   Volume
 };

package/dist/misc/VolumeSlice.js

@@ -1,62 +1,61 @@
 "use strict";
 Object.defineProperty(exports, Symbol.toStringTag, { value: "Module" });
 const THREE = require("three");
-var VolumeSlice = function(volume, index, axis) {
-  var slice = this;
-  this.volume = volume;
-  index = index || 0;
-  Object.defineProperty(this, "index", {
-    get: function() {
-      return index;
-    },
-    set: function(value) {
-      index = value;
-      slice.geometryNeedsUpdate = true;
-      return index;
-    }
-  });
-  this.axis = axis || "z";
-  this.canvas = document.createElement("canvas");
-  this.canvasBuffer = document.createElement("canvas");
-  this.updateGeometry();
-  var canvasMap = new THREE.Texture(this.canvas);
-  canvasMap.minFilter = THREE.LinearFilter;
-  canvasMap.wrapS = canvasMap.wrapT = THREE.ClampToEdgeWrapping;
-  var material = new THREE.MeshBasicMaterial({
-    map: canvasMap,
-    side: THREE.DoubleSide,
-    transparent: true
-  });
-  this.mesh = new THREE.Mesh(this.geometry, material);
-  this.mesh.matrixAutoUpdate = false;
-  this.geometryNeedsUpdate = true;
-  this.repaint();
-};
-VolumeSlice.prototype = {
-  constructor: VolumeSlice,
+class VolumeSlice {
+  constructor(volume, index, axis) {
+    const slice = this;
+    this.volume = volume;
+    index = index || 0;
+    Object.defineProperty(this, "index", {
+      get: function() {
+        return index;
+      },
+      set: function(value) {
+        index = value;
+        slice.geometryNeedsUpdate = true;
+        return index;
+      }
+    });
+    this.axis = axis || "z";
+    this.canvas = document.createElement("canvas");
+    this.canvasBuffer = document.createElement("canvas");
+    this.updateGeometry();
+    const canvasMap = new THREE.Texture(this.canvas);
+    canvasMap.minFilter = THREE.LinearFilter;
+    canvasMap.wrapS = canvasMap.wrapT = THREE.ClampToEdgeWrapping;
+    if ("colorSpace" in canvasMap)
+      canvasMap.colorSpace = "srgb";
+    else
+      canvasMap.encoding = 3001;
+    const material = new THREE.MeshBasicMaterial({ map: canvasMap, side: THREE.DoubleSide, transparent: true });
+    this.mesh = new THREE.Mesh(this.geometry, material);
+    this.mesh.matrixAutoUpdate = false;
+    this.geometryNeedsUpdate = true;
+    this.repaint();
+  }
   /**
    * @member {Function} repaint Refresh the texture and the geometry if geometryNeedsUpdate is set to true
    * @memberof VolumeSlice
    */
-  repaint: function() {
+  repaint() {
     if (this.geometryNeedsUpdate) {
       this.updateGeometry();
     }
-    var iLength = this.iLength, jLength = this.jLength, sliceAccess = this.sliceAccess, volume = this.volume, canvas = this.canvasBuffer, ctx = this.ctxBuffer;
-    var imgData = ctx.getImageData(0, 0, iLength, jLength);
-    var data = imgData.data;
-    var volumeData = volume.data;
-    var upperThreshold = volume.upperThreshold;
-    var lowerThreshold = volume.lowerThreshold;
-    var windowLow = volume.windowLow;
-    var windowHigh = volume.windowHigh;
-    var pixelCount = 0;
+    const iLength = this.iLength, jLength = this.jLength, sliceAccess = this.sliceAccess, volume = this.volume, canvas = this.canvasBuffer, ctx = this.ctxBuffer;
+    const imgData = ctx.getImageData(0, 0, iLength, jLength);
+    const data = imgData.data;
+    const volumeData = volume.data;
+    const upperThreshold = volume.upperThreshold;
+    const lowerThreshold = volume.lowerThreshold;
+    const windowLow = volume.windowLow;
+    const windowHigh = volume.windowHigh;
+    let pixelCount = 0;
     if (volume.dataType === "label") {
       for (let j = 0; j < jLength; j++) {
         for (let i = 0; i < iLength; i++) {
-          var label = volumeData[sliceAccess(i, j)];
+          let label = volumeData[sliceAccess(i, j)];
           label = label >= this.colorMap.length ? label % this.colorMap.length + 1 : label;
-          var color = this.colorMap[label];
+          const color = this.colorMap[label];
           data[4 * pixelCount] = color >> 24 & 255;
           data[4 * pixelCount + 1] = color >> 16 & 255;
           data[4 * pixelCount + 2] = color >> 8 & 255;
@@ -67,8 +66,8 @@ VolumeSlice.prototype = {
     } else {
       for (let j = 0; j < jLength; j++) {
         for (let i = 0; i < iLength; i++) {
-          var value = volumeData[sliceAccess(i, j)];
-          var alpha = 255;
+          let value = volumeData[sliceAccess(i, j)];
+          let alpha = 255;
           alpha = upperThreshold >= value ? lowerThreshold <= value ? alpha : 0 : 0;
           value = Math.floor(255 * (value - windowLow) / (windowHigh - windowLow));
           value = value > 255 ? 255 : value < 0 ? 0 : value | 0;
@@ -83,14 +82,14 @@ VolumeSlice.prototype = {
     ctx.putImageData(imgData, 0, 0);
     this.ctx.drawImage(canvas, 0, 0, iLength, jLength, 0, 0, this.canvas.width, this.canvas.height);
     this.mesh.material.map.needsUpdate = true;
-  },
+  }
   /**
    * @member {Function} Refresh the geometry according to axis and index
    * @see Volume.extractPerpendicularPlane
    * @memberof VolumeSlice
    */
-  updateGeometry: function() {
-    var extracted = this.volume.extractPerpendicularPlane(this.axis, this.index);
+  updateGeometry() {
+    const extracted = this.volume.extractPerpendicularPlane(this.axis, this.index);
     this.sliceAccess = extracted.sliceAccess;
     this.jLength = extracted.jLength;
     this.iLength = extracted.iLength;
@@ -111,5 +110,5 @@ VolumeSlice.prototype = {
     }
     this.geometryNeedsUpdate = false;
   }
-};
+}
 exports.VolumeSlice = VolumeSlice;