image-js 0.35.1 → 0.35.3

package/lib/image/roi/RoiLayer.js

@@ -4,11 +4,8 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
-
 var _Roi = _interopRequireDefault(require("./Roi"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 /**
  * A layer that is caracterised by a {@link RoiMap} and that will
  * generated automatically the corresponding ROI.
@@ -28,6 +25,7 @@ class RoiLayer {
     this.options = options;
     this.roi = this.createRoi();
   }
+
   /**
    * Roi are created from a roiMap
    * The roiMap contains mainty an array of identifiers that define
@@ -36,19 +34,15 @@ class RoiLayer {
    * @instance
    * @return {Roi[]}
    */
-
-
   createRoi() {
     // we need to find all all the different IDs there is in the data
     let data = this.roiMap.data;
     let mapIDs = {};
     this.roiMap.positive = 0;
     this.roiMap.negative = 0;
-
     for (let i = 0; i < data.length; i++) {
       if (data[i] && !mapIDs[data[i]]) {
         mapIDs[data[i]] = true;
-
         if (data[i] > 0) {
           this.roiMap.positive++;
         } else {
@@ -56,58 +50,43 @@ class RoiLayer {
         }
       }
     }
-
     let rois = {};
-
     for (let mapID in mapIDs) {
       rois[mapID] = new _Roi.default(this.roiMap, mapID * 1);
     }
-
     let width = this.roiMap.width;
     let height = this.roiMap.height;
-
     for (let y = 0; y < height; y++) {
       for (let x = 0; x < width; x++) {
         let target = y * width + x;
-
         if (data[target] !== 0) {
           const mapID = data[target];
           const roi = rois[mapID];
-
           if (x < roi.minX) {
             roi.minX = x;
           }
-
           if (x > roi.maxX) {
             roi.maxX = x;
           }
-
           if (y < roi.minY) {
             roi.minY = y;
           }
-
           if (y > roi.maxY) {
             roi.maxY = y;
           }
-
           roi.meanX += x;
           roi.meanY += y;
           roi.surface++;
         }
       }
     }
-
     let roiArray = [];
-
     for (let mapID in mapIDs) {
       rois[mapID].meanX /= rois[mapID].surface;
       rois[mapID].meanY /= rois[mapID].surface;
       roiArray.push(rois[mapID]);
     }
-
     return roiArray;
   }
-
 }
-
 exports.default = RoiLayer;

package/lib/image/roi/RoiMap.js

@@ -4,13 +4,9 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
-
 var _commonBorderLength = _interopRequireDefault(require("./util/commonBorderLength"));
-
 var _mergeRoi = _interopRequireDefault(require("./util/mergeRoi"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 /**
  * The roiMap is an array of the size of the original image data that contains
  * positive and negative numbers. When the number is common, it corresponds
@@ -19,6 +15,7 @@ function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { de
  * @class RoiMap
  * @private
  */
+
 class RoiMap {
   constructor(parent, data) {
     this.parent = parent;
@@ -28,49 +25,39 @@ class RoiMap {
     this.negative = 0;
     this.positive = 0;
   }
-
   get total() {
     return this.negative + this.positive;
   }
-
   get minMax() {
     let min = Number.MAX_SAFE_INTEGER;
     let max = Number.MIN_SAFE_INTEGER;
-
     for (let i = 0; i < this.data.length; i++) {
       if (this.data[i] < min) min = this.data[i];
       if (this.data[i] > max) max = this.data[i];
     }
-
     return {
       min,
       max
     };
   }
-
   get commonBorderLength() {
     return (0, _commonBorderLength.default)(this);
   }
-
   mergeRoi(options = {}) {
     return _mergeRoi.default.call(this, options);
   }
-
   mergeRois(rois) {
     const first = rois[0];
     const others = rois.slice(1);
-
     for (let i = 0; i < this.data.length; i++) {
       if (others.includes(this.data[i])) {
         this.data[i] = first;
       }
     }
   }
-
   rowsInfo() {
     let rowsInfo = new Array(this.height);
     let currentRow = 0;
-
     for (let i = 0; i < this.data.length; i += this.width) {
       let info = {
         row: currentRow,
@@ -87,27 +74,21 @@ class RoiMap {
       let changes = [];
       let previous = this.data[i];
       let current = 0;
-
       for (let j = i; j < i + this.width; j++) {
         let value = this.data[j];
-
         if (previous !== value) {
           previous = value;
           changes.push(current);
           current = 0;
         }
-
         current++;
-
         if (value > 0) {
           info.positivePixel++;
-
           if (!positives[value]) {
             positives[value] = true;
           }
         } else if (value < 0) {
           info.negativePixel++;
-
           if (!negatives[value]) {
             negatives[value] = true;
           }
@@ -115,23 +96,19 @@ class RoiMap {
           info.zeroPixel++;
         }
       }
-
-      changes.push(current); // TODO use median package
-
+      changes.push(current);
+      // TODO use median package
       info.medianChange = changes.sort((a, b) => a - b)[Math.floor(changes.length / 2)];
       info.positiveRoiIDs = Object.keys(positives);
       info.negativeRoiIDs = Object.keys(negatives);
       info.positiveRoi = info.positiveRoiIDs.length;
       info.negativeRoi = info.negativeRoiIDs.length;
     }
-
     return rowsInfo;
   }
-
   colsInfo() {
     let colsInfo = new Array(this.width);
     let currentCol = 0;
-
     for (let i = 0; i < this.width; i++) {
       let info = {
         col: currentCol,
@@ -148,27 +125,21 @@ class RoiMap {
       let changes = [];
       let previous = this.data[i];
       let current = 0;
-
       for (let j = i; j < i + this.data.length; j += this.width) {
         let value = this.data[j];
-
         if (previous !== value) {
           previous = value;
           changes.push(current);
           current = 0;
         }
-
         current++;
-
         if (value > 0) {
           info.positivePixel++;
-
           if (!positives[value]) {
             positives[value] = true;
           }
         } else if (value < 0) {
           info.negativePixel++;
-
           if (!negatives[value]) {
             negatives[value] = true;
           }
@@ -176,19 +147,15 @@ class RoiMap {
           info.zeroPixel++;
         }
       }
-
-      changes.push(current); // TODO use median package
-
+      changes.push(current);
+      // TODO use median package
       info.medianChange = changes.sort((a, b) => a - b)[Math.floor(changes.length / 2)];
       info.positiveRoiIDs = Object.keys(positives);
       info.negativeRoiIDs = Object.keys(negatives);
       info.positiveRoi = info.positiveRoiIDs.length;
       info.negativeRoi = info.negativeRoiIDs.length;
     }
-
     return colsInfo;
   }
-
 }
-
 exports.default = RoiMap;

package/lib/image/roi/creator/fromMask.js

@@ -4,11 +4,8 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = fromMask;
-
 var _RoiMap = _interopRequireDefault(require("../RoiMap"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 /**
  * @memberof RoiManager
  * @instance
@@ -21,15 +18,14 @@ function fromMask(mask, options = {}) {
     allowCorners = false
   } = options;
   const MAX_ARRAY = 0x00ffff; // 65535 should be enough for most of the cases
-  // based on a binary image we will create plenty of small images
 
+  // based on a binary image we will create plenty of small images
   let data = new Int16Array(mask.size); // maxValue: 32767, minValue: -32768
-  // split will always return an array of images
 
+  // split will always return an array of images
   let positiveID = 0;
   let negativeID = 0;
   let xToProcess = new Uint16Array(MAX_ARRAY + 1); // assign dynamically ????
-
   let yToProcess = new Uint16Array(MAX_ARRAY + 1); // mask +1 is of course mandatory !!!
 
   for (let x = 0; x < mask.width; x++) {
@@ -40,25 +36,21 @@ function fromMask(mask, options = {}) {
       }
     }
   }
-
   function analyseSurface(x, y) {
     let from = 0;
     let to = 0;
     let targetState = mask.getBitXY(x, y);
     let id = targetState ? ++positiveID : --negativeID;
-
     if (positiveID > 32767 || negativeID < -32768) {
       throw new Error('Too many regions of interest');
     }
-
     xToProcess[0] = x;
     yToProcess[0] = y;
-
     while (from <= to) {
       let currentX = xToProcess[from & MAX_ARRAY];
       let currentY = yToProcess[from & MAX_ARRAY];
-      data[currentY * mask.width + currentX] = id; // need to check all around mask pixel
-
+      data[currentY * mask.width + currentX] = id;
+      // need to check all around mask pixel
       if (currentX > 0 && data[currentY * mask.width + currentX - 1] === 0 && mask.getBitXY(currentX - 1, currentY) === targetState) {
         // LEFT
         to++;
@@ -66,7 +58,6 @@ function fromMask(mask, options = {}) {
         yToProcess[to & MAX_ARRAY] = currentY;
         data[currentY * mask.width + currentX - 1] = -32768;
       }
-
       if (currentY > 0 && data[(currentY - 1) * mask.width + currentX] === 0 && mask.getBitXY(currentX, currentY - 1) === targetState) {
         // TOP
         to++;
@@ -74,7 +65,6 @@ function fromMask(mask, options = {}) {
         yToProcess[to & MAX_ARRAY] = currentY - 1;
         data[(currentY - 1) * mask.width + currentX] = -32768;
       }
-
       if (currentX < mask.width - 1 && data[currentY * mask.width + currentX + 1] === 0 && mask.getBitXY(currentX + 1, currentY) === targetState) {
         // RIGHT
         to++;
@@ -82,7 +72,6 @@ function fromMask(mask, options = {}) {
         yToProcess[to & MAX_ARRAY] = currentY;
         data[currentY * mask.width + currentX + 1] = -32768;
       }
-
       if (currentY < mask.height - 1 && data[(currentY + 1) * mask.width + currentX] === 0 && mask.getBitXY(currentX, currentY + 1) === targetState) {
         // BOTTOM
         to++;
@@ -90,7 +79,6 @@ function fromMask(mask, options = {}) {
         yToProcess[to & MAX_ARRAY] = currentY + 1;
         data[(currentY + 1) * mask.width + currentX] = -32768;
       }
-
       if (allowCorners) {
         if (currentX > 0 && currentY > 0 && data[(currentY - 1) * mask.width + currentX - 1] === 0 && mask.getBitXY(currentX - 1, currentY - 1) === targetState) {
           // TOP LEFT
@@ -99,7 +87,6 @@ function fromMask(mask, options = {}) {
           yToProcess[to & MAX_ARRAY] = currentY - 1;
           data[(currentY - 1) * mask.width + currentX - 1] = -32768;
         }
-
         if (currentX < mask.width - 1 && currentY > 0 && data[(currentY - 1) * mask.width + currentX + 1] === 0 && mask.getBitXY(currentX + 1, currentY - 1) === targetState) {
           // TOP RIGHT
           to++;
@@ -107,7 +94,6 @@ function fromMask(mask, options = {}) {
           yToProcess[to & MAX_ARRAY] = currentY - 1;
           data[(currentY - 1) * mask.width + currentX + 1] = -32768;
         }
-
         if (currentX > 0 && currentY < mask.height - 1 && data[(currentY + 1) * mask.width + currentX - 1] === 0 && mask.getBitXY(currentX - 1, currentY + 1) === targetState) {
           // BOTTOM LEFT
           to++;
@@ -115,7 +101,6 @@ function fromMask(mask, options = {}) {
           yToProcess[to & MAX_ARRAY] = currentY + 1;
           data[(currentY + 1) * mask.width + currentX - 1] = -32768;
         }
-
         if (currentX < mask.width - 1 && currentY < mask.height - 1 && data[(currentY + 1) * mask.width + currentX + 1] === 0 && mask.getBitXY(currentX + 1, currentY + 1) === targetState) {
           // BOTTOM RIGHT
           to++;
@@ -124,14 +109,11 @@ function fromMask(mask, options = {}) {
           data[(currentY + 1) * mask.width + currentX + 1] = -32768;
         }
       }
-
       from++;
-
       if (to - from > MAX_ARRAY) {
         throw new Error('analyseMask can not finish, the array to manage internal data is not big enough.' + 'You could improve mask by changing MAX_ARRAY');
       }
     }
   }
-
   return new _RoiMap.default(mask, data);
 }

package/lib/image/roi/creator/fromMaskConnectedComponentLabelingAlgorithm.js

@@ -4,43 +4,37 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = fromMaskConnectedComponentLabelingAlgorithm;
-
 var _mlDisjointSet = _interopRequireDefault(require("ml-disjoint-set"));
-
 var _RoiMap = _interopRequireDefault(require("../RoiMap"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 /*
 This algorithm is nice and is therefore kept here
 However it seems to be slower than the get mask and
 also provides only the positive ROI
 We therefore don't expose it in the roiManager
  */
+
 const direction4X = [-1, 0];
 const direction4Y = [0, -1];
 const neighbours4 = [null, null];
 const direction8X = [-1, -1, 0, 1];
 const direction8Y = [0, -1, -1, -1];
 const neighbours8 = [null, null, null, null];
+
 /*
 Implementation of the connected-component labeling algorithm
  */
-
 function fromMaskConnectedComponentLabelingAlgorithm(mask, options = {}) {
   const {
     allowCorners = false
   } = options;
   let neighbours = 4;
-
   if (allowCorners) {
     neighbours = 8;
   }
-
   let directionX;
   let directionY;
   let neighboursList;
-
   if (neighbours === 8) {
     directionX = direction8X;
     directionY = direction8Y;
@@ -52,7 +46,6 @@ function fromMaskConnectedComponentLabelingAlgorithm(mask, options = {}) {
   } else {
     throw new RangeError(`unsupported neighbours count: ${neighbours}`);
   }
-
   const size = mask.size;
   const width = mask.width;
   const height = mask.height;
@@ -60,40 +53,32 @@ function fromMaskConnectedComponentLabelingAlgorithm(mask, options = {}) {
   const data = new Uint32Array(size);
   const linked = new _mlDisjointSet.default();
   let currentLabel = 1;
-
   for (let j = 0; j < height; j++) {
     for (let i = 0; i < width; i++) {
       // true means out of background
       const index = i + j * width;
-
       if (mask.getBit(index)) {
         let smallestNeighbour = null;
-
         for (let k = 0; k < neighboursList.length; k++) {
           const ii = i + directionX[k];
           const jj = j + directionY[k];
-
           if (ii >= 0 && jj >= 0 && ii < width && jj < height) {
             const index = ii + jj * width;
             let neighbour = labels[index];
-
             if (!neighbour) {
               neighboursList[k] = null;
             } else {
               neighboursList[k] = neighbour;
-
               if (!smallestNeighbour || neighboursList[k].value < smallestNeighbour.value) {
                 smallestNeighbour = neighboursList[k];
               }
             }
           }
         }
-
         if (!smallestNeighbour) {
           labels[index] = linked.add(currentLabel++);
         } else {
           labels[index] = smallestNeighbour;
-
           for (let k = 0; k < neighboursList.length; k++) {
             if (neighboursList[k] && neighboursList[k] !== smallestNeighbour) {
               linked.union(smallestNeighbour, neighboursList[k]);
@@ -103,16 +88,13 @@ function fromMaskConnectedComponentLabelingAlgorithm(mask, options = {}) {
       }
     }
   }
-
   for (let j = 0; j < height; j++) {
     for (let i = 0; i < width; i++) {
       const index = i + j * width;
-
       if (mask.getBit(index)) {
         data[index] = linked.find(labels[index]).value;
       }
     }
   }
-
   return new _RoiMap.default(mask, data);
 }