image-js 0.35.1 → 0.35.3

package/lib/image/roi/manager.js

@@ -4,29 +4,17 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
-
 var _jsQuantities = _interopRequireDefault(require("js-quantities"));
-
 var _deepValue = _interopRequireDefault(require("../../util/deepValue"));
-
 var _Image = _interopRequireDefault(require("../Image"));
-
 var _RoiLayer = _interopRequireDefault(require("./RoiLayer"));
-
 var _RoiMap = _interopRequireDefault(require("./RoiMap"));
-
 var _fromMask = _interopRequireDefault(require("./creator/fromMask"));
-
 var _fromMaskConnectedComponentLabelingAlgorithm = _interopRequireDefault(require("./creator/fromMaskConnectedComponentLabelingAlgorithm"));
-
 var _fromMaxima = _interopRequireDefault(require("./creator/fromMaxima"));
-
 var _fromPoints = _interopRequireDefault(require("./creator/fromPoints"));
-
 var _fromWaterShed = _interopRequireDefault(require("./creator/fromWaterShed"));
-
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
 /**
  * A manager of Regions of Interest. A RoiManager is related to a specific Image
  * and may contain multiple layers. Each layer is characterized by a label whose is
@@ -39,130 +27,107 @@ class RoiManager {
   constructor(image, options = {}) {
     this._image = image;
     this._options = options;
-
     if (!this._options.label) {
       this._options.label = 'default';
     }
-
     this._layers = {};
     this._painted = null;
-  } // docs is in the corresponding file
-
+  }
 
+  // docs is in the corresponding file
   fromMaxima(options = {}) {
     let opt = Object.assign({}, this._options, options);
-
     let roiMap = _fromMaxima.default.call(this._image, options);
-
     this._layers[opt.label] = new _RoiLayer.default(roiMap, opt);
-  } // docs is in the corresponding file
-
+  }
 
+  // docs is in the corresponding file
   fromPoints(points, options = {}) {
     let opt = Object.assign({}, this._options, options);
-
     let roiMap = _fromPoints.default.call(this._image, points, options);
-
     this._layers[opt.label] = new _RoiLayer.default(roiMap, opt);
     return this;
   }
+
   /**
    * @param {number[]} map
    * @param {object} [options]
    * @return {this}
    */
-
-
   putMap(map, options = {}) {
     let roiMap = new _RoiMap.default(this._image, map);
     let opt = Object.assign({}, this._options, options);
     this._layers[opt.label] = new _RoiLayer.default(roiMap, opt);
     return this;
-  } // docs is in the corresponding file
-
+  }
 
+  // docs is in the corresponding file
   fromWaterShed(options = {}) {
     let opt = Object.assign({}, this._options, options);
-
     let roiMap = _fromWaterShed.default.call(this._image, options);
-
     this._layers[opt.label] = new _RoiLayer.default(roiMap, opt);
-  } // docs is in the corresponding file
-
+  }
 
+  // docs is in the corresponding file
   fromMask(mask, options = {}) {
     let opt = Object.assign({}, this._options, options);
-
     let roiMap = _fromMask.default.call(this._image, mask, options);
-
     this._layers[opt.label] = new _RoiLayer.default(roiMap, opt);
     return this;
   }
-
   fromMaskConnectedComponentLabelingAlgorithm(mask, options = {}) {
     let opt = Object.assign({}, this._options, options);
-
     let roiMap = _fromMaskConnectedComponentLabelingAlgorithm.default.call(this._image, mask, options);
-
     this._layers[opt.label] = new _RoiLayer.default(roiMap, opt);
     return this;
   }
+
   /**
    *
    * @param {object} [options]
    * @return {RoiMap}
    */
-
-
   getMap(options = {}) {
     let opt = Object.assign({}, this._options, options);
-
     this._assertLayerWithLabel(opt.label);
-
     return this._layers[opt.label].roiMap;
   }
+
   /**
    * Return statistics about rows
    * @param {object} [options]
    * @return {object[]}
    */
-
-
   rowsInfo(options = {}) {
     return this.getMap(options).rowsInfo();
   }
+
   /**
    * Return statistics about columns
    * @param {object} [options]
    * @return {object[]}
    */
-
-
   colsInfo(options = {}) {
     return this.getMap(options).rowsInfo();
   }
+
   /**
    * Return the IDs of the Regions Of Interest (Roi) as an array of number
    * @param {object} [options]
    * @return {number[]}
    */
-
-
   getRoiIds(options = {}) {
     let rois = this.getRois(options);
-
     if (rois) {
       let ids = new Array(rois.length);
-
       for (let i = 0; i < rois.length; i++) {
         ids[i] = rois[i].id;
       }
-
       return ids;
     }
-
     throw new Error('ROIs not found');
   }
+
   /**
    * Allows to select ROI based on size, label and sign.
    * @param {object} [options={}]
@@ -179,8 +144,6 @@ class RoiManager {
    * @param {number} [options.maxRatio=Number.POSITIVE_INFINITY]
    * @return {Roi[]}
    */
-
-
   getRois(options = {}) {
     let {
       label = this._options.label,
@@ -195,22 +158,19 @@ class RoiManager {
       minRatio = 0,
       maxRatio = Number.POSITIVE_INFINITY
     } = options;
-
     if (!this._layers[label]) {
       throw new Error(`this Roi layer (${label}) does not exist`);
     }
-
     const allRois = this._layers[label].roi;
     const rois = [];
-
     for (const roi of allRois) {
       if ((roi.id < 0 && negative || roi.id > 0 && positive) && roi.surface >= minSurface && roi.surface <= maxSurface && roi.width >= minWidth && roi.width <= maxWidth && roi.height >= minHeight && roi.height <= maxHeight && roi.ratio >= minRatio && roi.ratio <= maxRatio) {
         rois.push(roi);
       }
     }
-
     return rois;
   }
+
   /**
    * Get an ROI by its id.
    * @param {number} roiId
@@ -218,51 +178,41 @@ class RoiManager {
    * @param {string} [options.label='default'] Label of the layer containing the ROI
    * @return {Roi}
    */
-
-
   getRoi(roiId, options = {}) {
     const {
       label = this._options.label
     } = options;
-
     if (!this._layers[label]) {
       throw new Error(`this Roi layer (${label}) does not exist`);
     }
-
     const roi = this._layers[label].roi.find(roi => roi.id === roiId);
-
     if (!roi) {
       throw new Error(`found no Roi with id ${roiId}`);
     }
-
     return roi;
   }
+
   /**
    * Returns an array of masks
    * See {@link Roi.getMask} for the options
    * @param {object} [options]
    * @return {Image[]} Retuns an array of masks (1 bit Image)
    */
-
-
   getMasks(options = {}) {
     let rois = this.getRois(options);
     let masks = new Array(rois.length);
-
     for (let i = 0; i < rois.length; i++) {
       masks[i] = rois[i].getMask(options);
     }
-
     return masks;
   }
+
   /**
    * Returns an array of masks
    * See {@link Roi.getAnalysisMasks} for the options
    * @param {object} [options]
    * @return {Image[]} Retuns an array of masks (1 bit Image)
    */
-
-
   getAnalysisMasks(options = {}) {
     const {
       analysisProperty
@@ -272,20 +222,18 @@ class RoiManager {
     if (rois.length === 0 || !rois[0][maskProperty]) return [];
     return rois.map(roi => roi[maskProperty]);
   }
+
   /**
    *
    * @param {object} [options]
    * @return {number[]}
    */
-
-
   getData(options = {}) {
     let opt = Object.assign({}, this._options, options);
-
     this._assertLayerWithLabel(opt.label);
-
     return this._layers[opt.label].roiMap.data;
   }
+
   /**
    * Paint the ROI on a copy of the image and return this image.
    * For painting options {@link Image.paintMasks}
@@ -298,48 +246,37 @@ class RoiManager {
    * @param {string} [options.unit="pixel"] Unit in which to display the values
    * @return {Image} - The painted RGBA 8 bits image
    */
-
-
   paint(options = {}) {
     let {
       labelProperty,
       analysisProperty
     } = options;
-
     if (!this._painted) {
       this._painted = this._image.rgba8();
     }
-
     let masks = this.getMasks(options);
-
     if (labelProperty) {
       const rois = this.getRois(options);
       options.labels = rois.map(roi => (0, _deepValue.default)(roi, labelProperty));
       const max = Math.max(...options.labels);
       let isSurface = false;
       let isDistance = false;
-
       if (labelProperty.includes('surface')) {
         isSurface = true;
       } else if (/(?:perimeter|min|max|external|width|height|length)/.test(labelProperty)) {
         isDistance = true;
       }
-
       if (isFinite(max)) {
         let unitLabel = '';
-
         if (options.unit !== 'pixel' && options.pixelSize && (isDistance || isSurface)) {
           unitLabel = isSurface ? `${options.unit}^2` : options.unit;
           let siLabel = isSurface ? 'm^2' : 'm';
           let factor = isSurface ? options.pixelSize ** 2 : options.pixelSize;
-
           const convert = _jsQuantities.default.swiftConverter(siLabel, unitLabel);
-
           options.labels = options.labels.map(value => {
             return convert(factor * value);
           });
         }
-
         if (max > 50) {
           options.labels = options.labels.map(number => Math.round(number) + unitLabel);
         } else if (max > 10) {
@@ -348,33 +285,28 @@ class RoiManager {
           options.labels = options.labels.map(number => number.toFixed(2) + unitLabel);
         }
       }
-
       options.labelsPosition = rois.map(roi => [roi.meanX, roi.meanY]);
     }
-
     this._painted.paintMasks(masks, options);
-
     if (analysisProperty) {
       let analysisMasks = this.getAnalysisMasks(options);
-
       this._painted.paintMasks(analysisMasks, {
         color: options.analysisColor,
         alpha: options.analysisAlpha
       });
     }
-
     return this._painted;
-  } // return a mask corresponding to all the selected masks
-
+  }
 
+  // return a mask corresponding to all the selected masks
   getMask(options = {}) {
     let mask = new _Image.default(this._image.width, this._image.height, {
       kind: 'BINARY'
     });
     let masks = this.getMasks(options);
-
     for (let i = 0; i < masks.length; i++) {
-      let roi = masks[i]; // we need to find the parent image to calculate the relative position
+      let roi = masks[i];
+      // we need to find the parent image to calculate the relative position
 
       for (let x = 0; x < roi.width; x++) {
         for (let y = 0; y < roi.height; y++) {
@@ -384,9 +316,9 @@ class RoiManager {
         }
       }
     }
-
     return mask;
   }
+
   /**
    * Reset the changes to the current painted iamge to the image that was
    * used during the creation of the RoiManager except if a new image is
@@ -394,19 +326,17 @@ class RoiManager {
    * @param {object} [options]
    * @param {Image} [options.image] A new iamge that you would like to sue for painting over
    */
-
-
   resetPainted(options = {}) {
     const {
       image
     } = options;
-
     if (image) {
       this._painted = this.image.rgba8();
     } else {
       this._painted = this._image.rgba8();
     }
   }
+
   /**
    * In place modification of the roiMap that joins regions of interest
    * @param {object} [options]
@@ -420,54 +350,46 @@ class RoiManager {
    * @param {number} [options.maxCommonBorderRatio=1] maximal common border ratio for merging
    * @return {this}
    */
-
-
   mergeRoi(options = {}) {
     const roiMap = this.getMap(options);
     roiMap.mergeRoi(options);
     this.putMap(roiMap.data, options);
     return this;
   }
+
   /**
    * Merge multiple rois into one.
    * All rois in the provided array will be merged into the first one.
    * @param {Array<number>} roiIds - A list of Roi ids to merge
    * @param {object} [options]
    */
-
-
   mergeRois(roiIds, options = {}) {
     if (!Array.isArray(roiIds) || roiIds.some(id => !Number.isInteger(id))) {
       throw new Error('Roi ids must be an array of integers');
     }
-
     if (roiIds.length < 2) {
       throw new Error('Roi ids must have at least two elements');
     }
-
     if (new Set(roiIds).size !== roiIds.length) {
       throw new Error('Roi ids must be all different');
-    } // Throws if one of the ids is wrong
-
-
+    }
+    // Throws if one of the ids is wrong
     roiIds.forEach(roiId => this.getRoi(roiId));
     const roiMap = this.getMap(options);
     roiMap.mergeRois(roiIds);
     this.putMap(roiMap.data, options);
     return this;
   }
+
   /**
    * Finds all corresponding ROIs for all ROIs in the manager
    * @param {number[]} roiMap
    * @param {object} [options]
    * @return {Array} array of objects returned in correspondingRoisInformation
    */
-
-
   findCorrespondingRoi(roiMap, options = {}) {
     let allRois = this.getRois(options);
     let allRelated = [];
-
     for (let i = 0; i < allRois.length; i++) {
       let currentRoi = allRois[i];
       let x = currentRoi.minX;
@@ -477,17 +399,15 @@ class RoiManager {
       let currentRelated = correspondingRoisInformation(x, y, allPoints, roiMap, roiSign);
       allRelated.push(currentRelated);
     }
-
     return allRelated;
   }
-
   _assertLayerWithLabel(label) {
     if (!this._layers[label]) {
       throw new Error(`no layer with label ${label}`);
     }
   }
-
 }
+
 /**
  * For a given ROI, find corresponding ROIs and properties in given ROIMap.
  * Returns an object containing the ID of ROIs, the surface shared by given and corresponding ROIs,
@@ -501,10 +421,7 @@ class RoiManager {
  * @return {object} {{id: Array, surface: Array, roiSurfaceCovered: Array, same: number, opposite: number, total: number}}
  * @private
  */
-
-
 exports.default = RoiManager;
-
 function correspondingRoisInformation(x, y, points, roiMap, roiSign) {
   let correspondingRois = {
     id: [],
@@ -514,14 +431,12 @@ function correspondingRoisInformation(x, y, points, roiMap, roiSign) {
     opposite: 0,
     total: 0
   };
-
   for (let i = 0; i < points.length; i++) {
     let currentPoint = points[i];
     let currentX = currentPoint[0];
     let currentY = currentPoint[1];
     let correspondingRoiMapIndex = currentX + x + (currentY + y) * roiMap.width;
     let value = roiMap.data[correspondingRoiMapIndex];
-
     if (value > 0 || value < 0) {
       if (correspondingRois.id.includes(value)) {
         correspondingRois.surface[correspondingRois.id.indexOf(value)] += 1;
@@ -531,19 +446,15 @@ function correspondingRoisInformation(x, y, points, roiMap, roiSign) {
       }
     }
   }
-
   for (let i = 0; i < correspondingRois.id.length; i++) {
     let currentSign = Math.sign(correspondingRois.id[i]);
-
     if (currentSign === roiSign) {
       correspondingRois.same += correspondingRois.surface[i];
     } else {
       correspondingRois.opposite += correspondingRois.surface[i];
     }
-
     correspondingRois.roiSurfaceCovered[i] = correspondingRois.surface[i] / points.length;
   }
-
   correspondingRois.total = correspondingRois.opposite + correspondingRois.same;
   return correspondingRois;
 }

package/lib/image/roi/util/commonBorderLength.js

@@ -4,8 +4,8 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = commonBorderLength;
-
 // We calculate all the border length with the neighbours
+
 function commonBorderLength(roiMap) {
   let data = roiMap.data;
   let dx = [+1, 0, -1, 0];
@@ -14,34 +14,26 @@ function commonBorderLength(roiMap) {
   let shift = -minMax.min;
   let max = minMax.max + shift;
   let borderInfo = [];
-
   for (let i = 0; i <= max; i++) {
     borderInfo.push(Object.create(null));
   }
-
   for (let x = 0; x < roiMap.width; x++) {
     for (let y = 0; y < roiMap.height; y++) {
       let target = x + y * roiMap.width;
       let currentRoiID = data[target];
-
       if (currentRoiID !== 0) {
         // each pixel may only contribute one time to a border
         let used = Object.create(null);
         let isBorder = false;
-
         for (let dir = 0; dir < 4; dir++) {
           let newX = x + dx[dir];
           let newY = y + dy[dir];
-
           if (newX >= 0 && newY >= 0 && newX < roiMap.width && newY < roiMap.height) {
             let neighbourRoiID = data[newX + newY * roiMap.width];
-
             if (currentRoiID !== neighbourRoiID) {
               isBorder = true;
-
               if (neighbourRoiID !== 0 && used[neighbourRoiID] === undefined) {
                 used[neighbourRoiID] = true;
-
                 if (!borderInfo[neighbourRoiID + shift][currentRoiID]) {
                   borderInfo[neighbourRoiID + shift][currentRoiID] = 1;
                 } else {
@@ -52,9 +44,8 @@ function commonBorderLength(roiMap) {
           } else {
             isBorder = true;
           }
-        } // we will also add an information to specify the border length
-
-
+        }
+        // we will also add an information to specify the border length
         if (isBorder) {
           if (!borderInfo[currentRoiID + shift][currentRoiID]) {
             borderInfo[currentRoiID + shift][currentRoiID] = 1;
@@ -64,16 +55,14 @@ function commonBorderLength(roiMap) {
         }
       }
     }
-  } // we convert now the result to an object for fast lookup and we will reshift the result
-
+  }
 
+  // we convert now the result to an object for fast lookup and we will reshift the result
   let result = {};
-
   for (let i = 0; i < borderInfo.length; i++) {
     if (Object.keys(borderInfo[i]).length > 0) {
       result[i - shift] = borderInfo[i];
     }
   }
-
   return result;
 }

package/lib/image/roi/util/mergeRoi.js

@@ -4,7 +4,6 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = mergeRoi;
-
 /**
  * In place modification of the roiMap that joins regions of interest
  * @param {object} [options]
@@ -27,31 +26,25 @@ function mergeRoi(options = {}) {
     minCommonBorderRatio = 0.3,
     maxCommonBorderRatio = 1
   } = options;
-
   let checkFunction = function (currentInfo, currentID, neighbourID) {
     return currentInfo[neighbourID] >= minCommonBorderLength && currentInfo[neighbourID] <= maxCommonBorderLength;
   };
-
   if (typeof algorithm === 'function') {
     checkFunction = algorithm;
   }
-
   if (algorithm.toLowerCase() === 'commonborderratio') {
     checkFunction = function (currentInfo, currentID, neighbourID) {
       let ratio = Math.min(currentInfo[neighbourID] / currentInfo[currentID], 1);
       return ratio >= minCommonBorderRatio && ratio <= maxCommonBorderRatio;
     };
   }
-
   const roiMap = this;
   const borderLengths = roiMap.commonBorderLength;
   let newMap = {};
   let oldToNew = {};
-
   for (let currentID of Object.keys(borderLengths)) {
     let currentInfo = borderLengths[currentID];
     let neighbourIDs = Object.keys(currentInfo);
-
     for (let neighbourID of neighbourIDs) {
       if (neighbourID !== currentID) {
         // it is not myself ...
@@ -61,25 +54,20 @@ function mergeRoi(options = {}) {
           if (oldToNew[neighbourID]) newNeighbourID = oldToNew[neighbourID];
           let newCurrentID = currentID;
           if (oldToNew[currentID]) newCurrentID = oldToNew[currentID];
-
           if (Number(newNeighbourID) !== newCurrentID) {
             let smallerID = Math.min(newNeighbourID, newCurrentID);
             let largerID = Math.max(newNeighbourID, newCurrentID);
-
             if (!newMap[smallerID]) {
               newMap[smallerID] = {};
             }
-
             newMap[smallerID][largerID] = true;
             oldToNew[largerID] = smallerID;
-
             if (newMap[largerID]) {
               // need to put everything to smallerID and remove property
               for (let id of Object.keys(newMap[largerID])) {
                 newMap[smallerID][id] = true;
                 oldToNew[id] = smallerID;
               }
-
               delete newMap[largerID];
             }
           }
@@ -87,31 +75,24 @@ function mergeRoi(options = {}) {
       }
     }
   }
-
   let minMax = roiMap.minMax;
   let shift = -minMax.min;
   let max = minMax.max + shift;
   let oldToNewArray = new Array(max + 1).fill(0);
-
   for (let key of Object.keys(oldToNew)) {
     oldToNewArray[Number(key) + shift] = oldToNew[key];
-  } // time to change the roiMap
-
-
+  }
+  // time to change the roiMap
   let data = roiMap.data;
-
   for (let i = 0; i < data.length; i++) {
     let currentValue = data[i];
-
     if (currentValue !== 0) {
       let newValue = oldToNewArray[currentValue + shift];
-
       if (newValue !== 0) {
         data[i] = newValue;
       }
     }
   }
-
   roiMap.computed = {};
   return roiMap;
 }