feat!: refactor points and add absolute coords calculation (#472)

src/roi/Roi.ts

@@ -11,19 +11,15 @@ import { getMask, GetMaskOptions } from './getMask';
 import { getEllipse } from './properties/getEllipse';
 import { Border, Ellipse } from './roi.types';
 
-/**
- * Properties of borders of ROI.
- *
- */
-
 interface Computed {
   perimeter: number;
   borders: Border[]; // external and internal ids which are not equal to the current roi ID
   perimeterInfo: { one: number; two: number; three: number; four: number };
   externalLengths: number[];
   borderLengths: number[];
   box: number;
-  points: number[][];
+  relativePoints: Point[];
+  absolutePoints: Point[];
   holesInfo: { number: number; surface: number };
   boxIDs: number[];
   externalBorders: Border[];
@@ -291,26 +287,26 @@ export class Roi {
     );
   }
   /**
-   * Computes current ROI points.
-   * @returns Array of points. It's an array of tuples, each tuple being the x and y coordinates of the ROI point.
+   * Computes ROI points relative to ROIs point of `origin`.
+   * @returns Array of points with relative ROI coordinates.
    */
-  get points() {
-    return this.#getComputed('points', () => {
-      const points = [];
-      for (let row = 0; row < this.height; row++) {
-        for (let column = 0; column < this.width; column++) {
-          const target =
-            (row + this.origin.row) * this.map.width +
-            column +
-            this.origin.column;
-          if (this.map.data[target] === this.id) {
-            points.push([column, row]);
-          }
-        }
-      }
+  get relativePoints() {
+    return this.#getComputed(`relativePoints`, () => {
+      const points = Array.from(this.points(false));
+      return points;
+    });
+  }
+  /**
+   * Computes ROI points relative to Image's/Mask's point of `origin`.
+   * @returns Array of points with absolute ROI coordinates.
+   */
+  get absolutePoints() {
+    return this.#getComputed(`absolutePoints`, () => {
+      const points = Array.from(this.points(true));
       return points;
     });
   }
+
   get boxIDs() {
     return this.#getComputed('boxIDs', () => {
       const surroundingIDs = new Set<number>(); // Allows to get a unique list without indexOf.
@@ -631,4 +627,30 @@ export class Roi {
     const roiMap = this.map;
     return (y + this.origin.row) * roiMap.width + x + this.origin.column;
   }
+
+  /**
+   * Generator function to calculate point's coordinates.
+   * @param absolute - controls whether coordinates should be relative to ROI's point of `origin` (relative), or relative to ROI's position on the Image/Mask (absolute).
+   * @yields Coordinates of each point of ROI.
+   */
+  *points(absolute: boolean) {
+    for (let row = 0; row < this.height; row++) {
+      for (let column = 0; column < this.width; column++) {
+        const target =
+          (row + this.origin.row) * this.map.width +
+          column +
+          this.origin.column;
+        if (this.map.data[target] === this.id) {
+          if (absolute) {
+            yield {
+              column: this.origin.column + column,
+              row: this.origin.row + row,
+            };
+          } else {
+            yield { column, row };
+          }
+        }
+      }
+    }
+  }
 }

src/roi/__tests__/points.test.ts

@@ -9,36 +9,84 @@ test('points 1st test', () => {
   ]);
   const roiMapManager = fromMask(mask);
   const rois = roiMapManager.getRois();
-  expect(rois[0].points).toStrictEqual([
-    [0, 0],
-    [1, 0],
-    [0, 1],
-    [1, 1],
-    [0, 2],
-    [1, 2],
-    [0, 3],
-    [1, 3],
+  expect(rois[0].relativePoints).toStrictEqual([
+    { column: 0, row: 0 },
+    { column: 1, row: 0 },
+    { column: 0, row: 1 },
+    { column: 1, row: 1 },
+    { column: 0, row: 2 },
+    { column: 1, row: 2 },
+    { column: 0, row: 3 },
+    { column: 1, row: 3 },
   ]);
 });
-
-test('points 2nd test', () => {
+test('points 2nt test for absolute coordinates', () => {
   const mask = testUtils.createMask([
-    [0, 0, 1, 0],
     [0, 1, 1, 0],
-    [1, 1, 1, 1],
-    [0, 0, 1, 0],
+    [0, 1, 1, 0],
+    [0, 1, 1, 0],
+    [0, 1, 1, 0],
   ]);
   const roiMapManager = fromMask(mask);
   const rois = roiMapManager.getRois();
+  expect(rois[0].absolutePoints).toStrictEqual([
+    { column: 1, row: 0 },
+    { column: 2, row: 0 },
+    { column: 1, row: 1 },
+    { column: 2, row: 1 },
+    { column: 1, row: 2 },
+    { column: 2, row: 2 },
+    { column: 1, row: 3 },
+    { column: 2, row: 3 },
+  ]);
+});
 
-  expect(rois[0].points).toStrictEqual([
-    [2, 0],
-    [1, 1],
-    [2, 1],
-    [0, 2],
-    [1, 2],
-    [2, 2],
-    [3, 2],
-    [2, 3],
+test('points 3rd test for relative coordinates', () => {
+  const mask = testUtils.createMask([
+    [0, 0, 0, 1, 1, 1],
+    [0, 1, 0, 1, 0, 1],
+    [0, 1, 0, 1, 0, 1],
+    [1, 1, 0, 1, 1, 1],
+    [0, 0, 0, 0, 0, 0],
+    [0, 0, 0, 0, 0, 0],
+  ]);
+  const roiMapManager = fromMask(mask);
+  const rois = roiMapManager.getRois();
+  expect(rois[1].relativePoints).toStrictEqual([
+    { column: 0, row: 0 },
+    { column: 1, row: 0 },
+    { column: 2, row: 0 },
+    { column: 0, row: 1 },
+    { column: 2, row: 1 },
+    { column: 0, row: 2 },
+    { column: 2, row: 2 },
+    { column: 0, row: 3 },
+    { column: 1, row: 3 },
+    { column: 2, row: 3 },
+  ]);
+});
+
+test('points 4th test for absolute coordinates', () => {
+  const mask = testUtils.createMask([
+    [0, 0, 0, 1, 1, 1],
+    [0, 1, 0, 1, 0, 1],
+    [0, 1, 0, 1, 0, 1],
+    [1, 1, 0, 1, 1, 1],
+    [0, 0, 0, 0, 0, 0],
+    [0, 0, 0, 0, 0, 0],
+  ]);
+  const roiMapManager = fromMask(mask);
+  const rois = roiMapManager.getRois();
+  expect(rois[1].absolutePoints).toStrictEqual([
+    { column: 3, row: 0 },
+    { column: 4, row: 0 },
+    { column: 5, row: 0 },
+    { column: 3, row: 1 },
+    { column: 5, row: 1 },
+    { column: 3, row: 2 },
+    { column: 5, row: 2 },
+    { column: 3, row: 3 },
+    { column: 4, row: 3 },
+    { column: 5, row: 3 },
   ]);
 });

src/roi/properties/getEllipse.ts

@@ -1,12 +1,12 @@
 import { EigenvalueDecomposition } from 'ml-matrix';
 import { xVariance, xyCovariance } from 'ml-spectra-processing';
 
+import { Point } from '../../geometry';
 import { getAngle } from '../../maskAnalysis/utils/getAngle';
 import { toDegrees } from '../../utils/geometry/angles';
 import { assert } from '../../utils/validators/assert';
 import { Roi } from '../Roi';
 import { Ellipse } from '../roi.types';
-
 /**
  * Calculates ellipse on around ROI.
  * @param roi - Region of interest.
@@ -16,8 +16,12 @@ export function getEllipse(roi: Roi): Ellipse {
   const xCenter = roi.centroid.column;
   const yCenter = roi.centroid.row;
 
-  const xCentered = roi.points.map((point: number[]) => point[0] - xCenter);
-  const yCentered = roi.points.map((point: number[]) => point[1] - yCenter);
+  const xCentered = roi.relativePoints.map(
+    (point: Point) => point.column - xCenter,
+  );
+  const yCentered = roi.relativePoints.map(
+    (point: Point) => point.row - yCenter,
+  );
 
   const centeredXVariance = xVariance(xCentered, { unbiased: false });
   const centeredYVariance = xVariance(yCentered, { unbiased: false });