feat: RoiMap could too easily contain over 2^15 rois (#388)

In order to solve this issue we are using Int32Array instead of Int16Array typed array

Author: lpatiny

src/roi/RoiMapManager.ts

@@ -23,7 +23,7 @@ export interface RoiMap {
    * Data of the ROIs. Each ROI is associated with a negative or a positive value,
    * depending if it derives from a zone made of zeros or ones in the original mask.
    */
-  data: Int16Array;
+  data: Int32Array;
   /**
    * Number of distinct positive values in the ROI map.
    *

src/roi/__tests__/Roi.test.ts

@@ -24,6 +24,6 @@ test('getMap', () => {
   // @ts-expect-error the map property is private
   const result = rois[0].map.data;
 
-  const expected = new Int16Array([-1, 1, -3, 1, 1, 1, -2, -2, -2]);
+  const expected = new Int32Array([-1, 1, -3, 1, 1, 1, -2, -2, -2]);
   expect(result).toStrictEqual(expected);
 });

src/roi/__tests__/waterShed.test.ts

@@ -1,5 +1,5 @@
 import { computeThreshold } from '../..';
-import { createGreyImage, getInt16Array } from '../../../test/testUtils';
+import { createGreyImage, getInt32Array } from '../../../test/testUtils';
 import { waterShed } from '../waterShed';
 
 describe('Test WaterShed Roi generation', () => {
@@ -12,7 +12,7 @@ describe('Test WaterShed Roi generation', () => {
       [3, 3, 3, 3, 3],
     ]);
     const roiMapManager = waterShed(image, {});
-    const resultArray = testUtils.getInt16Array(`
+    const resultArray = testUtils.getInt32Array(`
       -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1,
@@ -47,7 +47,7 @@ describe('Test WaterShed Roi generation', () => {
 
     const roiMapManager = waterShed(image, { threshold: 2 / 255 });
 
-    const resultArray = getInt16Array(`
+    const resultArray = getInt32Array(`
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0,-2,-2,-2, 0, 0, 0, 0, 0,
       0, 0,-2,-2,-2,-2, 0, 0, 0, 0,
@@ -86,7 +86,7 @@ describe('Test WaterShed Roi generation', () => {
     const roiMapManager = waterShed(invertedImage, {
       threshold: 253 / image.maxValue,
     });
-    const resultArray = getInt16Array(`
+    const resultArray = getInt32Array(`
       0, 0, 0, 0, 0,
       0,-1,-1,-1, 0, 
       0,-1,-1,-1, 0, 
@@ -127,7 +127,7 @@ describe('Test WaterShed Roi generation', () => {
     const roiMapManager = waterShed(image, {
       threshold: threshold / image.maxValue,
     });
-    const resultArray = getInt16Array(`
+    const resultArray = getInt32Array(`
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0,-2,-2,-2, 0, 0, 0, 0, 0, 
       0, 0,-2,-2,-2,-2, 0, 0, 0, 0,
@@ -167,7 +167,7 @@ describe('Test WaterShed Roi generation', () => {
 
     const mask = image.threshold({ algorithm: 'otsu' });
     const roiMapManager = waterShed(image, { mask });
-    const resultArray = getInt16Array(`
+    const resultArray = getInt32Array(`
       -2, -2, -2, -2, -2, -2, -2, -2, -2, -1,
       -2, -2, -2, -2, -2, -2, -2,  0, -1, -1,
       -2, -2, -2, -2, -2, -2, -2, -2, -1, -1, 

src/roi/fromMask.ts

@@ -30,7 +30,7 @@ export function fromMask(
   const maxNegativeId = -maxRoiId;
 
   // based on a binary image we will create plenty of small images
-  const data = new Int16Array(mask.size); // maxValue: maxPositiveId, minValue: maxNegativeId
+  const data = new Int32Array(mask.size); // maxValue: maxPositiveId, minValue: maxNegativeId
 
   // split will always return an array of images
   let positiveId = 0;

src/roi/waterShed.ts

@@ -81,7 +81,7 @@ export function waterShed(
 
   const maskExpectedValue = 0;
 
-  const data = new Int16Array(currentImage.size);
+  const data = new Int32Array(currentImage.size);
   const width = currentImage.width;
   const height = currentImage.height;
   const toProcess = new PriorityQueue({

test/testUtils.ts

@@ -9,10 +9,6 @@ import { TestImagePath } from './TestImagePath';
 import { createImageFromData, CreateImageOptions } from './createImageFromData';
 import { createMask } from './createMask';
 
-
-
-
-
 /**
  * Return the path to a given image.
  * @param name - Test image name.
@@ -142,6 +138,20 @@ export function getInt16Array(string: string) {
       .map(Number),
   );
 }
+
+/**
+ * Creates an Int32Array from string
+ * @param string - represents Int32Array data
+ * @returns Int32Array
+ */
+export function getInt32Array(string: string) {
+  return new Int32Array(
+    string
+      .split(/[\n\r ,]+/)
+      .filter(Boolean)
+      .map(Number),
+  );
+}
 declare global {
   // eslint-disable-next-line no-var
   var testUtils: {
@@ -157,8 +167,8 @@ declare global {
     makeTmpDir: typeof makeTmpDir;
     cleanTmpDir: typeof cleanTmpDir;
     getInt16Array: typeof getInt16Array;
+    getInt32Array: typeof getInt32Array;
   };
 }
 
-export {createMask} from './createMask';
-
+export { createMask } from './createMask';