Fix principal curve (#70)

Author: ishii-norimi

js/view/principal_curve.js

@@ -20,7 +20,6 @@ var dispPC = function (elm, platform) {
 }
 
 export default function (platform) {
-	platform.setting.ml.draft = true
 	platform.setting.ml.usage = 'Click and add data point. Next, click "Fit" button.'
 	dispPC(platform.setting.ml.configElement, platform)
 }

lib/model/principal_curve.js

@@ -4,8 +4,6 @@ import SmoothingSpline from './spline.js'
 
 /**
  * Principal curves
- *
- * @deprecated Does not work properly
  */
 export default class PrincipalCurve {
 	// https://omedstu.jimdofree.com/2019/09/29/principal-curve-%E5%85%A5%E9%96%80/
@@ -39,10 +37,13 @@ export default class PrincipalCurve {
 		const ln = 1000
 
 		for (let i = 0; i < 1; i++) {
+			const uniql = l.copy()
+			const lidx = uniql.unique()
+			const xidx = x.row(lidx)
 			const f = []
 			for (let k = 0; k < m; k++) {
-				const spl = new SmoothingSpline(0)
-				spl.fit(l.value, x.col(k).value)
+				const spl = new SmoothingSpline(0.1)
+				spl.fit(uniql.value, xidx.col(k).value)
 				f.push(spl)
 			}
 

lib/util/matrix.js

@@ -864,6 +864,69 @@ export default class Matrix {
 		return idx
 	}
 
+	/**
+	 * Make it unique in the specified axis.
+	 *
+	 * @param {number} [axis=0]
+	 * @param {number} [tol=0]
+	 * @returns {number[]}
+	 */
+	unique(axis = 0, tol = 0) {
+		const idx = []
+		if (axis === 0) {
+			let r = 0
+			for (let i = 0; i < this.rows; i++) {
+				let same_k = -1
+				for (let k = 0; k < i; k++) {
+					let issame = true
+					for (let j = 0; issame && j < this.cols; j++) {
+						if (Math.abs(this._value[i * this.cols + j] - this._value[k * this.cols + j]) > tol) {
+							issame = false
+						}
+					}
+					if (issame) {
+						same_k = k
+						break
+					}
+				}
+				if (same_k < 0) {
+					for (let j = 0; j < this.cols; j++) {
+						this._value[r * this.cols + j] = this._value[i * this.cols + j]
+					}
+					idx.push(i)
+					r++
+				}
+			}
+			this._size[0] = r
+			this._value.length = this.length
+		} else if (axis === 1) {
+			for (let j = 0; j < this.cols; j++) {
+				let hasSame = false
+				for (let k = 0; !hasSame && k < idx.length; k++) {
+					hasSame = true
+					for (let i = 0; hasSame && i < this.rows; i++) {
+						if (Math.abs(this._value[i * this.cols + j] - this._value[i * this.cols + idx[k]]) > tol) {
+							hasSame = false
+						}
+					}
+				}
+				if (!hasSame) {
+					idx.push(j)
+				}
+			}
+			for (let i = 0, p = 0; i < this.rows; i++) {
+				for (let j = 0; j < idx.length; j++, p++) {
+					this._value[p] = this._value[i * this.cols + idx[j]]
+				}
+			}
+			this._size[1] = idx.length
+			this._value.length = this.length
+		} else {
+			throw new MatrixException('Invalid axis.')
+		}
+		return idx
+	}
+
 	/**
 	 * Returns resized matrix.
 	 *

tests/lib/model/principal_curve.test.js

@@ -0,0 +1,16 @@
+import Matrix from '../../../lib/util/matrix.js'
+import PrincipalCurve from '../../../lib/model/principal_curve.js'
+
+import { coRankingMatrix } from '../../../lib/evaluate/dimensionality_reduction.js'
+
+test('dimensionality reduction', () => {
+	const x = Matrix.randn(50, 5, 0, 0.2).concat(Matrix.randn(50, 5, 5, 0.2)).toArray()
+	const model = new PrincipalCurve()
+
+	for (let i = 0; i < 10; i++) {
+		model.fit(x)
+	}
+	const y = model.predict()
+	const q = coRankingMatrix(x, y, 30, 20)
+	expect(q).toBeGreaterThan(0.9)
+})

tests/lib/util/matrix.test.js

@@ -1296,6 +1296,81 @@ describe('Matrix', () => {
 		})
 	})
 
+	describe('unique', () => {
+		test('axis 0', () => {
+			const org = Matrix.randn(10, 5)
+			org.set(1, 0, org.row(3))
+			const mat = org.copy()
+
+			const idx = mat.unique(0)
+			expect(mat.sizes).toEqual([9, 5])
+			expect(idx).toEqual([0, 1, 2, 4, 5, 6, 7, 8, 9])
+			for (let i = 0; i < mat.rows; i++) {
+				for (let j = 0; j < mat.cols; j++) {
+					expect(mat.at(i, j)).toBe(org.at(idx[i], j))
+				}
+			}
+		})
+
+		test('axis 0 tol', () => {
+			const org = Matrix.randn(10, 5)
+			org.set(
+				1,
+				0,
+				org.row(3).copyMap(v => v + (Math.random() * 2 - 1) * 1.0e-4)
+			)
+			const mat = org.copy()
+
+			const idx = mat.unique(0, 1.0e-4)
+			expect(mat.sizes).toEqual([9, 5])
+			expect(idx).toEqual([0, 1, 2, 4, 5, 6, 7, 8, 9])
+			for (let i = 0; i < mat.rows; i++) {
+				for (let j = 0; j < mat.cols; j++) {
+					expect(mat.at(i, j)).toBeCloseTo(org.at(idx[i], j))
+				}
+			}
+		})
+
+		test('axis 1', () => {
+			const org = Matrix.randn(5, 10)
+			org.set(0, 1, org.col(3))
+			const mat = org.copy()
+
+			const idx = mat.unique(1)
+			expect(mat.sizes).toEqual([5, 9])
+			expect(idx).toEqual([0, 1, 2, 4, 5, 6, 7, 8, 9])
+			for (let i = 0; i < mat.rows; i++) {
+				for (let j = 0; j < mat.cols; j++) {
+					expect(mat.at(i, j)).toBe(org.at(i, idx[j]))
+				}
+			}
+		})
+
+		test('axis 1 tol', () => {
+			const org = Matrix.randn(5, 10)
+			org.set(
+				0,
+				1,
+				org.col(3).copyMap(v => v + (Math.random() * 2 - 1) * 1.0e-4)
+			)
+			const mat = org.copy()
+
+			const idx = mat.unique(1, 1.0e-4)
+			expect(mat.sizes).toEqual([5, 9])
+			expect(idx).toEqual([0, 1, 2, 4, 5, 6, 7, 8, 9])
+			for (let i = 0; i < mat.rows; i++) {
+				for (let j = 0; j < mat.cols; j++) {
+					expect(mat.at(i, j)).toBeCloseTo(org.at(i, idx[j]))
+				}
+			}
+		})
+
+		test('fail invalid axis', () => {
+			const mat = Matrix.randn(5, 10)
+			expect(() => mat.unique(2)).toThrowError('Invalid axis.')
+		})
+	})
+
 	describe('resize', () => {
 		test.each([
 			[5, 6],