@datagrok/eda 1.4.3 → 1.4.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (152) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/dist/_d4c0.js +279 -0
  3. package/dist/_d4c0.js.map +1 -0
  4. package/dist/node_modules_datagrok-libraries_math_src_dbscan_wasm_clustering-worker_js.js +279 -0
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  6. package/dist/node_modules_datagrok-libraries_ml_src_MCL_mcl-sparse-matrix-mult-worker_js.js +59 -0
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  18. package/dist/src_workers_softmax-worker_ts.js +154 -0
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  24. package/dist/vendors-node_modules_datagrok-libraries_math_src_dbscan_wasm_dbscan_js.js +1253 -0
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  48. package/dist/wasm_EDAForWebWorker_js-wasm_callWasmForWebWorker_js.js +779 -0
  49. package/dist/wasm_EDAForWebWorker_js-wasm_callWasmForWebWorker_js.js.map +1 -0
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  52. package/dist/wasm_workers_fitLinearRegressionParamsWithDataNormalizingWorker_js.js +267 -0
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  70. package/dist/wasm_workers_trainAndAnalyzeLSSVMWorker_js.js +267 -0
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  74. package/dist/wasm_workers_xgboostWorker_js.js +279 -0
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  76. package/package.json +5 -4
  77. package/src/package-api.ts +259 -0
  78. package/src/package.g.ts +522 -0
  79. package/src/package.ts +907 -678
  80. package/test-console-output-1.log +78 -93
  81. package/test-record-1.mp4 +0 -0
  82. package/tsconfig.json +2 -2
  83. package/webpack.config.js +5 -0
  84. package/dist/111.js +0 -2
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  129. package/dist/738.js.LICENSE.txt +0 -51
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package/dist/vendors-node_modules_umap-js_dist_index_js.js.map ADDED
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(function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });\n}) : (function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n o[k2] = m[k];\n}));\nvar __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? 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i < nSamples; i++) {\n var rejectSample = true;\n var j = 0;\n while (rejectSample) {\n j = utils.tauRandInt(poolSize, random);\n var broken = false;\n for (var k = 0; k < i; k++) {\n if (j === result[k]) {\n broken = true;\n break;\n }\n }\n if (!broken)\n rejectSample = false;\n }\n result[i] = j;\n }\n return result;\n}\nexports.rejectionSample = rejectionSample;\nfunction heapPush(heap, row, weight, index, flag) {\n row = Math.floor(row);\n var indices = heap[0][row];\n var weights = heap[1][row];\n var isNew = heap[2][row];\n if (weight >= weights[0]) {\n return 0;\n }\n for (var i = 0; i < indices.length; i++) {\n if (index === indices[i]) {\n return 0;\n }\n }\n return uncheckedHeapPush(heap, row, weight, index, flag);\n}\nexports.heapPush = heapPush;\nfunction uncheckedHeapPush(heap, row, weight, index, flag) {\n var indices = heap[0][row];\n var weights = heap[1][row];\n var isNew = heap[2][row];\n if (weight >= weights[0]) {\n return 0;\n }\n weights[0] = weight;\n indices[0] = index;\n isNew[0] = flag;\n var i = 0;\n var iSwap = 0;\n while (true) {\n var ic1 = 2 * i + 1;\n var ic2 = ic1 + 1;\n var heapShape2 = heap[0][0].length;\n if (ic1 >= heapShape2) {\n break;\n }\n else if (ic2 >= heapShape2) {\n if (weights[ic1] > weight) {\n iSwap = ic1;\n }\n else {\n break;\n }\n }\n else if (weights[ic1] >= weights[ic2]) {\n if (weight < weights[ic1]) {\n iSwap = ic1;\n }\n else {\n break;\n }\n }\n else {\n if (weight < weights[ic2]) {\n iSwap = ic2;\n }\n else {\n break;\n }\n }\n weights[i] = weights[iSwap];\n indices[i] = indices[iSwap];\n isNew[i] = isNew[iSwap];\n i = iSwap;\n }\n weights[i] = weight;\n indices[i] = index;\n isNew[i] = flag;\n return 1;\n}\nexports.uncheckedHeapPush = uncheckedHeapPush;\nfunction buildCandidates(currentGraph, nVertices, nNeighbors, maxCandidates, random) {\n var candidateNeighbors = makeHeap(nVertices, maxCandidates);\n for (var i = 0; i < nVertices; i++) {\n for (var j = 0; j < nNeighbors; j++) {\n if (currentGraph[0][i][j] < 0) {\n continue;\n }\n var idx = currentGraph[0][i][j];\n var isn = currentGraph[2][i][j];\n var d = utils.tauRand(random);\n heapPush(candidateNeighbors, i, d, idx, isn);\n heapPush(candidateNeighbors, idx, d, i, isn);\n currentGraph[2][i][j] = 0;\n }\n }\n return candidateNeighbors;\n}\nexports.buildCandidates = buildCandidates;\nfunction deheapSort(heap) {\n var indices = heap[0];\n var weights = heap[1];\n for (var i = 0; i < indices.length; i++) {\n var indHeap = indices[i];\n var distHeap = weights[i];\n for (var j = 0; j < indHeap.length - 1; j++) {\n var indHeapIndex = indHeap.length - j - 1;\n var distHeapIndex = distHeap.length - j - 1;\n var temp1 = indHeap[0];\n indHeap[0] = indHeap[indHeapIndex];\n indHeap[indHeapIndex] = temp1;\n var temp2 = distHeap[0];\n distHeap[0] = distHeap[distHeapIndex];\n distHeap[distHeapIndex] = temp2;\n siftDown(distHeap, indHeap, distHeapIndex, 0);\n }\n }\n return { indices: indices, weights: weights };\n}\nexports.deheapSort = deheapSort;\nfunction siftDown(heap1, heap2, ceiling, elt) {\n while (elt * 2 + 1 < ceiling) {\n var leftChild = elt * 2 + 1;\n var rightChild = leftChild + 1;\n var swap = elt;\n if (heap1[swap] < heap1[leftChild]) {\n swap = leftChild;\n }\n if (rightChild < ceiling && heap1[swap] < heap1[rightChild]) {\n swap = rightChild;\n }\n if (swap === elt) {\n break;\n }\n else {\n var temp1 = heap1[elt];\n heap1[elt] = heap1[swap];\n heap1[swap] = temp1;\n var temp2 = heap2[elt];\n heap2[elt] = heap2[swap];\n heap2[swap] = temp2;\n elt = swap;\n }\n }\n}\nfunction smallestFlagged(heap, row) {\n var ind = heap[0][row];\n var dist = heap[1][row];\n var flag = heap[2][row];\n var minDist = Infinity;\n var resultIndex = -1;\n for (var i = 0; i > ind.length; i++) {\n if (flag[i] === 1 && dist[i] < minDist) {\n minDist = dist[i];\n resultIndex = i;\n }\n }\n if (resultIndex >= 0) {\n flag[resultIndex] = 0;\n return Math.floor(ind[resultIndex]);\n }\n else {\n return -1;\n }\n}\nexports.smallestFlagged = smallestFlagged;\n","\"use strict\";\nObject.defineProperty(exports, \"__esModule\", { value: true });\nvar umap_1 = require(\"./umap\");\nObject.defineProperty(exports, \"UMAP\", { enumerable: true, get: function () { return umap_1.UMAP; } });\n","\"use strict\";\nvar __createBinding = (this && this.__createBinding) || (Object.create ? 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\"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n};\nvar _a;\nObject.defineProperty(exports, \"__esModule\", { value: true });\nexports.getCSR = exports.normalize = exports.eliminateZeros = exports.multiplyScalar = exports.maximum = exports.subtract = exports.add = exports.pairwiseMultiply = exports.identity = exports.transpose = exports.SparseMatrix = void 0;\nvar utils = __importStar(require(\"./utils\"));\nvar SparseMatrix = (function () {\n function SparseMatrix(rows, cols, values, dims) {\n this.entries = new Map();\n this.nRows = 0;\n this.nCols = 0;\n if (rows.length !== cols.length || rows.length !== values.length) {\n throw new Error('rows, cols and values arrays must all have the same length');\n }\n this.nRows = dims[0];\n this.nCols = dims[1];\n for (var i = 0; i < values.length; i++) {\n var row = rows[i];\n var col = cols[i];\n this.checkDims(row, col);\n var key = this.makeKey(row, col);\n this.entries.set(key, { value: values[i], row: row, col: col });\n }\n }\n SparseMatrix.prototype.makeKey = function (row, col) {\n return row + \":\" + col;\n };\n SparseMatrix.prototype.checkDims = function (row, col) {\n var withinBounds = row < this.nRows && col < this.nCols;\n if (!withinBounds) {\n throw new Error('row and/or col specified outside of matrix dimensions');\n }\n };\n SparseMatrix.prototype.set = function (row, col, value) {\n this.checkDims(row, col);\n var key = this.makeKey(row, col);\n if (!this.entries.has(key)) {\n this.entries.set(key, { value: value, row: row, col: col });\n }\n else {\n this.entries.get(key).value = value;\n }\n };\n SparseMatrix.prototype.get = function (row, col, defaultValue) {\n if (defaultValue === void 0) { defaultValue = 0; }\n this.checkDims(row, col);\n var key = this.makeKey(row, col);\n if (this.entries.has(key)) {\n return this.entries.get(key).value;\n }\n else {\n return defaultValue;\n }\n };\n SparseMatrix.prototype.getAll = function (ordered) {\n if (ordered === void 0) { ordered = true; }\n var rowColValues = [];\n this.entries.forEach(function (value) {\n rowColValues.push(value);\n });\n if (ordered) {\n rowColValues.sort(function (a, b) {\n if (a.row === b.row) {\n return a.col - b.col;\n }\n else {\n return a.row - b.row;\n }\n });\n }\n return rowColValues;\n };\n SparseMatrix.prototype.getDims = function () {\n return [this.nRows, this.nCols];\n };\n SparseMatrix.prototype.getRows = function () {\n return Array.from(this.entries, function (_a) {\n var _b = __read(_a, 2), key = _b[0], value = _b[1];\n return value.row;\n });\n };\n SparseMatrix.prototype.getCols = function () {\n return Array.from(this.entries, function (_a) {\n var _b = __read(_a, 2), key = _b[0], value = _b[1];\n return value.col;\n });\n };\n SparseMatrix.prototype.getValues = function () {\n return Array.from(this.entries, function (_a) {\n var _b = __read(_a, 2), key = _b[0], value = _b[1];\n return value.value;\n });\n };\n SparseMatrix.prototype.forEach = function (fn) {\n this.entries.forEach(function (value) { return fn(value.value, value.row, value.col); });\n };\n SparseMatrix.prototype.map = function (fn) {\n var vals = [];\n this.entries.forEach(function (value) {\n vals.push(fn(value.value, value.row, value.col));\n });\n var dims = [this.nRows, this.nCols];\n return new SparseMatrix(this.getRows(), this.getCols(), vals, dims);\n };\n SparseMatrix.prototype.toArray = function () {\n var _this = this;\n var rows = utils.empty(this.nRows);\n var output = rows.map(function () {\n return utils.zeros(_this.nCols);\n });\n this.entries.forEach(function (value) {\n output[value.row][value.col] = value.value;\n });\n return output;\n };\n return SparseMatrix;\n}());\nexports.SparseMatrix = SparseMatrix;\nfunction transpose(matrix) {\n var cols = [];\n var rows = [];\n var vals = [];\n matrix.forEach(function (value, row, col) {\n cols.push(row);\n rows.push(col);\n vals.push(value);\n });\n var dims = [matrix.nCols, matrix.nRows];\n return new SparseMatrix(rows, cols, vals, dims);\n}\nexports.transpose = transpose;\nfunction identity(size) {\n var _a = __read(size, 1), rows = _a[0];\n var matrix = new SparseMatrix([], [], [], size);\n for (var i = 0; i < rows; i++) {\n matrix.set(i, i, 1);\n }\n return matrix;\n}\nexports.identity = identity;\nfunction pairwiseMultiply(a, b) {\n return elementWise(a, b, function (x, y) { return x * y; });\n}\nexports.pairwiseMultiply = pairwiseMultiply;\nfunction add(a, b) {\n return elementWise(a, b, function (x, y) { return x + y; });\n}\nexports.add = add;\nfunction subtract(a, b) {\n return elementWise(a, b, function (x, y) { return x - y; });\n}\nexports.subtract = subtract;\nfunction maximum(a, b) {\n return elementWise(a, b, function (x, y) { return (x > y ? x : y); });\n}\nexports.maximum = maximum;\nfunction multiplyScalar(a, scalar) {\n return a.map(function (value) {\n return value * scalar;\n });\n}\nexports.multiplyScalar = multiplyScalar;\nfunction eliminateZeros(m) {\n var zeroIndices = new Set();\n var values = m.getValues();\n var rows = m.getRows();\n var cols = m.getCols();\n for (var i = 0; i < values.length; i++) {\n if (values[i] === 0) {\n zeroIndices.add(i);\n }\n }\n var removeByZeroIndex = function (_, index) { return !zeroIndices.has(index); };\n var nextValues = values.filter(removeByZeroIndex);\n var nextRows = rows.filter(removeByZeroIndex);\n var nextCols = cols.filter(removeByZeroIndex);\n return new SparseMatrix(nextRows, nextCols, nextValues, m.getDims());\n}\nexports.eliminateZeros = eliminateZeros;\nfunction normalize(m, normType) {\n var e_1, _a;\n if (normType === void 0) { normType = \"l2\"; }\n var normFn = normFns[normType];\n var colsByRow = new Map();\n m.forEach(function (_, row, col) {\n var cols = colsByRow.get(row) || [];\n cols.push(col);\n colsByRow.set(row, cols);\n });\n var nextMatrix = new SparseMatrix([], [], [], m.getDims());\n var _loop_1 = function (row) {\n var cols = colsByRow.get(row).sort();\n var vals = cols.map(function (col) { return m.get(row, col); });\n var norm = normFn(vals);\n for (var i = 0; i < norm.length; i++) {\n nextMatrix.set(row, cols[i], norm[i]);\n }\n };\n try {\n for (var _b = __values(colsByRow.keys()), _c = _b.next(); !_c.done; _c = _b.next()) {\n var row = _c.value;\n _loop_1(row);\n }\n }\n catch (e_1_1) { e_1 = { error: e_1_1 }; }\n finally {\n try {\n if (_c && !_c.done && (_a = _b.return)) _a.call(_b);\n }\n finally { if (e_1) throw e_1.error; }\n }\n return nextMatrix;\n}\nexports.normalize = normalize;\nvar normFns = (_a = {},\n _a[\"max\"] = function (xs) {\n var max = -Infinity;\n for (var i = 0; i < xs.length; i++) {\n max = xs[i] > max ? xs[i] : max;\n }\n return xs.map(function (x) { return x / max; });\n },\n _a[\"l1\"] = function (xs) {\n var sum = 0;\n for (var i = 0; i < xs.length; i++) {\n sum += xs[i];\n }\n return xs.map(function (x) { return x / sum; });\n },\n _a[\"l2\"] = function (xs) {\n var sum = 0;\n for (var i = 0; i < xs.length; i++) {\n sum += Math.pow(xs[i], 2);\n }\n return xs.map(function (x) { return Math.sqrt(Math.pow(x, 2) / sum); });\n },\n _a);\nfunction elementWise(a, b, op) {\n var visited = new Set();\n var rows = [];\n var cols = [];\n var vals = [];\n var operate = function (row, col) {\n rows.push(row);\n cols.push(col);\n var nextValue = op(a.get(row, col), b.get(row, col));\n vals.push(nextValue);\n };\n var valuesA = a.getValues();\n var rowsA = a.getRows();\n var colsA = a.getCols();\n for (var i = 0; i < valuesA.length; i++) {\n var row = rowsA[i];\n var col = colsA[i];\n var key = row + \":\" + col;\n visited.add(key);\n operate(row, col);\n }\n var valuesB = b.getValues();\n var rowsB = b.getRows();\n var colsB = b.getCols();\n for (var i = 0; i < valuesB.length; i++) {\n var row = rowsB[i];\n var col = colsB[i];\n var key = row + \":\" + col;\n if (visited.has(key))\n continue;\n operate(row, col);\n }\n var dims = [a.nRows, a.nCols];\n return new SparseMatrix(rows, cols, vals, dims);\n}\nfunction getCSR(x) {\n var entries = [];\n x.forEach(function (value, row, col) {\n entries.push({ value: value, row: row, col: col });\n });\n entries.sort(function (a, b) {\n if (a.row === b.row) {\n return a.col - b.col;\n }\n else {\n return a.row - b.row;\n }\n });\n var indices = [];\n var values = [];\n var indptr = [];\n var currentRow = -1;\n for (var i = 0; i < entries.length; i++) {\n var _a = entries[i], row = _a.row, col = _a.col, value = _a.value;\n if (row !== currentRow) {\n currentRow = row;\n indptr.push(i);\n }\n indices.push(col);\n values.push(value);\n }\n return { indices: indices, values: values, indptr: indptr };\n}\nexports.getCSR = getCSR;\n","\"use strict\";\nvar __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });\n}) : (function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n o[k2] = m[k];\n}));\nvar __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {\n Object.defineProperty(o, \"default\", { enumerable: true, value: v });\n}) : function(o, v) {\n o[\"default\"] = v;\n});\nvar __importStar = (this && this.__importStar) || function (mod) {\n if (mod && mod.__esModule) return mod;\n var result = {};\n if (mod != null) for (var k in mod) if (k !== \"default\" && Object.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);\n __setModuleDefault(result, mod);\n return result;\n};\nvar __values = (this && this.__values) || function(o) {\n var s = typeof Symbol === \"function\" && Symbol.iterator, m = s && o[s], i = 0;\n if (m) return m.call(o);\n if (o && typeof o.length === \"number\") return {\n next: function () {\n if (o && i >= o.length) o = void 0;\n return { value: o && o[i++], done: !o };\n }\n };\n throw new TypeError(s ? \"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n};\nObject.defineProperty(exports, \"__esModule\", { value: true });\nexports.initializeSearch = exports.makeInitializedNNSearch = exports.makeInitializations = exports.makeNNDescent = void 0;\nvar heap = __importStar(require(\"./heap\"));\nvar matrix = __importStar(require(\"./matrix\"));\nvar tree = __importStar(require(\"./tree\"));\nvar utils = __importStar(require(\"./utils\"));\nfunction makeNNDescent(distanceFn, random) {\n return function nNDescent(data, leafArray, nNeighbors, nIters, maxCandidates, delta, rho, rpTreeInit) {\n if (nIters === void 0) { nIters = 10; }\n if (maxCandidates === void 0) { maxCandidates = 50; }\n if (delta === void 0) { delta = 0.001; }\n if (rho === void 0) { rho = 0.5; }\n if (rpTreeInit === void 0) { rpTreeInit = true; }\n var nVertices = data.length;\n var currentGraph = heap.makeHeap(data.length, nNeighbors);\n for (var i = 0; i < data.length; i++) {\n var indices = heap.rejectionSample(nNeighbors, data.length, random);\n for (var j = 0; j < indices.length; j++) {\n var d = distanceFn(data[i], data[indices[j]]);\n heap.heapPush(currentGraph, i, d, indices[j], 1);\n heap.heapPush(currentGraph, indices[j], d, i, 1);\n }\n }\n if (rpTreeInit) {\n for (var n = 0; n < leafArray.length; n++) {\n for (var i = 0; i < leafArray[n].length; i++) {\n if (leafArray[n][i] < 0) {\n break;\n }\n for (var j = i + 1; j < leafArray[n].length; j++) {\n if (leafArray[n][j] < 0) {\n break;\n }\n var d = distanceFn(data[leafArray[n][i]], data[leafArray[n][j]]);\n heap.heapPush(currentGraph, leafArray[n][i], d, leafArray[n][j], 1);\n heap.heapPush(currentGraph, leafArray[n][j], d, leafArray[n][i], 1);\n }\n }\n }\n }\n for (var n = 0; n < nIters; n++) {\n var candidateNeighbors = heap.buildCandidates(currentGraph, nVertices, nNeighbors, maxCandidates, random);\n var c = 0;\n for (var i = 0; i < nVertices; i++) {\n for (var j = 0; j < maxCandidates; j++) {\n var p = Math.floor(candidateNeighbors[0][i][j]);\n if (p < 0 || utils.tauRand(random) < rho) {\n continue;\n }\n for (var k = 0; k < maxCandidates; k++) {\n var q = Math.floor(candidateNeighbors[0][i][k]);\n var cj = candidateNeighbors[2][i][j];\n var ck = candidateNeighbors[2][i][k];\n if (q < 0 || (!cj && !ck)) {\n continue;\n }\n var d = distanceFn(data[p], data[q]);\n c += heap.heapPush(currentGraph, p, d, q, 1);\n c += heap.heapPush(currentGraph, q, d, p, 1);\n }\n }\n }\n if (c <= delta * nNeighbors * data.length) {\n break;\n }\n }\n var sorted = heap.deheapSort(currentGraph);\n return sorted;\n };\n}\nexports.makeNNDescent = makeNNDescent;\nfunction makeInitializations(distanceFn) {\n function initFromRandom(nNeighbors, data, queryPoints, _heap, random) {\n for (var i = 0; i < queryPoints.length; i++) {\n var indices = utils.rejectionSample(nNeighbors, data.length, random);\n for (var j = 0; j < indices.length; j++) {\n if (indices[j] < 0) {\n continue;\n }\n var d = distanceFn(data[indices[j]], queryPoints[i]);\n heap.heapPush(_heap, i, d, indices[j], 1);\n }\n }\n }\n function initFromTree(_tree, data, queryPoints, _heap, random) {\n for (var i = 0; i < queryPoints.length; i++) {\n var indices = tree.searchFlatTree(queryPoints[i], _tree, random);\n for (var j = 0; j < indices.length; j++) {\n if (indices[j] < 0) {\n return;\n }\n var d = distanceFn(data[indices[j]], queryPoints[i]);\n heap.heapPush(_heap, i, d, indices[j], 1);\n }\n }\n return;\n }\n return { initFromRandom: initFromRandom, initFromTree: initFromTree };\n}\nexports.makeInitializations = makeInitializations;\nfunction makeInitializedNNSearch(distanceFn) {\n return function nnSearchFn(data, graph, initialization, queryPoints) {\n var e_1, _a;\n var _b = matrix.getCSR(graph), indices = _b.indices, indptr = _b.indptr;\n for (var i = 0; i < queryPoints.length; i++) {\n var tried = new Set(initialization[0][i]);\n while (true) {\n var vertex = heap.smallestFlagged(initialization, i);\n if (vertex === -1) {\n break;\n }\n var candidates = indices.slice(indptr[vertex], indptr[vertex + 1]);\n try {\n for (var candidates_1 = (e_1 = void 0, __values(candidates)), candidates_1_1 = candidates_1.next(); !candidates_1_1.done; candidates_1_1 = candidates_1.next()) {\n var candidate = candidates_1_1.value;\n if (candidate === vertex ||\n candidate === -1 ||\n tried.has(candidate)) {\n continue;\n }\n var d = distanceFn(data[candidate], queryPoints[i]);\n heap.uncheckedHeapPush(initialization, i, d, candidate, 1);\n tried.add(candidate);\n }\n }\n catch (e_1_1) { e_1 = { error: e_1_1 }; }\n finally {\n try {\n if (candidates_1_1 && !candidates_1_1.done && (_a = candidates_1.return)) _a.call(candidates_1);\n }\n finally { if (e_1) throw e_1.error; }\n }\n }\n }\n return initialization;\n };\n}\nexports.makeInitializedNNSearch = makeInitializedNNSearch;\nfunction initializeSearch(forest, data, queryPoints, nNeighbors, initFromRandom, initFromTree, random) {\n var e_2, _a;\n var results = heap.makeHeap(queryPoints.length, nNeighbors);\n initFromRandom(nNeighbors, data, queryPoints, results, random);\n if (forest) {\n try {\n for (var forest_1 = __values(forest), forest_1_1 = forest_1.next(); !forest_1_1.done; forest_1_1 = forest_1.next()) {\n var tree_1 = forest_1_1.value;\n initFromTree(tree_1, data, queryPoints, results, random);\n }\n }\n catch (e_2_1) { e_2 = { error: e_2_1 }; }\n finally {\n try {\n if (forest_1_1 && !forest_1_1.done && (_a = forest_1.return)) _a.call(forest_1);\n }\n finally { if (e_2) throw e_2.error; }\n }\n }\n return results;\n}\nexports.initializeSearch = initializeSearch;\n","\"use strict\";\nvar __createBinding = (this && this.__createBinding) || (Object.create ? 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\"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n};\nObject.defineProperty(exports, \"__esModule\", { value: true });\nexports.searchFlatTree = exports.makeLeafArray = exports.makeForest = exports.FlatTree = void 0;\nvar utils = __importStar(require(\"./utils\"));\nvar FlatTree = (function () {\n function FlatTree(hyperplanes, offsets, children, indices) {\n this.hyperplanes = hyperplanes;\n this.offsets = offsets;\n this.children = children;\n this.indices = indices;\n }\n return FlatTree;\n}());\nexports.FlatTree = FlatTree;\nfunction makeForest(data, nNeighbors, nTrees, random) {\n var leafSize = Math.max(10, nNeighbors);\n var trees = utils\n .range(nTrees)\n .map(function (_, i) { return makeTree(data, leafSize, i, random); });\n var forest = trees.map(function (tree) { return flattenTree(tree, leafSize); });\n return forest;\n}\nexports.makeForest = makeForest;\nfunction makeTree(data, leafSize, n, random) {\n if (leafSize === void 0) { leafSize = 30; }\n var indices = utils.range(data.length);\n var tree = makeEuclideanTree(data, indices, leafSize, n, random);\n return tree;\n}\nfunction makeEuclideanTree(data, indices, leafSize, q, random) {\n if (leafSize === void 0) { leafSize = 30; }\n if (indices.length > leafSize) {\n var splitResults = euclideanRandomProjectionSplit(data, indices, random);\n var indicesLeft = splitResults.indicesLeft, indicesRight = splitResults.indicesRight, hyperplane = splitResults.hyperplane, offset = splitResults.offset;\n var leftChild = makeEuclideanTree(data, indicesLeft, leafSize, q + 1, random);\n var rightChild = makeEuclideanTree(data, indicesRight, leafSize, q + 1, random);\n var node = { leftChild: leftChild, rightChild: rightChild, isLeaf: false, hyperplane: hyperplane, offset: offset };\n return node;\n }\n else {\n var node = { indices: indices, isLeaf: true };\n return node;\n }\n}\nfunction euclideanRandomProjectionSplit(data, indices, random) {\n var dim = data[0].length;\n var leftIndex = utils.tauRandInt(indices.length, random);\n var rightIndex = utils.tauRandInt(indices.length, random);\n rightIndex += leftIndex === rightIndex ? 1 : 0;\n rightIndex = rightIndex % indices.length;\n var left = indices[leftIndex];\n var right = indices[rightIndex];\n var hyperplaneOffset = 0;\n var hyperplaneVector = utils.zeros(dim);\n for (var i = 0; i < hyperplaneVector.length; i++) {\n hyperplaneVector[i] = data[left][i] - data[right][i];\n hyperplaneOffset -=\n (hyperplaneVector[i] * (data[left][i] + data[right][i])) / 2.0;\n }\n var nLeft = 0;\n var nRight = 0;\n var side = utils.zeros(indices.length);\n for (var i = 0; i < indices.length; i++) {\n var margin = hyperplaneOffset;\n for (var d = 0; d < dim; d++) {\n margin += hyperplaneVector[d] * data[indices[i]][d];\n }\n if (margin === 0) {\n side[i] = utils.tauRandInt(2, random);\n if (side[i] === 0) {\n nLeft += 1;\n }\n else {\n nRight += 1;\n }\n }\n else if (margin > 0) {\n side[i] = 0;\n nLeft += 1;\n }\n else {\n side[i] = 1;\n nRight += 1;\n }\n }\n var indicesLeft = utils.zeros(nLeft);\n var indicesRight = utils.zeros(nRight);\n nLeft = 0;\n nRight = 0;\n for (var i = 0; i < side.length; i++) {\n if (side[i] === 0) {\n indicesLeft[nLeft] = indices[i];\n nLeft += 1;\n }\n else {\n indicesRight[nRight] = indices[i];\n nRight += 1;\n }\n }\n return {\n indicesLeft: indicesLeft,\n indicesRight: indicesRight,\n hyperplane: hyperplaneVector,\n offset: hyperplaneOffset,\n };\n}\nfunction flattenTree(tree, leafSize) {\n var nNodes = numNodes(tree);\n var nLeaves = numLeaves(tree);\n var hyperplanes = utils\n .range(nNodes)\n .map(function () { return utils.zeros(tree.hyperplane ? tree.hyperplane.length : 0); });\n var offsets = utils.zeros(nNodes);\n var children = utils.range(nNodes).map(function () { return [-1, -1]; });\n var indices = utils\n .range(nLeaves)\n .map(function () { return utils.range(leafSize).map(function () { return -1; }); });\n recursiveFlatten(tree, hyperplanes, offsets, children, indices, 0, 0);\n return new FlatTree(hyperplanes, offsets, children, indices);\n}\nfunction recursiveFlatten(tree, hyperplanes, offsets, children, indices, nodeNum, leafNum) {\n var _a;\n if (tree.isLeaf) {\n children[nodeNum][0] = -leafNum;\n (_a = indices[leafNum]).splice.apply(_a, __spread([0, tree.indices.length], tree.indices));\n leafNum += 1;\n return { nodeNum: nodeNum, leafNum: leafNum };\n }\n else {\n hyperplanes[nodeNum] = tree.hyperplane;\n offsets[nodeNum] = tree.offset;\n children[nodeNum][0] = nodeNum + 1;\n var oldNodeNum = nodeNum;\n var res = recursiveFlatten(tree.leftChild, hyperplanes, offsets, children, indices, nodeNum + 1, leafNum);\n nodeNum = res.nodeNum;\n leafNum = res.leafNum;\n children[oldNodeNum][1] = nodeNum + 1;\n res = recursiveFlatten(tree.rightChild, hyperplanes, offsets, children, indices, nodeNum + 1, leafNum);\n return { nodeNum: res.nodeNum, leafNum: res.leafNum };\n }\n}\nfunction numNodes(tree) {\n if (tree.isLeaf) {\n return 1;\n }\n else {\n return 1 + numNodes(tree.leftChild) + numNodes(tree.rightChild);\n }\n}\nfunction numLeaves(tree) {\n if (tree.isLeaf) {\n return 1;\n }\n else {\n return numLeaves(tree.leftChild) + numLeaves(tree.rightChild);\n }\n}\nfunction makeLeafArray(rpForest) {\n var e_1, _a;\n if (rpForest.length > 0) {\n var output = [];\n try {\n for (var rpForest_1 = __values(rpForest), rpForest_1_1 = rpForest_1.next(); !rpForest_1_1.done; rpForest_1_1 = rpForest_1.next()) {\n var tree = rpForest_1_1.value;\n output.push.apply(output, __spread(tree.indices));\n }\n }\n catch (e_1_1) { e_1 = { error: e_1_1 }; }\n finally {\n try {\n if (rpForest_1_1 && !rpForest_1_1.done && (_a = rpForest_1.return)) _a.call(rpForest_1);\n }\n finally { if (e_1) throw e_1.error; }\n }\n return output;\n }\n else {\n return [[-1]];\n }\n}\nexports.makeLeafArray = makeLeafArray;\nfunction selectSide(hyperplane, offset, point, random) {\n var margin = offset;\n for (var d = 0; d < point.length; d++) {\n margin += hyperplane[d] * point[d];\n }\n if (margin === 0) {\n var side = utils.tauRandInt(2, random);\n return side;\n }\n else if (margin > 0) {\n return 0;\n }\n else {\n return 1;\n }\n}\nfunction searchFlatTree(point, tree, random) {\n var node = 0;\n while (tree.children[node][0] > 0) {\n var side = selectSide(tree.hyperplanes[node], tree.offsets[node], point, random);\n if (side === 0) {\n node = tree.children[node][0];\n }\n else {\n node = tree.children[node][1];\n }\n }\n var index = -1 * tree.children[node][0];\n return tree.indices[index];\n}\nexports.searchFlatTree = searchFlatTree;\n","\"use strict\";\nvar __createBinding = (this && this.__createBinding) || (Object.create ? 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mod : { \"default\": mod };\n};\nObject.defineProperty(exports, \"__esModule\", { value: true });\nexports.initTransform = exports.resetLocalConnectivity = exports.fastIntersection = exports.findABParams = exports.cosine = exports.euclidean = exports.UMAP = void 0;\nvar heap = __importStar(require(\"./heap\"));\nvar matrix = __importStar(require(\"./matrix\"));\nvar nnDescent = __importStar(require(\"./nn_descent\"));\nvar tree = __importStar(require(\"./tree\"));\nvar utils = __importStar(require(\"./utils\"));\nvar ml_levenberg_marquardt_1 = __importDefault(require(\"ml-levenberg-marquardt\"));\nvar SMOOTH_K_TOLERANCE = 1e-5;\nvar MIN_K_DIST_SCALE = 1e-3;\nvar UMAP = (function () {\n function UMAP(params) {\n var _this = this;\n if (params === void 0) { params = {}; }\n this.learningRate = 1.0;\n this.localConnectivity = 1.0;\n this.minDist = 0.1;\n this.nComponents = 2;\n this.nEpochs = 0;\n this.nNeighbors = 15;\n this.negativeSampleRate = 5;\n this.random = Math.random;\n this.repulsionStrength = 1.0;\n this.setOpMixRatio = 1.0;\n this.spread = 1.0;\n this.transformQueueSize = 4.0;\n this.targetMetric = \"categorical\";\n this.targetWeight = 0.5;\n this.targetNNeighbors = this.nNeighbors;\n this.distanceFn = euclidean;\n this.isInitialized = false;\n this.rpForest = [];\n this.embedding = [];\n this.optimizationState = new OptimizationState();\n var setParam = function (key) {\n if (params[key] !== undefined)\n _this[key] = params[key];\n };\n setParam('distanceFn');\n setParam('learningRate');\n setParam('localConnectivity');\n setParam('minDist');\n setParam('nComponents');\n setParam('nEpochs');\n setParam('nNeighbors');\n setParam('negativeSampleRate');\n setParam('random');\n setParam('repulsionStrength');\n setParam('setOpMixRatio');\n setParam('spread');\n setParam('transformQueueSize');\n }\n UMAP.prototype.fit = function (X) {\n this.initializeFit(X);\n this.optimizeLayout();\n return this.embedding;\n };\n UMAP.prototype.fitAsync = function (X, callback) {\n if (callback === void 0) { callback = function () { return true; }; }\n return __awaiter(this, void 0, void 0, function () {\n return __generator(this, function (_a) {\n switch (_a.label) {\n case 0:\n this.initializeFit(X);\n return [4, this.optimizeLayoutAsync(callback)];\n case 1:\n _a.sent();\n return [2, this.embedding];\n }\n });\n });\n };\n UMAP.prototype.setSupervisedProjection = function (Y, params) {\n if (params === void 0) { params = {}; }\n this.Y = Y;\n this.targetMetric = params.targetMetric || this.targetMetric;\n this.targetWeight = params.targetWeight || this.targetWeight;\n this.targetNNeighbors = params.targetNNeighbors || this.targetNNeighbors;\n };\n UMAP.prototype.setPrecomputedKNN = function (knnIndices, knnDistances) {\n this.knnIndices = knnIndices;\n this.knnDistances = knnDistances;\n };\n UMAP.prototype.initializeFit = function (X) {\n if (X.length <= this.nNeighbors) {\n throw new Error(\"Not enough data points (\" + X.length + \") to create nNeighbors: \" + this.nNeighbors + \". Add more data points or adjust the configuration.\");\n }\n if (this.X === X && this.isInitialized) {\n return this.getNEpochs();\n }\n this.X = X;\n if (!this.knnIndices && !this.knnDistances) {\n var knnResults = this.nearestNeighbors(X);\n this.knnIndices = knnResults.knnIndices;\n this.knnDistances = knnResults.knnDistances;\n }\n this.graph = this.fuzzySimplicialSet(X, this.nNeighbors, this.setOpMixRatio);\n this.makeSearchFns();\n this.searchGraph = this.makeSearchGraph(X);\n this.processGraphForSupervisedProjection();\n var _a = this.initializeSimplicialSetEmbedding(), head = _a.head, tail = _a.tail, epochsPerSample = _a.epochsPerSample;\n this.optimizationState.head = head;\n this.optimizationState.tail = tail;\n this.optimizationState.epochsPerSample = epochsPerSample;\n this.initializeOptimization();\n this.prepareForOptimizationLoop();\n this.isInitialized = true;\n return this.getNEpochs();\n };\n UMAP.prototype.makeSearchFns = function () {\n var _a = nnDescent.makeInitializations(this.distanceFn), initFromTree = _a.initFromTree, initFromRandom = _a.initFromRandom;\n this.initFromTree = initFromTree;\n this.initFromRandom = initFromRandom;\n this.search = nnDescent.makeInitializedNNSearch(this.distanceFn);\n };\n UMAP.prototype.makeSearchGraph = function (X) {\n var knnIndices = this.knnIndices;\n var knnDistances = this.knnDistances;\n var dims = [X.length, X.length];\n var searchGraph = new matrix.SparseMatrix([], [], [], dims);\n for (var i = 0; i < knnIndices.length; i++) {\n var knn = knnIndices[i];\n var distances = knnDistances[i];\n for (var j = 0; j < knn.length; j++) {\n var neighbor = knn[j];\n var distance = distances[j];\n if (distance > 0) {\n searchGraph.set(i, neighbor, distance);\n }\n }\n }\n var transpose = matrix.transpose(searchGraph);\n return matrix.maximum(searchGraph, transpose);\n };\n UMAP.prototype.transform = function (toTransform) {\n var _this = this;\n var rawData = this.X;\n if (rawData === undefined || rawData.length === 0) {\n throw new Error('No data has been fit.');\n }\n var nNeighbors = Math.floor(this.nNeighbors * this.transformQueueSize);\n nNeighbors = Math.min(rawData.length, nNeighbors);\n var init = nnDescent.initializeSearch(this.rpForest, rawData, toTransform, nNeighbors, this.initFromRandom, this.initFromTree, this.random);\n var result = this.search(rawData, this.searchGraph, init, toTransform);\n var _a = heap.deheapSort(result), indices = _a.indices, distances = _a.weights;\n indices = indices.map(function (x) { return x.slice(0, _this.nNeighbors); });\n distances = distances.map(function (x) { return x.slice(0, _this.nNeighbors); });\n var adjustedLocalConnectivity = Math.max(0, this.localConnectivity - 1);\n var _b = this.smoothKNNDistance(distances, this.nNeighbors, adjustedLocalConnectivity), sigmas = _b.sigmas, rhos = _b.rhos;\n var _c = this.computeMembershipStrengths(indices, distances, sigmas, rhos), rows = _c.rows, cols = _c.cols, vals = _c.vals;\n var size = [toTransform.length, rawData.length];\n var graph = new matrix.SparseMatrix(rows, cols, vals, size);\n var normed = matrix.normalize(graph, \"l1\");\n var csrMatrix = matrix.getCSR(normed);\n var nPoints = toTransform.length;\n var eIndices = utils.reshape2d(csrMatrix.indices, nPoints, this.nNeighbors);\n var eWeights = utils.reshape2d(csrMatrix.values, nPoints, this.nNeighbors);\n var embedding = initTransform(eIndices, eWeights, this.embedding);\n var nEpochs = this.nEpochs\n ? this.nEpochs / 3\n : graph.nRows <= 10000\n ? 100\n : 30;\n var graphMax = graph\n .getValues()\n .reduce(function (max, val) { return (val > max ? val : max); }, 0);\n graph = graph.map(function (value) { return (value < graphMax / nEpochs ? 0 : value); });\n graph = matrix.eliminateZeros(graph);\n var epochsPerSample = this.makeEpochsPerSample(graph.getValues(), nEpochs);\n var head = graph.getRows();\n var tail = graph.getCols();\n this.assignOptimizationStateParameters({\n headEmbedding: embedding,\n tailEmbedding: this.embedding,\n head: head,\n tail: tail,\n currentEpoch: 0,\n nEpochs: nEpochs,\n nVertices: graph.getDims()[1],\n epochsPerSample: epochsPerSample,\n });\n this.prepareForOptimizationLoop();\n return this.optimizeLayout();\n };\n UMAP.prototype.processGraphForSupervisedProjection = function () {\n var _a = this, Y = _a.Y, X = _a.X;\n if (Y) {\n if (Y.length !== X.length) {\n throw new Error('Length of X and y must be equal');\n }\n if (this.targetMetric === \"categorical\") {\n var lt = this.targetWeight < 1.0;\n var farDist = lt ? 2.5 * (1.0 / (1.0 - this.targetWeight)) : 1.0e12;\n this.graph = this.categoricalSimplicialSetIntersection(this.graph, Y, farDist);\n }\n }\n };\n UMAP.prototype.step = function () {\n var currentEpoch = this.optimizationState.currentEpoch;\n if (currentEpoch < this.getNEpochs()) {\n this.optimizeLayoutStep(currentEpoch);\n }\n return this.optimizationState.currentEpoch;\n };\n UMAP.prototype.getEmbedding = function () {\n return this.embedding;\n };\n UMAP.prototype.nearestNeighbors = function (X) {\n var _a = this, distanceFn = _a.distanceFn, nNeighbors = _a.nNeighbors;\n var log2 = function (n) { return Math.log(n) / Math.log(2); };\n var metricNNDescent = nnDescent.makeNNDescent(distanceFn, this.random);\n var round = function (n) {\n return n === 0.5 ? 0 : Math.round(n);\n };\n var nTrees = 5 + Math.floor(round(Math.pow(X.length, 0.5) / 20.0));\n var nIters = Math.max(5, Math.floor(Math.round(log2(X.length))));\n this.rpForest = tree.makeForest(X, nNeighbors, nTrees, this.random);\n var leafArray = tree.makeLeafArray(this.rpForest);\n var _b = metricNNDescent(X, leafArray, nNeighbors, nIters), indices = _b.indices, weights = _b.weights;\n return { knnIndices: indices, knnDistances: weights };\n };\n UMAP.prototype.fuzzySimplicialSet = function (X, nNeighbors, setOpMixRatio) {\n if (setOpMixRatio === void 0) { setOpMixRatio = 1.0; }\n var _a = this, _b = _a.knnIndices, knnIndices = _b === void 0 ? [] : _b, _c = _a.knnDistances, knnDistances = _c === void 0 ? [] : _c, localConnectivity = _a.localConnectivity;\n var _d = this.smoothKNNDistance(knnDistances, nNeighbors, localConnectivity), sigmas = _d.sigmas, rhos = _d.rhos;\n var _e = this.computeMembershipStrengths(knnIndices, knnDistances, sigmas, rhos), rows = _e.rows, cols = _e.cols, vals = _e.vals;\n var size = [X.length, X.length];\n var sparseMatrix = new matrix.SparseMatrix(rows, cols, vals, size);\n var transpose = matrix.transpose(sparseMatrix);\n var prodMatrix = matrix.pairwiseMultiply(sparseMatrix, transpose);\n var a = matrix.subtract(matrix.add(sparseMatrix, transpose), prodMatrix);\n var b = matrix.multiplyScalar(a, setOpMixRatio);\n var c = matrix.multiplyScalar(prodMatrix, 1.0 - setOpMixRatio);\n var result = matrix.add(b, c);\n return result;\n };\n UMAP.prototype.categoricalSimplicialSetIntersection = function (simplicialSet, target, farDist, unknownDist) {\n if (unknownDist === void 0) { unknownDist = 1.0; }\n var intersection = fastIntersection(simplicialSet, target, unknownDist, farDist);\n intersection = matrix.eliminateZeros(intersection);\n return resetLocalConnectivity(intersection);\n };\n UMAP.prototype.smoothKNNDistance = function (distances, k, localConnectivity, nIter, bandwidth) {\n if (localConnectivity === void 0) { localConnectivity = 1.0; }\n if (nIter === void 0) { nIter = 64; }\n if (bandwidth === void 0) { bandwidth = 1.0; }\n var target = (Math.log(k) / Math.log(2)) * bandwidth;\n var rho = utils.zeros(distances.length);\n var result = utils.zeros(distances.length);\n for (var i = 0; i < distances.length; i++) {\n var lo = 0.0;\n var hi = Infinity;\n var mid = 1.0;\n var ithDistances = distances[i];\n var nonZeroDists = ithDistances.filter(function (d) { return d > 0.0; });\n if (nonZeroDists.length >= localConnectivity) {\n var index = Math.floor(localConnectivity);\n var interpolation = localConnectivity - index;\n if (index > 0) {\n rho[i] = nonZeroDists[index - 1];\n if (interpolation > SMOOTH_K_TOLERANCE) {\n rho[i] +=\n interpolation * (nonZeroDists[index] - nonZeroDists[index - 1]);\n }\n }\n else {\n rho[i] = interpolation * nonZeroDists[0];\n }\n }\n else if (nonZeroDists.length > 0) {\n rho[i] = utils.max(nonZeroDists);\n }\n for (var n = 0; n < nIter; n++) {\n var psum = 0.0;\n for (var j = 1; j < distances[i].length; j++) {\n var d = distances[i][j] - rho[i];\n if (d > 0) {\n psum += Math.exp(-(d / mid));\n }\n else {\n psum += 1.0;\n }\n }\n if (Math.abs(psum - target) < SMOOTH_K_TOLERANCE) {\n break;\n }\n if (psum > target) {\n hi = mid;\n mid = (lo + hi) / 2.0;\n }\n else {\n lo = mid;\n if (hi === Infinity) {\n mid *= 2;\n }\n else {\n mid = (lo + hi) / 2.0;\n }\n }\n }\n result[i] = mid;\n if (rho[i] > 0.0) {\n var meanIthDistances = utils.mean(ithDistances);\n if (result[i] < MIN_K_DIST_SCALE * meanIthDistances) {\n result[i] = MIN_K_DIST_SCALE * meanIthDistances;\n }\n }\n else {\n var meanDistances = utils.mean(distances.map(utils.mean));\n if (result[i] < MIN_K_DIST_SCALE * meanDistances) {\n result[i] = MIN_K_DIST_SCALE * meanDistances;\n }\n }\n }\n return { sigmas: result, rhos: rho };\n };\n UMAP.prototype.computeMembershipStrengths = function (knnIndices, knnDistances, sigmas, rhos) {\n var nSamples = knnIndices.length;\n var nNeighbors = knnIndices[0].length;\n var rows = utils.zeros(nSamples * nNeighbors);\n var cols = utils.zeros(nSamples * nNeighbors);\n var vals = utils.zeros(nSamples * nNeighbors);\n for (var i = 0; i < nSamples; i++) {\n for (var j = 0; j < nNeighbors; j++) {\n var val = 0;\n if (knnIndices[i][j] === -1) {\n continue;\n }\n if (knnIndices[i][j] === i) {\n val = 0.0;\n }\n else if (knnDistances[i][j] - rhos[i] <= 0.0) {\n val = 1.0;\n }\n else {\n val = Math.exp(-((knnDistances[i][j] - rhos[i]) / sigmas[i]));\n }\n rows[i * nNeighbors + j] = i;\n cols[i * nNeighbors + j] = knnIndices[i][j];\n vals[i * nNeighbors + j] = val;\n }\n }\n return { rows: rows, cols: cols, vals: vals };\n };\n UMAP.prototype.initializeSimplicialSetEmbedding = function () {\n var _this = this;\n var nEpochs = this.getNEpochs();\n var nComponents = this.nComponents;\n var graphValues = this.graph.getValues();\n var graphMax = 0;\n for (var i = 0; i < graphValues.length; i++) {\n var value = graphValues[i];\n if (graphMax < graphValues[i]) {\n graphMax = value;\n }\n }\n var graph = this.graph.map(function (value) {\n if (value < graphMax / nEpochs) {\n return 0;\n }\n else {\n return value;\n }\n });\n this.embedding = utils.zeros(graph.nRows).map(function () {\n return utils.zeros(nComponents).map(function () {\n return utils.tauRand(_this.random) * 20 + -10;\n });\n });\n var weights = [];\n var head = [];\n var tail = [];\n var rowColValues = graph.getAll();\n for (var i = 0; i < rowColValues.length; i++) {\n var entry = rowColValues[i];\n if (entry.value) {\n weights.push(entry.value);\n tail.push(entry.row);\n head.push(entry.col);\n }\n }\n var epochsPerSample = this.makeEpochsPerSample(weights, nEpochs);\n return { head: head, tail: tail, epochsPerSample: epochsPerSample };\n };\n UMAP.prototype.makeEpochsPerSample = function (weights, nEpochs) {\n var result = utils.filled(weights.length, -1.0);\n var max = utils.max(weights);\n var nSamples = weights.map(function (w) { return (w / max) * nEpochs; });\n nSamples.forEach(function (n, i) {\n if (n > 0)\n result[i] = nEpochs / nSamples[i];\n });\n return result;\n };\n UMAP.prototype.assignOptimizationStateParameters = function (state) {\n Object.assign(this.optimizationState, state);\n };\n UMAP.prototype.prepareForOptimizationLoop = function () {\n var _a = this, repulsionStrength = _a.repulsionStrength, learningRate = _a.learningRate, negativeSampleRate = _a.negativeSampleRate;\n var _b = this.optimizationState, epochsPerSample = _b.epochsPerSample, headEmbedding = _b.headEmbedding, tailEmbedding = _b.tailEmbedding;\n var dim = headEmbedding[0].length;\n var moveOther = headEmbedding.length === tailEmbedding.length;\n var epochsPerNegativeSample = epochsPerSample.map(function (e) { return e / negativeSampleRate; });\n var epochOfNextNegativeSample = __spread(epochsPerNegativeSample);\n var epochOfNextSample = __spread(epochsPerSample);\n this.assignOptimizationStateParameters({\n epochOfNextSample: epochOfNextSample,\n epochOfNextNegativeSample: epochOfNextNegativeSample,\n epochsPerNegativeSample: epochsPerNegativeSample,\n moveOther: moveOther,\n initialAlpha: learningRate,\n alpha: learningRate,\n gamma: repulsionStrength,\n dim: dim,\n });\n };\n UMAP.prototype.initializeOptimization = function () {\n var headEmbedding = this.embedding;\n var tailEmbedding = this.embedding;\n var _a = this.optimizationState, head = _a.head, tail = _a.tail, epochsPerSample = _a.epochsPerSample;\n var nEpochs = this.getNEpochs();\n var nVertices = this.graph.nCols;\n var _b = findABParams(this.spread, this.minDist), a = _b.a, b = _b.b;\n this.assignOptimizationStateParameters({\n headEmbedding: headEmbedding,\n tailEmbedding: tailEmbedding,\n head: head,\n tail: tail,\n epochsPerSample: epochsPerSample,\n a: a,\n b: b,\n nEpochs: nEpochs,\n nVertices: nVertices,\n });\n };\n UMAP.prototype.optimizeLayoutStep = function (n) {\n var optimizationState = this.optimizationState;\n var head = optimizationState.head, tail = optimizationState.tail, headEmbedding = optimizationState.headEmbedding, tailEmbedding = optimizationState.tailEmbedding, epochsPerSample = optimizationState.epochsPerSample, epochOfNextSample = optimizationState.epochOfNextSample, epochOfNextNegativeSample = optimizationState.epochOfNextNegativeSample, epochsPerNegativeSample = optimizationState.epochsPerNegativeSample, moveOther = optimizationState.moveOther, initialAlpha = optimizationState.initialAlpha, alpha = optimizationState.alpha, gamma = optimizationState.gamma, a = optimizationState.a, b = optimizationState.b, dim = optimizationState.dim, nEpochs = optimizationState.nEpochs, nVertices = optimizationState.nVertices;\n var clipValue = 4.0;\n for (var i = 0; i < epochsPerSample.length; i++) {\n if (epochOfNextSample[i] > n) {\n continue;\n }\n var j = head[i];\n var k = tail[i];\n var current = headEmbedding[j];\n var other = tailEmbedding[k];\n var distSquared = rDist(current, other);\n var gradCoeff = 0;\n if (distSquared > 0) {\n gradCoeff = -2.0 * a * b * Math.pow(distSquared, b - 1.0);\n gradCoeff /= a * Math.pow(distSquared, b) + 1.0;\n }\n for (var d = 0; d < dim; d++) {\n var gradD = clip(gradCoeff * (current[d] - other[d]), clipValue);\n current[d] += gradD * alpha;\n if (moveOther) {\n other[d] += -gradD * alpha;\n }\n }\n epochOfNextSample[i] += epochsPerSample[i];\n var nNegSamples = Math.floor((n - epochOfNextNegativeSample[i]) / epochsPerNegativeSample[i]);\n for (var p = 0; p < nNegSamples; p++) {\n var k_1 = utils.tauRandInt(nVertices, this.random);\n var other_1 = tailEmbedding[k_1];\n var distSquared_1 = rDist(current, other_1);\n var gradCoeff_1 = 0.0;\n if (distSquared_1 > 0.0) {\n gradCoeff_1 = 2.0 * gamma * b;\n gradCoeff_1 /=\n (0.001 + distSquared_1) * (a * Math.pow(distSquared_1, b) + 1);\n }\n else if (j === k_1) {\n continue;\n }\n for (var d = 0; d < dim; d++) {\n var gradD = 4.0;\n if (gradCoeff_1 > 0.0) {\n gradD = clip(gradCoeff_1 * (current[d] - other_1[d]), clipValue);\n }\n current[d] += gradD * alpha;\n }\n }\n epochOfNextNegativeSample[i] += nNegSamples * epochsPerNegativeSample[i];\n }\n optimizationState.alpha = initialAlpha * (1.0 - n / nEpochs);\n optimizationState.currentEpoch += 1;\n return headEmbedding;\n };\n UMAP.prototype.optimizeLayoutAsync = function (epochCallback) {\n var _this = this;\n if (epochCallback === void 0) { epochCallback = function () { return true; }; }\n return new Promise(function (resolve, reject) {\n var step = function () { return __awaiter(_this, void 0, void 0, function () {\n var _a, nEpochs, currentEpoch, epochCompleted, shouldStop, isFinished;\n return __generator(this, function (_b) {\n try {\n _a = this.optimizationState, nEpochs = _a.nEpochs, currentEpoch = _a.currentEpoch;\n this.embedding = this.optimizeLayoutStep(currentEpoch);\n epochCompleted = this.optimizationState.currentEpoch;\n shouldStop = epochCallback(epochCompleted) === false;\n isFinished = epochCompleted === nEpochs;\n if (!shouldStop && !isFinished) {\n setTimeout(function () { return step(); }, 0);\n }\n else {\n return [2, resolve(isFinished)];\n }\n }\n catch (err) {\n reject(err);\n }\n return [2];\n });\n }); };\n setTimeout(function () { return step(); }, 0);\n });\n };\n UMAP.prototype.optimizeLayout = function (epochCallback) {\n if (epochCallback === void 0) { epochCallback = function () { return true; }; }\n var isFinished = false;\n var embedding = [];\n while (!isFinished) {\n var _a = this.optimizationState, nEpochs = _a.nEpochs, currentEpoch = _a.currentEpoch;\n embedding = this.optimizeLayoutStep(currentEpoch);\n var epochCompleted = this.optimizationState.currentEpoch;\n var shouldStop = epochCallback(epochCompleted) === false;\n isFinished = epochCompleted === nEpochs || shouldStop;\n }\n return embedding;\n };\n UMAP.prototype.getNEpochs = function () {\n var graph = this.graph;\n if (this.nEpochs > 0) {\n return this.nEpochs;\n }\n var length = graph.nRows;\n if (length <= 2500) {\n return 500;\n }\n else if (length <= 5000) {\n return 400;\n }\n else if (length <= 7500) {\n return 300;\n }\n else {\n return 200;\n }\n };\n return UMAP;\n}());\nexports.UMAP = UMAP;\nfunction euclidean(x, y) {\n var result = 0;\n for (var i = 0; i < x.length; i++) {\n result += Math.pow((x[i] - y[i]), 2);\n }\n return Math.sqrt(result);\n}\nexports.euclidean = euclidean;\nfunction cosine(x, y) {\n var result = 0.0;\n var normX = 0.0;\n var normY = 0.0;\n for (var i = 0; i < x.length; i++) {\n result += x[i] * y[i];\n normX += Math.pow(x[i], 2);\n normY += Math.pow(y[i], 2);\n }\n if (normX === 0 && normY === 0) {\n return 0;\n }\n else if (normX === 0 || normY === 0) {\n return 1.0;\n }\n else {\n return 1.0 - result / Math.sqrt(normX * normY);\n }\n}\nexports.cosine = cosine;\nvar OptimizationState = (function () {\n function OptimizationState() {\n this.currentEpoch = 0;\n this.headEmbedding = [];\n this.tailEmbedding = [];\n this.head = [];\n this.tail = [];\n this.epochsPerSample = [];\n this.epochOfNextSample = [];\n this.epochOfNextNegativeSample = [];\n this.epochsPerNegativeSample = [];\n this.moveOther = true;\n this.initialAlpha = 1.0;\n this.alpha = 1.0;\n this.gamma = 1.0;\n this.a = 1.5769434603113077;\n this.b = 0.8950608779109733;\n this.dim = 2;\n this.nEpochs = 500;\n this.nVertices = 0;\n }\n return OptimizationState;\n}());\nfunction clip(x, clipValue) {\n if (x > clipValue)\n return clipValue;\n else if (x < -clipValue)\n return -clipValue;\n else\n return x;\n}\nfunction rDist(x, y) {\n var result = 0.0;\n for (var i = 0; i < x.length; i++) {\n result += Math.pow(x[i] - y[i], 2);\n }\n return result;\n}\nfunction findABParams(spread, minDist) {\n var curve = function (_a) {\n var _b = __read(_a, 2), a = _b[0], b = _b[1];\n return function (x) {\n return 1.0 / (1.0 + a * Math.pow(x, (2 * b)));\n };\n };\n var xv = utils\n .linear(0, spread * 3, 300)\n .map(function (val) { return (val < minDist ? 1.0 : val); });\n var yv = utils.zeros(xv.length).map(function (val, index) {\n var gte = xv[index] >= minDist;\n return gte ? Math.exp(-(xv[index] - minDist) / spread) : val;\n });\n var initialValues = [0.5, 0.5];\n var data = { x: xv, y: yv };\n var options = {\n damping: 1.5,\n initialValues: initialValues,\n gradientDifference: 10e-2,\n maxIterations: 100,\n errorTolerance: 10e-3,\n };\n var parameterValues = ml_levenberg_marquardt_1.default(data, curve, options).parameterValues;\n var _a = __read(parameterValues, 2), a = _a[0], b = _a[1];\n return { a: a, b: b };\n}\nexports.findABParams = findABParams;\nfunction fastIntersection(graph, target, unknownDist, farDist) {\n if (unknownDist === void 0) { unknownDist = 1.0; }\n if (farDist === void 0) { farDist = 5.0; }\n return graph.map(function (value, row, col) {\n if (target[row] === -1 || target[col] === -1) {\n return value * Math.exp(-unknownDist);\n }\n else if (target[row] !== target[col]) {\n return value * Math.exp(-farDist);\n }\n else {\n return value;\n }\n });\n}\nexports.fastIntersection = fastIntersection;\nfunction resetLocalConnectivity(simplicialSet) {\n simplicialSet = matrix.normalize(simplicialSet, \"max\");\n var transpose = matrix.transpose(simplicialSet);\n var prodMatrix = matrix.pairwiseMultiply(transpose, simplicialSet);\n simplicialSet = matrix.add(simplicialSet, matrix.subtract(transpose, prodMatrix));\n return matrix.eliminateZeros(simplicialSet);\n}\nexports.resetLocalConnectivity = resetLocalConnectivity;\nfunction initTransform(indices, weights, embedding) {\n var result = utils\n .zeros(indices.length)\n .map(function (z) { return utils.zeros(embedding[0].length); });\n for (var i = 0; i < indices.length; i++) {\n for (var j = 0; j < indices[0].length; j++) {\n for (var d = 0; d < embedding[0].length; d++) {\n var a = indices[i][j];\n result[i][d] += weights[i][j] * embedding[a][d];\n }\n }\n }\n return result;\n}\nexports.initTransform = initTransform;\n","\"use strict\";\nvar __values = (this && this.__values) || function(o) {\n var s = typeof Symbol === \"function\" && Symbol.iterator, m = s && o[s], i = 0;\n if (m) return m.call(o);\n if (o && typeof o.length === \"number\") return {\n next: function () {\n if (o && i >= o.length) o = void 0;\n return { value: o && o[i++], done: !o };\n }\n };\n throw new TypeError(s ? \"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n};\nObject.defineProperty(exports, \"__esModule\", { value: true });\nexports.reshape2d = exports.rejectionSample = exports.max2d = exports.max = exports.mean = exports.sum = exports.linear = exports.ones = exports.zeros = exports.filled = exports.range = exports.empty = exports.norm = exports.tauRand = exports.tauRandInt = void 0;\nfunction tauRandInt(n, random) {\n return Math.floor(random() * n);\n}\nexports.tauRandInt = tauRandInt;\nfunction tauRand(random) {\n return random();\n}\nexports.tauRand = tauRand;\nfunction norm(vec) {\n var e_1, _a;\n var result = 0;\n try {\n for (var vec_1 = __values(vec), vec_1_1 = vec_1.next(); !vec_1_1.done; vec_1_1 = vec_1.next()) {\n var item = vec_1_1.value;\n result += Math.pow(item, 2);\n }\n }\n catch (e_1_1) { e_1 = { error: e_1_1 }; }\n finally {\n try {\n if (vec_1_1 && !vec_1_1.done && (_a = vec_1.return)) _a.call(vec_1);\n }\n finally { if (e_1) throw e_1.error; }\n }\n return Math.sqrt(result);\n}\nexports.norm = norm;\nfunction empty(n) {\n var output = [];\n for (var i = 0; i < n; i++) {\n output.push(undefined);\n }\n return output;\n}\nexports.empty = empty;\nfunction range(n) {\n return empty(n).map(function (_, i) { return i; });\n}\nexports.range = range;\nfunction filled(n, v) {\n return empty(n).map(function () { return v; });\n}\nexports.filled = filled;\nfunction zeros(n) {\n return filled(n, 0);\n}\nexports.zeros = zeros;\nfunction ones(n) {\n return filled(n, 1);\n}\nexports.ones = ones;\nfunction linear(a, b, len) {\n return empty(len).map(function (_, i) {\n return a + i * ((b - a) / (len - 1));\n });\n}\nexports.linear = linear;\nfunction sum(input) {\n return input.reduce(function (sum, val) { return sum + val; });\n}\nexports.sum = sum;\nfunction mean(input) {\n return sum(input) / input.length;\n}\nexports.mean = mean;\nfunction max(input) {\n var max = 0;\n for (var i = 0; i < input.length; i++) {\n max = input[i] > max ? input[i] : max;\n }\n return max;\n}\nexports.max = max;\nfunction max2d(input) {\n var max = 0;\n for (var i = 0; i < input.length; i++) {\n for (var j = 0; j < input[i].length; j++) {\n max = input[i][j] > max ? input[i][j] : max;\n }\n }\n return max;\n}\nexports.max2d = max2d;\nfunction rejectionSample(nSamples, poolSize, random) {\n var result = zeros(nSamples);\n for (var i = 0; i < nSamples; i++) {\n var rejectSample = true;\n while (rejectSample) {\n var j = tauRandInt(poolSize, random);\n var broken = false;\n for (var k = 0; k < i; k++) {\n if (j === result[k]) {\n broken = true;\n break;\n }\n }\n if (!broken) {\n rejectSample = false;\n }\n result[i] = j;\n }\n }\n return result;\n}\nexports.rejectionSample = rejectionSample;\nfunction reshape2d(x, a, b) {\n var rows = [];\n var count = 0;\n var index = 0;\n if (x.length !== a * b) {\n throw new Error('Array dimensions must match input length.');\n }\n for (var i = 0; i < a; i++) {\n var col = [];\n for (var j = 0; j < b; j++) {\n col.push(x[index]);\n index += 1;\n }\n rows.push(col);\n count += 1;\n }\n return rows;\n}\nexports.reshape2d = reshape2d;\n","const toString = Object.prototype.toString;\n\nexport default function isAnyArray(object) {\n return toString.call(object).endsWith('Array]');\n}\n","/**\n * Calculate current error\n * @ignore\n * @param {{x:Array<number>, y:Array<number>}} data - Array of points to fit in the format [x1, x2, ... ], [y1, y2, ... ]\n * @param {Array<number>} parameters - Array of current parameter values\n * @param {function} parameterizedFunction - The parameters and returns a function with the independent variable as a parameter\n * @return {number}\n */\nexport default function errorCalculation(\n data,\n parameters,\n parameterizedFunction,\n) {\n let error = 0;\n const func = parameterizedFunction(parameters);\n\n for (let i = 0; i < data.x.length; i++) {\n error += Math.abs(data.y[i] - func(data.x[i]));\n }\n\n return error;\n}\n","import isArray from 'is-any-array';\n\nimport errorCalculation from './errorCalculation';\nimport step from './step';\n\n/**\n * Curve fitting algorithm\n * @param {{x:Array<number>, y:Array<number>}} data - Array of points to fit in the format [x1, x2, ... ], [y1, y2, ... ]\n * @param {function} parameterizedFunction - The parameters and returns a function with the independent variable as a parameter\n * @param {object} [options] - Options object\n * @param {number} [options.damping] - Levenberg-Marquardt parameter\n * @param {number} [options.gradientDifference = 10e-2] - Adjustment for decrease the damping parameter\n * @param {Array<number>} [options.minValues] - Minimum allowed values for parameters\n * @param {Array<number>} [options.maxValues] - Maximum allowed values for parameters\n * @param {Array<number>} [options.initialValues] - Array of initial parameter values\n * @param {number} [options.maxIterations = 100] - Maximum of allowed iterations\n * @param {number} [options.errorTolerance = 10e-3] - Minimum uncertainty allowed for each point\n * @return {{parameterValues: Array<number>, parameterError: number, iterations: number}}\n */\nexport default function levenbergMarquardt(\n data,\n parameterizedFunction,\n options = {},\n) {\n let {\n maxIterations = 100,\n gradientDifference = 10e-2,\n damping = 0,\n errorTolerance = 10e-3,\n minValues,\n maxValues,\n initialValues,\n } = options;\n\n if (damping <= 0) {\n throw new Error('The damping option must be a positive number');\n } else if (!data.x || !data.y) {\n throw new Error('The data parameter must have x and y elements');\n } else if (\n !isArray(data.x) ||\n data.x.length < 2 ||\n !isArray(data.y) ||\n data.y.length < 2\n ) {\n throw new Error(\n 'The data parameter elements must be an array with more than 2 points',\n );\n } else if (data.x.length !== data.y.length) {\n throw new Error('The data parameter elements must have the same size');\n }\n\n let parameters =\n initialValues || new Array(parameterizedFunction.length).fill(1);\n let parLen = parameters.length;\n maxValues = maxValues || new Array(parLen).fill(Number.MAX_SAFE_INTEGER);\n minValues = minValues || new Array(parLen).fill(Number.MIN_SAFE_INTEGER);\n\n if (maxValues.length !== minValues.length) {\n throw new Error('minValues and maxValues must be the same size');\n }\n\n if (!isArray(parameters)) {\n throw new Error('initialValues must be an array');\n }\n\n let error = errorCalculation(data, parameters, parameterizedFunction);\n\n let converged = error <= errorTolerance;\n\n let iteration;\n for (iteration = 0; iteration < maxIterations && !converged; iteration++) {\n parameters = step(\n data,\n parameters,\n damping,\n gradientDifference,\n parameterizedFunction,\n );\n\n for (let k = 0; k < parLen; k++) {\n parameters[k] = Math.min(\n Math.max(minValues[k], parameters[k]),\n maxValues[k],\n );\n }\n\n error = errorCalculation(data, parameters, parameterizedFunction);\n if (isNaN(error)) break;\n converged = error <= errorTolerance;\n }\n\n return {\n parameterValues: parameters,\n parameterError: error,\n iterations: iteration,\n };\n}\n","import { inverse, Matrix } from 'ml-matrix';\n\n/**\n * Difference of the matrix function over the parameters\n * @ignore\n * @param {{x:Array<number>, y:Array<number>}} data - Array of points to fit in the format [x1, x2, ... ], [y1, y2, ... ]\n * @param {Array<number>} evaluatedData - Array of previous evaluated function values\n * @param {Array<number>} params - Array of previous parameter values\n * @param {number} gradientDifference - Adjustment for decrease the damping parameter\n * @param {function} paramFunction - The parameters and returns a function with the independent variable as a parameter\n * @return {Matrix}\n */\nfunction gradientFunction(\n data,\n evaluatedData,\n params,\n gradientDifference,\n paramFunction,\n) {\n const n = params.length;\n const m = data.x.length;\n\n let ans = new Array(n);\n\n for (let param = 0; param < n; param++) {\n ans[param] = new Array(m);\n let auxParams = params.slice();\n auxParams[param] += gradientDifference;\n let funcParam = paramFunction(auxParams);\n\n for (let point = 0; point < m; point++) {\n ans[param][point] = evaluatedData[point] - funcParam(data.x[point]);\n }\n }\n return new Matrix(ans);\n}\n\n/**\n * Matrix function over the samples\n * @ignore\n * @param {{x:Array<number>, y:Array<number>}} data - Array of points to fit in the format [x1, x2, ... ], [y1, y2, ... ]\n * @param {Array<number>} evaluatedData - Array of previous evaluated function values\n * @return {Matrix}\n */\nfunction matrixFunction(data, evaluatedData) {\n const m = data.x.length;\n\n let ans = new Array(m);\n\n for (let point = 0; point < m; point++) {\n ans[point] = [data.y[point] - evaluatedData[point]];\n }\n\n return new Matrix(ans);\n}\n\n/**\n * Iteration for Levenberg-Marquardt\n * @ignore\n * @param {{x:Array<number>, y:Array<number>}} data - Array of points to fit in the format [x1, x2, ... ], [y1, y2, ... ]\n * @param {Array<number>} params - Array of previous parameter values\n * @param {number} damping - Levenberg-Marquardt parameter\n * @param {number} gradientDifference - Adjustment for decrease the damping parameter\n * @param {function} parameterizedFunction - The parameters and returns a function with the independent variable as a parameter\n * @return {Array<number>}\n */\nexport default function step(\n data,\n params,\n damping,\n gradientDifference,\n parameterizedFunction,\n) {\n let value = damping * gradientDifference * gradientDifference;\n let identity = Matrix.eye(params.length, params.length, value);\n\n const func = parameterizedFunction(params);\n\n let evaluatedData = new Float64Array(data.x.length);\n for (let i = 0; i < data.x.length; i++) {\n evaluatedData[i] = func(data.x[i]);\n }\n\n let gradientFunc = gradientFunction(\n data,\n evaluatedData,\n params,\n gradientDifference,\n parameterizedFunction,\n );\n let matrixFunc = matrixFunction(data, evaluatedData);\n let inverseMatrix = inverse(\n identity.add(gradientFunc.mmul(gradientFunc.transpose())),\n );\n\n params = new Matrix([params]);\n params = params.sub(\n inverseMatrix\n .mmul(gradientFunc)\n .mmul(matrixFunc)\n .mul(gradientDifference)\n .transpose(),\n );\n\n return params.to1DArray();\n}\n"],"names":[],"sourceRoot":""}