@elarsaks/umap-wasm 0.1.2 → 0.1.4

package/dist/src/matrix.js

@@ -1,360 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
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-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
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-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
-var __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
-        }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
-var _a;
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.SparseMatrix = void 0;
-exports.transpose = transpose;
-exports.identity = identity;
-exports.pairwiseMultiply = pairwiseMultiply;
-exports.add = add;
-exports.subtract = subtract;
-exports.maximum = maximum;
-exports.multiplyScalar = multiplyScalar;
-exports.eliminateZeros = eliminateZeros;
-exports.normalize = normalize;
-exports.getCSR = getCSR;
-var utils = __importStar(require("./utils"));
-var SparseMatrix = (function () {
-    function SparseMatrix(rows, cols, values, dims) {
-        this.entries = new Map();
-        this.nRows = 0;
-        this.nCols = 0;
-        if (rows.length !== cols.length || rows.length !== values.length) {
-            throw new Error('rows, cols and values arrays must all have the same length');
-        }
-        this.nRows = dims[0];
-        this.nCols = dims[1];
-        for (var i = 0; i < values.length; i++) {
-            var row = rows[i];
-            var col = cols[i];
-            this.checkDims(row, col);
-            var key = this.makeKey(row, col);
-            this.entries.set(key, { value: values[i], row: row, col: col });
-        }
-    }
-    SparseMatrix.prototype.makeKey = function (row, col) {
-        return "".concat(row, ":").concat(col);
-    };
-    SparseMatrix.prototype.checkDims = function (row, col) {
-        var withinBounds = row < this.nRows && col < this.nCols;
-        if (!withinBounds) {
-            throw new Error('row and/or col specified outside of matrix dimensions');
-        }
-    };
-    SparseMatrix.prototype.set = function (row, col, value) {
-        this.checkDims(row, col);
-        var key = this.makeKey(row, col);
-        if (!this.entries.has(key)) {
-            this.entries.set(key, { value: value, row: row, col: col });
-        }
-        else {
-            this.entries.get(key).value = value;
-        }
-    };
-    SparseMatrix.prototype.get = function (row, col, defaultValue) {
-        if (defaultValue === void 0) { defaultValue = 0; }
-        this.checkDims(row, col);
-        var key = this.makeKey(row, col);
-        if (this.entries.has(key)) {
-            return this.entries.get(key).value;
-        }
-        else {
-            return defaultValue;
-        }
-    };
-    SparseMatrix.prototype.getAll = function (ordered) {
-        if (ordered === void 0) { ordered = true; }
-        var rowColValues = [];
-        this.entries.forEach(function (value) {
-            rowColValues.push(value);
-        });
-        if (ordered) {
-            rowColValues.sort(function (a, b) {
-                if (a.row === b.row) {
-                    return a.col - b.col;
-                }
-                else {
-                    return a.row - b.row;
-                }
-            });
-        }
-        return rowColValues;
-    };
-    SparseMatrix.prototype.getDims = function () {
-        return [this.nRows, this.nCols];
-    };
-    SparseMatrix.prototype.getRows = function () {
-        return Array.from(this.entries, function (_a) {
-            var _b = __read(_a, 2), key = _b[0], value = _b[1];
-            return value.row;
-        });
-    };
-    SparseMatrix.prototype.getCols = function () {
-        return Array.from(this.entries, function (_a) {
-            var _b = __read(_a, 2), key = _b[0], value = _b[1];
-            return value.col;
-        });
-    };
-    SparseMatrix.prototype.getValues = function () {
-        return Array.from(this.entries, function (_a) {
-            var _b = __read(_a, 2), key = _b[0], value = _b[1];
-            return value.value;
-        });
-    };
-    SparseMatrix.prototype.forEach = function (fn) {
-        this.entries.forEach(function (value) { return fn(value.value, value.row, value.col); });
-    };
-    SparseMatrix.prototype.map = function (fn) {
-        var vals = [];
-        this.entries.forEach(function (value) {
-            vals.push(fn(value.value, value.row, value.col));
-        });
-        var dims = [this.nRows, this.nCols];
-        return new SparseMatrix(this.getRows(), this.getCols(), vals, dims);
-    };
-    SparseMatrix.prototype.toArray = function () {
-        var _this = this;
-        var rows = utils.empty(this.nRows);
-        var output = rows.map(function () {
-            return utils.zeros(_this.nCols);
-        });
-        this.entries.forEach(function (value) {
-            output[value.row][value.col] = value.value;
-        });
-        return output;
-    };
-    return SparseMatrix;
-}());
-exports.SparseMatrix = SparseMatrix;
-function transpose(matrix) {
-    var cols = [];
-    var rows = [];
-    var vals = [];
-    matrix.forEach(function (value, row, col) {
-        cols.push(row);
-        rows.push(col);
-        vals.push(value);
-    });
-    var dims = [matrix.nCols, matrix.nRows];
-    return new SparseMatrix(rows, cols, vals, dims);
-}
-function identity(size) {
-    var _a = __read(size, 1), rows = _a[0];
-    var matrix = new SparseMatrix([], [], [], size);
-    for (var i = 0; i < rows; i++) {
-        matrix.set(i, i, 1);
-    }
-    return matrix;
-}
-function pairwiseMultiply(a, b) {
-    return elementWise(a, b, function (x, y) { return x * y; });
-}
-function add(a, b) {
-    return elementWise(a, b, function (x, y) { return x + y; });
-}
-function subtract(a, b) {
-    return elementWise(a, b, function (x, y) { return x - y; });
-}
-function maximum(a, b) {
-    return elementWise(a, b, function (x, y) { return (x > y ? x : y); });
-}
-function multiplyScalar(a, scalar) {
-    return a.map(function (value) {
-        return value * scalar;
-    });
-}
-function eliminateZeros(m) {
-    var zeroIndices = new Set();
-    var values = m.getValues();
-    var rows = m.getRows();
-    var cols = m.getCols();
-    for (var i = 0; i < values.length; i++) {
-        if (values[i] === 0) {
-            zeroIndices.add(i);
-        }
-    }
-    var removeByZeroIndex = function (_, index) { return !zeroIndices.has(index); };
-    var nextValues = values.filter(removeByZeroIndex);
-    var nextRows = rows.filter(removeByZeroIndex);
-    var nextCols = cols.filter(removeByZeroIndex);
-    return new SparseMatrix(nextRows, nextCols, nextValues, m.getDims());
-}
-function normalize(m, normType) {
-    var e_1, _a;
-    if (normType === void 0) { normType = "l2"; }
-    var normFn = normFns[normType];
-    var colsByRow = new Map();
-    m.forEach(function (_, row, col) {
-        var cols = colsByRow.get(row) || [];
-        cols.push(col);
-        colsByRow.set(row, cols);
-    });
-    var nextMatrix = new SparseMatrix([], [], [], m.getDims());
-    var _loop_1 = function (row) {
-        var cols = colsByRow.get(row).sort();
-        var vals = cols.map(function (col) { return m.get(row, col); });
-        var norm = normFn(vals);
-        for (var i = 0; i < norm.length; i++) {
-            nextMatrix.set(row, cols[i], norm[i]);
-        }
-    };
-    try {
-        for (var _b = __values(colsByRow.keys()), _c = _b.next(); !_c.done; _c = _b.next()) {
-            var row = _c.value;
-            _loop_1(row);
-        }
-    }
-    catch (e_1_1) { e_1 = { error: e_1_1 }; }
-    finally {
-        try {
-            if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
-        }
-        finally { if (e_1) throw e_1.error; }
-    }
-    return nextMatrix;
-}
-var normFns = (_a = {},
-    _a["max"] = function (xs) {
-        var max = -Infinity;
-        for (var i = 0; i < xs.length; i++) {
-            max = xs[i] > max ? xs[i] : max;
-        }
-        return xs.map(function (x) { return x / max; });
-    },
-    _a["l1"] = function (xs) {
-        var sum = 0;
-        for (var i = 0; i < xs.length; i++) {
-            sum += xs[i];
-        }
-        return xs.map(function (x) { return x / sum; });
-    },
-    _a["l2"] = function (xs) {
-        var sum = 0;
-        for (var i = 0; i < xs.length; i++) {
-            sum += Math.pow(xs[i], 2);
-        }
-        return xs.map(function (x) { return Math.sqrt(Math.pow(x, 2) / sum); });
-    },
-    _a);
-function elementWise(a, b, op) {
-    var visited = new Set();
-    var rows = [];
-    var cols = [];
-    var vals = [];
-    var operate = function (row, col) {
-        rows.push(row);
-        cols.push(col);
-        var nextValue = op(a.get(row, col), b.get(row, col));
-        vals.push(nextValue);
-    };
-    var valuesA = a.getValues();
-    var rowsA = a.getRows();
-    var colsA = a.getCols();
-    for (var i = 0; i < valuesA.length; i++) {
-        var row = rowsA[i];
-        var col = colsA[i];
-        var key = "".concat(row, ":").concat(col);
-        visited.add(key);
-        operate(row, col);
-    }
-    var valuesB = b.getValues();
-    var rowsB = b.getRows();
-    var colsB = b.getCols();
-    for (var i = 0; i < valuesB.length; i++) {
-        var row = rowsB[i];
-        var col = colsB[i];
-        var key = "".concat(row, ":").concat(col);
-        if (visited.has(key))
-            continue;
-        operate(row, col);
-    }
-    var dims = [a.nRows, a.nCols];
-    return new SparseMatrix(rows, cols, vals, dims);
-}
-function getCSR(x) {
-    var entries = [];
-    x.forEach(function (value, row, col) {
-        entries.push({ value: value, row: row, col: col });
-    });
-    entries.sort(function (a, b) {
-        if (a.row === b.row) {
-            return a.col - b.col;
-        }
-        else {
-            return a.row - b.row;
-        }
-    });
-    var indices = [];
-    var values = [];
-    var indptr = [];
-    var currentRow = -1;
-    for (var i = 0; i < entries.length; i++) {
-        var _a = entries[i], row = _a.row, col = _a.col, value = _a.value;
-        if (row !== currentRow) {
-            currentRow = row;
-            indptr.push(i);
-        }
-        indices.push(col);
-        values.push(value);
-    }
-    return { indices: indices, values: values, indptr: indptr };
-}

package/dist/src/nn_descent.js

@@ -1,204 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
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-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeNNDescent = makeNNDescent;
-exports.makeInitializations = makeInitializations;
-exports.makeInitializedNNSearch = makeInitializedNNSearch;
-exports.initializeSearch = initializeSearch;
-var heap = __importStar(require("./heap"));
-var matrix = __importStar(require("./matrix"));
-var tree = __importStar(require("./tree"));
-var utils = __importStar(require("./utils"));
-function makeNNDescent(distanceFn, random) {
-    return function nNDescent(data, leafArray, nNeighbors, nIters, maxCandidates, delta, rho, rpTreeInit) {
-        if (nIters === void 0) { nIters = 10; }
-        if (maxCandidates === void 0) { maxCandidates = 50; }
-        if (delta === void 0) { delta = 0.001; }
-        if (rho === void 0) { rho = 0.5; }
-        if (rpTreeInit === void 0) { rpTreeInit = true; }
-        var nVertices = data.length;
-        var currentGraph = heap.makeHeap(data.length, nNeighbors);
-        for (var i = 0; i < data.length; i++) {
-            var indices = heap.rejectionSample(nNeighbors, data.length, random);
-            for (var j = 0; j < indices.length; j++) {
-                var d = distanceFn(data[i], data[indices[j]]);
-                heap.heapPush(currentGraph, i, d, indices[j], 1);
-                heap.heapPush(currentGraph, indices[j], d, i, 1);
-            }
-        }
-        if (rpTreeInit) {
-            for (var n = 0; n < leafArray.length; n++) {
-                for (var i = 0; i < leafArray[n].length; i++) {
-                    if (leafArray[n][i] < 0) {
-                        break;
-                    }
-                    for (var j = i + 1; j < leafArray[n].length; j++) {
-                        if (leafArray[n][j] < 0) {
-                            break;
-                        }
-                        var d = distanceFn(data[leafArray[n][i]], data[leafArray[n][j]]);
-                        heap.heapPush(currentGraph, leafArray[n][i], d, leafArray[n][j], 1);
-                        heap.heapPush(currentGraph, leafArray[n][j], d, leafArray[n][i], 1);
-                    }
-                }
-            }
-        }
-        for (var n = 0; n < nIters; n++) {
-            var candidateNeighbors = heap.buildCandidates(currentGraph, nVertices, nNeighbors, maxCandidates, random);
-            var c = 0;
-            for (var i = 0; i < nVertices; i++) {
-                for (var j = 0; j < maxCandidates; j++) {
-                    var p = Math.floor(candidateNeighbors[0][i][j]);
-                    if (p < 0 || utils.tauRand(random) < rho) {
-                        continue;
-                    }
-                    for (var k = 0; k < maxCandidates; k++) {
-                        var q = Math.floor(candidateNeighbors[0][i][k]);
-                        var cj = candidateNeighbors[2][i][j];
-                        var ck = candidateNeighbors[2][i][k];
-                        if (q < 0 || (!cj && !ck)) {
-                            continue;
-                        }
-                        var d = distanceFn(data[p], data[q]);
-                        c += heap.heapPush(currentGraph, p, d, q, 1);
-                        c += heap.heapPush(currentGraph, q, d, p, 1);
-                    }
-                }
-            }
-            if (c <= delta * nNeighbors * data.length) {
-                break;
-            }
-        }
-        var sorted = heap.deheapSort(currentGraph);
-        return sorted;
-    };
-}
-function makeInitializations(distanceFn) {
-    function initFromRandom(nNeighbors, data, queryPoints, _heap, random) {
-        for (var i = 0; i < queryPoints.length; i++) {
-            var indices = utils.rejectionSample(nNeighbors, data.length, random);
-            for (var j = 0; j < indices.length; j++) {
-                if (indices[j] < 0) {
-                    continue;
-                }
-                var d = distanceFn(data[indices[j]], queryPoints[i]);
-                heap.heapPush(_heap, i, d, indices[j], 1);
-            }
-        }
-    }
-    function initFromTree(_tree, data, queryPoints, _heap, random) {
-        for (var i = 0; i < queryPoints.length; i++) {
-            var indices = tree.searchFlatTree(queryPoints[i], _tree, random);
-            for (var j = 0; j < indices.length; j++) {
-                if (indices[j] < 0) {
-                    return;
-                }
-                var d = distanceFn(data[indices[j]], queryPoints[i]);
-                heap.heapPush(_heap, i, d, indices[j], 1);
-            }
-        }
-        return;
-    }
-    return { initFromRandom: initFromRandom, initFromTree: initFromTree };
-}
-function makeInitializedNNSearch(distanceFn) {
-    return function nnSearchFn(data, graph, initialization, queryPoints) {
-        var e_1, _a;
-        var _b = matrix.getCSR(graph), indices = _b.indices, indptr = _b.indptr;
-        for (var i = 0; i < queryPoints.length; i++) {
-            var tried = new Set(initialization[0][i]);
-            while (true) {
-                var vertex = heap.smallestFlagged(initialization, i);
-                if (vertex === -1) {
-                    break;
-                }
-                var candidates = indices.slice(indptr[vertex], indptr[vertex + 1]);
-                try {
-                    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()) {
-                        var candidate = candidates_1_1.value;
-                        if (candidate === vertex ||
-                            candidate === -1 ||
-                            tried.has(candidate)) {
-                            continue;
-                        }
-                        var d = distanceFn(data[candidate], queryPoints[i]);
-                        heap.uncheckedHeapPush(initialization, i, d, candidate, 1);
-                        tried.add(candidate);
-                    }
-                }
-                catch (e_1_1) { e_1 = { error: e_1_1 }; }
-                finally {
-                    try {
-                        if (candidates_1_1 && !candidates_1_1.done && (_a = candidates_1.return)) _a.call(candidates_1);
-                    }
-                    finally { if (e_1) throw e_1.error; }
-                }
-            }
-        }
-        return initialization;
-    };
-}
-function initializeSearch(forest, data, queryPoints, nNeighbors, initFromRandom, initFromTree, random) {
-    var e_2, _a;
-    var results = heap.makeHeap(queryPoints.length, nNeighbors);
-    initFromRandom(nNeighbors, data, queryPoints, results, random);
-    if (forest) {
-        try {
-            for (var forest_1 = __values(forest), forest_1_1 = forest_1.next(); !forest_1_1.done; forest_1_1 = forest_1.next()) {
-                var tree_1 = forest_1_1.value;
-                initFromTree(tree_1, data, queryPoints, results, random);
-            }
-        }
-        catch (e_2_1) { e_2 = { error: e_2_1 }; }
-        finally {
-            try {
-                if (forest_1_1 && !forest_1_1.done && (_a = forest_1.return)) _a.call(forest_1);
-            }
-            finally { if (e_2) throw e_2.error; }
-        }
-    }
-    return results;
-}