visualifyjs 2.5.3 → 3.0.0

package/src/core/components/visium.js

@@ -1,97 +1,114 @@
-/*
- * @Author       : Lihao leolihao@arizona.edu
- * @Date         : 2024-01-08 16:34:20
- * @FilePath     : /visualifyjs/src/core/components/Visium.js
- * @Description  :
- * Copyright (c) 2024 by Lihao (leolihao@arizona.edu), All Rights Reserved.
- */
-import React, { useEffect, useState } from 'react';
-import { useAppContext } from '../appContext';
-import conditionalFetch from '../fetch/condfetch';
-import EChartSwitcher from '../modules/echartswitcher';
-import Loading from '../pages/loading';
-import { isEmpty } from 'lodash';
-
-const Visium = ({ props, style }) => {
-	const [loading, setLoading] = useState({
-		active: true,
-		message: 'Please Select the Section',
-	});
-	const { sharedData } = useAppContext();
-	const [Options, setOptions] = useState(props);
-
-	useEffect(() => {
-		const { cellfrac, metadata, gene, image } = props.settings;
-		if (!metadata || !gene || !image)
-			throw new Error('missing metadata, gene, or image');
-		let trigger = {
-			metadata: metadata.trigger,
-			gene: gene.trigger,
-			image: image.trigger,
-		};
-
-		const updatePlot = async () => {
-			try {
-				const cellval = isEmpty(sharedData[cellfrac])
-					? 'All'
-					: sharedData[cellfrac][0];
-
-				if (sharedData?.[trigger.image]) {
-					console.log('image trigger', sharedData?.[trigger.image]);
-					const imageBuffer = await conditionalFetch(
-						image,
-						sharedData,
-						{},
-					);
-
-					const blob = new Blob([new Uint8Array(imageBuffer.data)], {
-						type: 'image/png',
-					});
-					const dataURL = URL.createObjectURL(blob);
-
-					console.log('image', dataURL);
-					setOptions((prev) => ({
-						...prev,
-						config: {
-							...prev.config,
-							overrides: {
-								...prev.config.overrides,
-								backgroundColor: {
-									image: dataURL,
-								},
-							},
-						},
-					}));
-				}
-
-				console.log('update plot', cellval, trigger);
-			} catch (e) {
-				setLoading({ active: true, message: e.message });
-			}
-		};
-
-		updatePlot();
-	}, [props, sharedData]);
-
-	return (
-		<div
-			id={props.id}
-			style={{ ...style, position: 'relative' }}>
-			{loading.active && (
-				<Loading
-					message={loading.message}
-					style={loading.style}
-				/>
-			)}
-			<EChartSwitcher
-				props={Options}
-				style={{
-					opacity: loading.active ? 0 : 1,
-					...style,
-				}}
-			/>
-		</div>
-	);
-};
-
-export default Visium;
+/*
+ * @Author       : Lihao leolihao@arizona.edu
+ * @Date         : 2024-01-08 16:34:20
+ * @FilePath     : /visualifyjs/src/core/components/Visium.js
+ * @Description  :
+ * Copyright (c) 2024 by Lihao (leolihao@arizona.edu), All Rights Reserved.
+ */
+import React, { useEffect, useState, useRef } from 'react';
+import { useAppContext } from '../appContext';
+import conditionalFetch from '../fetch/condfetch';
+import EChartSwitcher from '../modules/echartswitcher';
+import Loading from '../pages/loading';
+import { isEmpty } from 'lodash';
+
+const Visium = ({ props, style }) => {
+	const [loading, setLoading] = useState({
+		active: true,
+		message: 'Please Select the Section',
+	});
+	const { sharedData } = useAppContext();
+	const [Options, setOptions] = useState(props);
+
+	// Use ref for sharedData to access latest without depending on it
+	const sharedDataRef = useRef(sharedData);
+	sharedDataRef.current = sharedData;
+
+	// Extract stable trigger keys from props.settings
+	const { cellfrac, metadata, gene, image } = props.settings || {};
+	const imageTrigger = image?.trigger;
+	// Build a snapshot of only the sharedData keys we depend on
+	const relevantKeys = [imageTrigger, cellfrac].filter(Boolean);
+	const sharedDataSnapshot = JSON.stringify(
+		relevantKeys.reduce((acc, key) => {
+			acc[key] = sharedData[key];
+			return acc;
+		}, {}),
+	);
+
+	useEffect(() => {
+		if (!metadata || !gene || !image)
+			throw new Error('missing metadata, gene, or image');
+		const currentSharedData = sharedDataRef.current;
+		let trigger = {
+			metadata: metadata.trigger,
+			gene: gene.trigger,
+			image: image.trigger,
+		};
+
+		const updatePlot = async () => {
+			try {
+				const cellval = isEmpty(currentSharedData[cellfrac])
+					? 'All'
+					: currentSharedData[cellfrac][0];
+
+				if (currentSharedData?.[trigger.image]) {
+					console.log('image trigger', currentSharedData?.[trigger.image]);
+					const imageBuffer = await conditionalFetch(
+						image,
+						currentSharedData,
+						{},
+					);
+
+					const blob = new Blob([new Uint8Array(imageBuffer.data)], {
+						type: 'image/png',
+					});
+					const dataURL = URL.createObjectURL(blob);
+
+					console.log('image', dataURL);
+					setOptions((prev) => ({
+						...prev,
+						config: {
+							...prev.config,
+							overrides: {
+								...prev.config.overrides,
+								backgroundColor: {
+									image: dataURL,
+								},
+							},
+						},
+					}));
+				}
+
+				console.log('update plot', cellval, trigger);
+			} catch (e) {
+				setLoading({ active: true, message: e.message });
+			}
+		};
+
+		updatePlot();
+		// eslint-disable-next-line react-hooks/exhaustive-deps
+	}, [sharedDataSnapshot, cellfrac, imageTrigger]);
+
+	return (
+		<div
+			id={props.id}
+			style={{ ...style, position: 'relative' }}>
+			{loading.active && (
+				<Loading
+					message={loading.message}
+					style={loading.style}
+				/>
+			)}
+			<EChartSwitcher
+				props={Options}
+				style={{
+					opacity: loading.active ? 0 : 1,
+					...style,
+				}}
+			/>
+		</div>
+	);
+};
+
+export default Visium;

package/src/core/data-processor.js

@@ -0,0 +1,413 @@
+/**
+ * @fileoverview Data Processor - Main Thread Interface
+ * @module core/data-processor
+ *
+ * Provides a high-level API for offloading data processing to Web Workers.
+ * Handles worker pool management, task distribution, and result aggregation.
+ */
+
+import { getWorkerPool, terminateWorkerPool } from './workers/worker-pool';
+
+/**
+ * Default configuration for data processor
+ * @readonly
+ */
+const DEFAULT_CONFIG = {
+	workerScript: new URL('./workers/data-worker.js', import.meta.url).href,
+	minWorkers: 2,
+	maxWorkers: 4,
+	chunkSize: 10000,
+	enableChunking: true,
+};
+
+/**
+ * Data Processor class
+ * Manages data processing operations using Web Workers
+ */
+class DataProcessor {
+	/**
+	 * Create a new data processor
+	 * @param {Object} config - Processor configuration
+	 */
+	constructor(config = {}) {
+		this.config = { ...DEFAULT_CONFIG, ...config };
+		this.pool = getWorkerPool({
+			workerScript: this.config.workerScript,
+			minWorkers: this.config.minWorkers,
+			maxWorkers: this.config.maxWorkers,
+		});
+	}
+
+	/**
+	 * Check if data should be chunked for processing
+	 * @private
+	 * @param {Array} data - Data array
+	 * @returns {boolean} True if data should be chunked
+	 */
+	_shouldChunk(data) {
+		return this.config.enableChunking && data.length > this.config.chunkSize;
+	}
+
+	/**
+	 * Split data into chunks for parallel processing
+	 * @private
+	 * @param {Array} data - Data array
+	 * @param {number} chunkSize - Size of each chunk
+	 * @returns {Array<Array>} Array of chunks
+	 */
+	_chunkData(data, chunkSize) {
+		const chunks = [];
+		for (let i = 0; i < data.length; i += chunkSize) {
+			chunks.push(data.slice(i, i + chunkSize));
+		}
+		return chunks;
+	}
+
+	/**
+	 * Aggregate data using specified method
+	 * @param {Array} data - Input data
+	 * @param {Object} config - Aggregation config
+	 * @returns {Promise<number>} Aggregated value
+	 */
+	async aggregate(data, config) {
+		if (this._shouldChunk(data)) {
+			// Process in chunks and combine results
+			const chunks = this._chunkData(data, this.config.chunkSize);
+			const chunkResults = await this.pool.executeAll(
+				chunks.map((chunk) => ({
+					operation: 'aggregate',
+					data: chunk,
+					config: { ...config, method: 'sum' },
+				}))
+			);
+
+			// Combine chunk results
+			const total = chunkResults.reduce((a, b) => a + b, 0);
+
+			if (config.method === 'avg' || config.method === 'mean') {
+				return total / data.length;
+			}
+			if (config.method === 'count') {
+				return data.length;
+			}
+			return total;
+		}
+
+		return this.pool.execute({
+			operation: 'aggregate',
+			data,
+			config,
+		});
+	}
+
+	/**
+	 * Filter data based on criteria
+	 * @param {Array} data - Input data
+	 * @param {Object} criteria - Filter criteria
+	 * @returns {Promise<Array>} Filtered data
+	 */
+	async filter(data, criteria) {
+		if (this._shouldChunk(data)) {
+			const chunks = this._chunkData(data, this.config.chunkSize);
+			const results = await this.pool.executeAll(
+				chunks.map((chunk) => ({
+					operation: 'filter',
+					data: chunk,
+					config: criteria,
+				}))
+			);
+			return results.flat();
+		}
+
+		return this.pool.execute({
+			operation: 'filter',
+			data,
+			config: criteria,
+		});
+	}
+
+	/**
+	 * Sort data by fields
+	 * @param {Array} data - Input data
+	 * @param {Array|Object} sortConfig - Sort configuration
+	 * @returns {Promise<Array>} Sorted data
+	 */
+	async sort(data, sortConfig) {
+		// Sorting is typically done on full dataset
+		return this.pool.execute({
+			operation: 'sort',
+			data,
+			config: sortConfig,
+		});
+	}
+
+	/**
+	 * Group data by field(s)
+	 * @param {Array} data - Input data
+	 * @param {string|Array} fields - Field(s) to group by
+	 * @returns {Promise<Object>} Grouped data
+	 */
+	async groupBy(data, fields) {
+		return this.pool.execute({
+			operation: 'groupBy',
+			data,
+			config: fields,
+		});
+	}
+
+	/**
+	 * Sample data for preview
+	 * @param {Array} data - Input data
+	 * @param {number} sampleSize - Sample size
+	 * @returns {Promise<Array>} Sampled data
+	 */
+	async sample(data, sampleSize) {
+		return this.pool.execute({
+			operation: 'sample',
+			data,
+			config: { size: sampleSize },
+		});
+	}
+
+	/**
+	 * Calculate statistics for a field
+	 * @param {Array} data - Input data
+	 * @param {string} field - Field name
+	 * @returns {Promise<Object>} Statistics
+	 */
+	async statistics(data, field) {
+		if (this._shouldChunk(data)) {
+			// Process statistics in chunks and combine
+			const chunks = this._chunkData(data, this.config.chunkSize);
+			const chunkStats = await this.pool.executeAll(
+				chunks.map((chunk) => ({
+					operation: 'statistics',
+					data: chunk,
+					config: { field },
+				}))
+			);
+
+			// Combine statistics from chunks
+			return this._combineStatistics(chunkStats);
+		}
+
+		return this.pool.execute({
+			operation: 'statistics',
+			data,
+			config: { field },
+		});
+	}
+
+	/**
+	 * Combine statistics from multiple chunks
+	 * @private
+	 * @param {Array<Object>} statsArray - Array of statistics
+	 * @returns {Object} Combined statistics
+	 */
+	_combineStatistics(statsArray) {
+		const validStats = statsArray.filter((s) => s !== null);
+		if (validStats.length === 0) return null;
+
+		const totalCount = validStats.reduce((sum, s) => sum + s.count, 0);
+		const totalSum = validStats.reduce((sum, s) => sum + s.sum, 0);
+		const mean = totalSum / totalCount;
+
+		// Combine variance (using parallel algorithm)
+		let totalVariance = 0;
+		for (const s of validStats) {
+			totalVariance += s.variance * s.count + Math.pow(s.mean - mean, 2) * s.count;
+		}
+		totalVariance /= totalCount;
+
+		return {
+			count: totalCount,
+			sum: totalSum,
+			mean,
+			min: Math.min(...validStats.map((s) => s.min)),
+			max: Math.max(...validStats.map((s) => s.max)),
+			variance: totalVariance,
+			std: Math.sqrt(totalVariance),
+		};
+	}
+
+	/**
+	 * Parse CSV data
+	 * @param {string} csv - CSV content
+	 * @param {Object} options - Parse options
+	 * @returns {Promise<Array>} Parsed data
+	 */
+	async parseCSV(csv, options = {}) {
+		return this.pool.execute({
+			operation: 'parseCSV',
+			data: csv,
+			config: options,
+		});
+	}
+
+	/**
+	 * Execute a pipeline of operations
+	 * @param {Array} data - Input data
+	 * @param {Array} operations - Array of operations
+	 * @returns {Promise<Array>} Result data
+	 */
+	async pipeline(data, operations) {
+		return this.pool.execute({
+			operation: 'pipeline',
+			data,
+			config: operations,
+		});
+	}
+
+	/**
+	 * Process large dataset with progress callbacks
+	 * @param {Array} data - Input data
+	 * @param {Object} config - Processing config
+	 * @param {Function} onProgress - Progress callback
+	 * @returns {Promise<Object>} Processing result
+	 */
+	async processLargeDataset(data, config, onProgress) {
+		const { operation, operationConfig } = config;
+		const chunks = this._chunkData(data, this.config.chunkSize);
+		const totalChunks = chunks.length;
+		const results = [];
+
+		// Process chunks in batches to avoid overwhelming the worker pool
+		const batchSize = this.config.maxWorkers;
+		for (let i = 0; i < chunks.length; i += batchSize) {
+			const batch = chunks.slice(i, i + batchSize);
+			const batchResults = await this.pool.executeAll(
+				batch.map((chunk) => ({
+					operation,
+					data: chunk,
+					config: operationConfig,
+				}))
+			);
+			results.push(...batchResults);
+
+			if (onProgress) {
+				onProgress({
+					processed: Math.min(i + batchSize, totalChunks),
+					total: totalChunks,
+					percent: Math.round((Math.min(i + batchSize, totalChunks) / totalChunks) * 100),
+				});
+			}
+		}
+
+		return this._combineResults(results, operation);
+	}
+
+	/**
+	 * Combine results from chunked processing
+	 * @private
+	 * @param {Array} results - Chunk results
+	 * @param {string} operation - Operation type
+	 * @returns {any} Combined result
+	 */
+	_combineResults(results, operation) {
+		switch (operation) {
+			case 'filter':
+				return results.flat();
+			case 'aggregate':
+				return results.reduce((a, b) => a + b, 0);
+			case 'statistics':
+				return this._combineStatistics(results);
+			default:
+				return results;
+		}
+	}
+
+	/**
+	 * Get processor statistics
+	 * @returns {Object} Statistics
+	 */
+	getStats() {
+		return this.pool.getStats();
+	}
+
+	/**
+	 * Terminate the processor and clean up resources
+	 */
+	terminate() {
+		terminateWorkerPool();
+	}
+}
+
+// Singleton instance
+let globalProcessor = null;
+
+/**
+ * Get or create global data processor
+ * @param {Object} config - Processor configuration
+ * @returns {DataProcessor} Global processor instance
+ */
+export function getDataProcessor(config = {}) {
+	if (!globalProcessor) {
+		globalProcessor = new DataProcessor(config);
+	}
+	return globalProcessor;
+}
+
+/**
+ * Terminate global data processor
+ */
+export function terminateDataProcessor() {
+	if (globalProcessor) {
+		globalProcessor.terminate();
+		globalProcessor = null;
+	}
+}
+
+// Convenience functions for common operations
+
+/**
+ * Aggregate data using workers
+ * @param {Array} data - Input data
+ * @param {Object} config - Aggregation config
+ * @returns {Promise<number>} Aggregated value
+ */
+export function aggregateData(data, config) {
+	return getDataProcessor().aggregate(data, config);
+}
+
+/**
+ * Filter data using workers
+ * @param {Array} data - Input data
+ * @param {Object} criteria - Filter criteria
+ * @returns {Promise<Array>} Filtered data
+ */
+export function filterData(data, criteria) {
+	return getDataProcessor().filter(data, criteria);
+}
+
+/**
+ * Sort data using workers
+ * @param {Array} data - Input data
+ * @param {Object} sortConfig - Sort config
+ * @returns {Promise<Array>} Sorted data
+ */
+export function sortData(data, sortConfig) {
+	return getDataProcessor().sort(data, sortConfig);
+}
+
+/**
+ * Sample data for preview
+ * @param {Array} data - Input data
+ * @param {number} sampleSize - Sample size
+ * @returns {Promise<Array>} Sampled data
+ */
+export function sampleData(data, sampleSize) {
+	return getDataProcessor().sample(data, sampleSize);
+}
+
+/**
+ * Calculate statistics
+ * @param {Array} data - Input data
+ * @param {string} field - Field name
+ * @returns {Promise<Object>} Statistics
+ */
+export function calculateStatistics(data, field) {
+	return getDataProcessor().statistics(data, field);
+}
+
+export { DataProcessor };
+export default DataProcessor;