Tidyed up pyodide files and removed some jupyter dependencies

+38 -40

app/epics/pyodideEpics.js

··· 1 - import { combineEpics } from "redux-observable"; 2 - import { of } from "rxjs"; 3 - import { 4 - map, 5 - mergeMap, 6 - tap, 7 - pluck, 8 - filter 9 - } from "rxjs/operators"; 10 - import { getWorkspaceDir } from "../utils/filesystem/storage"; 11 - import { parseSingleQuoteJSON } from "../utils/pyodide/functions" 12 - import { readFiles } from "../utils/filesystem/read"; 1 + import { combineEpics } from 'redux-observable'; 2 + import { of } from 'rxjs'; 3 + import { map, mergeMap, tap, pluck, filter } from 'rxjs/operators'; 4 + import { getWorkspaceDir } from '../utils/filesystem/storage'; 5 + import { parseSingleQuoteJSON } from '../utils/pyodide/functions'; 6 + import { readFiles } from '../utils/filesystem/read'; 13 7 import { 14 8 LAUNCH, 15 9 LOAD_EPOCHS, ··· 20 14 CLEAN_EPOCHS, 21 15 loadTopo, 22 16 loadERP 23 - } from "../actions/pyodideActions"; 17 + } from '../actions/pyodideActions'; 24 18 import { 25 19 loadPackages, 26 20 utils, ··· 34 28 plotPSD, 35 29 plotERP, 36 30 plotTopoMap, 37 - saveEpochs, 38 - } from "../utils/pyodide/commands"; 31 + saveEpochs 32 + } from '../utils/pyodide'; 39 33 import { 40 34 EMOTIV_CHANNELS, 41 35 EVENTS, ··· 43 37 MUSE_CHANNELS, 44 38 PYODIDE_VARIABLE_NAMES, 45 39 PYODIDE_STATUS 46 - } from "../constants/constants"; 40 + } from '../constants/constants'; 47 41 48 - export const GET_EPOCHS_INFO = "GET_EPOCHS_INFO"; 49 - export const GET_CHANNEL_INFO = "GET_CHANNEL_INFO"; 50 - export const SET_MAIN_CHANNEL = "SET_MAIN_CHANNEL"; 51 - export const SET_EPOCH_INFO = "SET_EPOCH_INFO"; 52 - export const SET_CHANNEL_INFO = "SET_CHANNEL_INFO"; 53 - export const SET_PSD_PLOT = "SET_PSD_PLOT"; 54 - export const SET_ERP_PLOT = "SET_ERP_PLOT"; 55 - export const SET_TOPO_PLOT = "SET_TOPO_PLOT"; 56 - export const SET_PYODIDE_STATUS = "SET_PYODIDE_STATUS"; 57 - export const RECEIVE_EXECUTE_REPLY = "RECEIVE_EXECUTE_REPLY"; 58 - export const RECEIVE_EXECUTE_RESULT = "RECEIVE_EXECUTE_RESULT"; 59 - export const RECEIVE_STREAM = "RECEIVE_STREAM"; 60 - export const RECEIVE_DISPLAY_DATA = "RECEIVE_DISPLAY_DATA"; 42 + export const GET_EPOCHS_INFO = 'GET_EPOCHS_INFO'; 43 + export const GET_CHANNEL_INFO = 'GET_CHANNEL_INFO'; 44 + export const SET_MAIN_CHANNEL = 'SET_MAIN_CHANNEL'; 45 + export const SET_EPOCH_INFO = 'SET_EPOCH_INFO'; 46 + export const SET_CHANNEL_INFO = 'SET_CHANNEL_INFO'; 47 + export const SET_PSD_PLOT = 'SET_PSD_PLOT'; 48 + export const SET_ERP_PLOT = 'SET_ERP_PLOT'; 49 + export const SET_TOPO_PLOT = 'SET_TOPO_PLOT'; 50 + export const SET_PYODIDE_STATUS = 'SET_PYODIDE_STATUS'; 51 + export const RECEIVE_EXECUTE_REPLY = 'RECEIVE_EXECUTE_REPLY'; 52 + export const RECEIVE_EXECUTE_RESULT = 'RECEIVE_EXECUTE_RESULT'; 53 + export const RECEIVE_STREAM = 'RECEIVE_STREAM'; 54 + export const RECEIVE_DISPLAY_DATA = 'RECEIVE_DISPLAY_DATA'; 61 55 62 56 // ------------------------------------------------------------------------- 63 57 // Action Creators ··· 101 95 102 96 const launchEpic = action$ => 103 97 action$.ofType(LAUNCH).pipe( 104 - tap(() => console.log("launching")), 98 + tap(() => console.log('launching')), 105 99 mergeMap(loadPackages), 106 100 mergeMap(utils), 107 101 map(() => setPyodideStatus(PYODIDE_STATUS.LOADED)) ··· 109 103 110 104 const loadEpochsEpic = (action$, state$) => 111 105 action$.ofType(LOAD_EPOCHS).pipe( 112 - pluck("payload"), 106 + pluck('payload'), 113 107 filter(filePathsArray => filePathsArray.length >= 1), 114 108 tap(files => console.log('files:', files)), 115 - map((filePathsArray => readFiles(filePathsArray))), 109 + map(filePathsArray => readFiles(filePathsArray)), 116 110 tap(csvArray => console.log('csvs:', csvArray)), 117 111 mergeMap(csvArray => loadCSV(csvArray)), 118 112 mergeMap(() => filterIIR(1, 30)), ··· 131 125 map(() => getEpochsInfo(PYODIDE_VARIABLE_NAMES.RAW_EPOCHS)) 132 126 ); 133 127 134 - const loadCleanedEpochsEpic = (action$) => 128 + const loadCleanedEpochsEpic = action$ => 135 129 action$.ofType(LOAD_CLEANED_EPOCHS).pipe( 136 - pluck("payload"), 130 + pluck('payload'), 137 131 filter(filePathsArray => filePathsArray.length >= 1), 138 132 map(filePathsArray => loadCleanedEpochs(filePathsArray)), 139 133 mergeMap(() => ··· 157 151 map(() => getEpochsInfo(PYODIDE_VARIABLE_NAMES.RAW_EPOCHS)) 158 152 ); 159 153 160 - const getEpochsInfoEpic = (action$) => 154 + const getEpochsInfoEpic = action$ => 161 155 action$.ofType(GET_EPOCHS_INFO).pipe( 162 - pluck("payload"), 156 + pluck('payload'), 163 157 tap(payload => console.log('payload: ', payload)), 164 158 mergeMap(requestEpochsInfo), 165 159 map(epochInfoArray => ··· 171 165 map(setEpochInfo) 172 166 ); 173 167 174 - const getChannelInfoEpic = (action$, state$) => 168 + const getChannelInfoEpic = action$ => 175 169 action$.ofType(GET_CHANNEL_INFO).pipe( 176 170 map(requestChannelInfo), 177 171 map(channelInfoString => ··· 179 173 ) 180 174 ); 181 175 182 - const loadPSDEpic = (action$, state$) => 176 + const loadPSDEpic = action$ => 183 177 action$.ofType(LOAD_PSD).pipe( 184 178 map(plotPSD), 185 179 map(setPSDPlot) ··· 198 192 ) 199 193 ); 200 194 201 - const loadERPEpic = (action$, state$) => 195 + const loadERPEpic = action$ => 202 196 action$.ofType(LOAD_ERP).pipe( 197 + <<<<<<< HEAD 203 198 <<<<<<< HEAD 204 199 pluck('payload'), 205 200 map((channelName) => { 206 201 ======= 207 202 pluck("payload"), 203 + ======= 204 + pluck('payload'), 205 + >>>>>>> Tidyed up pyodide files and removed some jupyter dependencies 208 206 map(channelName => { 209 207 >>>>>>> Added loading of pyodide within app epics 210 208 if (MUSE_CHANNELS.includes(channelName)) { ··· 216 214 console.warn('channel name supplied to loadERPEpic does not belong to either device'); 217 215 ======= 218 216 console.warn( 219 - "channel name supplied to loadERPEpic does not belong to either device" 217 + 'channel name supplied to loadERPEpic does not belong to either device' 220 218 ); 221 219 >>>>>>> Added loading of pyodide within app epics 222 220 return EMOTIV_CHANNELS[0];

+1 -4

app/package.json

··· 19 19 "@neurosity/pipes": "^3.2.3", 20 20 "@babel/runtime": "7.10.2", 21 21 "@babel/runtime-corejs2": "^7.10.2", 22 - "enchannel-zmq-backend": "^9.1.22", 23 - "kernelspecs": "^2.0.0", 24 - "node-pre-gyp": "^0.15.0", 25 - "spawnteract": "^5.0.1" 22 + "node-pre-gyp": "^0.15.0" 26 23 }, 27 24 "devDependencies": { 28 25 "@babel/register": "^7.10.1"

-95

app/utils/pyodide/commands.js

··· 1 - import * as path from "path"; 2 - import { readFileSync } from "fs"; 3 - import { languagePluginLoader } from "./pyodide"; 4 - 5 - 6 - let pyodide; 7 - // ----------------------------- 8 - // Imports and Utility functions 9 - 10 - export const loadPackages = async () => { 11 - await languagePluginLoader; 12 - console.log("loaded language plugin"); 13 - // using window.pyodide instead of pyodide to get linter to stop yelling ;) 14 - await window.pyodide.loadPackage(["matplotlib", "mne", "pandas"]); 15 - await window.pyodide.runPython("import js"); 16 - console.log("loaded mne package"); 17 - 18 - } 19 - 20 - export const utils = async () => 21 - window.pyodide.runPython( 22 - readFileSync(path.join(__dirname, "/utils/pyodide/utils.py"), "utf8") 23 - ); 24 - 25 - export const loadCSV = async (csvArray: Array<any>) => { 26 - window.csvArray = csvArray; 27 - // TODO: Pass attached variable name as parameter to load_data 28 - await window.pyodide.runPython( 29 - `raw = load_data()`) 30 - } 31 - 32 - // --------------------------- 33 - // MNE-Related Data Processing 34 - export const loadCleanedEpochs = (epocsArray: Array<any>) => 35 - [ 36 - `clean_epochs = concatenate_epochs([read_epochs(file) for file in files])`, 37 - `conditions = OrderedDict({key: [value] for (key, value) in clean_epochs.event_id.items()})` 38 - ].join("\n"); 39 - 40 - // NOTE: this command includes a ';' to prevent returning data 41 - export const filterIIR = async (lowCutoff: number, highCutoff: number) => 42 - window.pyodide.runPython(`raw.filter(${lowCutoff}, ${highCutoff}, method='iir');`) 43 - 44 - export const epochEvents = async ( 45 - eventIDs: { [string]: number }, 46 - tmin: number, 47 - tmax: number, 48 - reject?: Array<string> | string = "None" 49 - ) => window.pyodide.runPython([ 50 - `event_id = ${JSON.stringify(eventIDs)}`, 51 - `tmin=${tmin}`, 52 - `tmax=${tmax}`, 53 - `baseline= (tmin, tmax)`, 54 - `picks = None`, 55 - `reject = ${reject}`, 56 - "events = find_events(raw)", 57 - `raw_epochs = Epochs(raw, events=events, event_id=event_id, 58 - tmin=tmin, tmax=tmax, baseline=baseline, reject=reject, preload=True, 59 - verbose=False, picks=picks)`, 60 - `conditions = OrderedDict({key: [value] for (key, value) in raw_epochs.event_id.items()})` 61 - ].join("\n")) 62 - 63 - export const requestEpochsInfo = async (variableName: string) => { 64 - const pyodideReturn = await window.pyodide.runPython(`get_epochs_info(${variableName})`); 65 - return pyodideReturn 66 - } 67 - 68 - export const requestChannelInfo = () => 69 - `[ch for ch in clean_epochs.ch_names if ch != 'Marker']`; 70 - 71 - // ----------------------------- 72 - // Plot functions 73 - 74 - export const cleanEpochsPlot = () => 75 - `raw_epochs.plot(scalings='auto', n_epochs=6, title="Clean Data", events=None)`; 76 - 77 - export const plotPSD = () => `raw.plot_psd(fmin=1, fmax=30)`; 78 - 79 - export const plotTopoMap = () => `plot_topo(clean_epochs, conditions)`; 80 - 81 - export const plotERP = (channelIndex: number) => 82 - `X, y = plot_conditions(clean_epochs, ch_ind=${channelIndex}, conditions=conditions, 83 - ci=97.5, n_boot=1000, title='', diff_waveform=None)`; 84 - 85 - export const saveEpochs = (workspaceDir: string, subject: string) => 86 - `raw_epochs.save(${formatFilePath( 87 - path.join( 88 - workspaceDir, 89 - "Data", 90 - subject, 91 - "EEG", 92 - `${subject}-cleaned-epo.fif` 93 - ) 94 - )})`; 95 -

+6

app/utils/pyodide/functions.js

··· 1 + // ------------------------------------------- 2 + // Helper & utility functions 3 + 1 4 export const parseSingleQuoteJSON = (string: string) => 2 5 JSON.parse(string.replace(/'/g, '"')); 3 6 ··· 31 34 } 32 35 return `${msg.channel} ${content}`; 33 36 }; 37 + 38 + export const formatFilePath = (filePath: string) => 39 + `"${filePath.replace(/\\/g, '/')}"`;

+118

app/utils/pyodide/index.js

··· 1 + import * as path from 'path'; 2 + import { readFileSync } from 'fs'; 3 + import { languagePluginLoader } from './pyodide'; 4 + import { formatFilePath } from './functions'; 5 + 6 + // --------------------------------- 7 + // This file contains the JS functions that allow the app to access python-wasm through pyodide 8 + // These functions wrap the python strings defined in the 9 + 10 + // ----------------------------- 11 + // Imports and Utility functions 12 + 13 + // Note: this takes an incredibly long time 14 + export const loadPackages = async () => { 15 + await languagePluginLoader; 16 + console.log('loaded language plugin'); 17 + // using window.pyodide instead of pyodide to get linter to stop yelling ;) 18 + await window.pyodide.loadPackage(['matplotlib', 'mne', 'pandas']); 19 + await window.pyodide.runPython('import js'); 20 + console.log('loaded mne package'); 21 + }; 22 + 23 + export const loadUtils = async () => 24 + window.pyodide.runPython( 25 + readFileSync(path.join(__dirname, '/utils/pyodide/utils.py'), 'utf8') 26 + ); 27 + 28 + export const loadCSV = async (csvArray: Array<any>) => { 29 + window.csvArray = csvArray; 30 + // TODO: Pass attached variable name as parameter to load_data 31 + await window.pyodide.runPython(`raw = load_data()`); 32 + }; 33 + 34 + // --------------------------- 35 + // MNE-Related Data Processing 36 + 37 + // export const loadCleanedEpochs = (epocsArray: Array<any>) => 38 + // [ 39 + // `clean_epochs = concatenate_epochs([read_epochs(file) for file in files])`, 40 + // `conditions = OrderedDict({key: [value] for (key, value) in clean_epochs.event_id.items()})` 41 + // ].join("\n"); 42 + 43 + // NOTE: this command includes a ';' to prevent returning data 44 + export const filterIIR = async (lowCutoff: number, highCutoff: number) => 45 + window.pyodide.runPython( 46 + `raw.filter(${lowCutoff}, ${highCutoff}, method='iir');` 47 + ); 48 + 49 + export const epochEvents = async ( 50 + eventIDs: { [string]: number }, 51 + tmin: number, 52 + tmax: number, 53 + reject?: Array<string> | string = 'None' 54 + ) => 55 + window.pyodide.runPython( 56 + [ 57 + `event_id = ${JSON.stringify(eventIDs)}`, 58 + `tmin=${tmin}`, 59 + `tmax=${tmax}`, 60 + `baseline= (tmin, tmax)`, 61 + `picks = None`, 62 + `reject = ${reject}`, 63 + 'events = find_events(raw)', 64 + `raw_epochs = Epochs(raw, events=events, event_id=event_id, 65 + tmin=tmin, tmax=tmax, baseline=baseline, reject=reject, preload=True, 66 + verbose=False, picks=picks)`, 67 + `conditions = OrderedDict({key: [value] for (key, value) in raw_epochs.event_id.items()})` 68 + ].join('\n') 69 + ); 70 + 71 + export const requestEpochsInfo = async (variableName: string) => { 72 + const pyodideReturn = await window.pyodide.runPython( 73 + `get_epochs_info(${variableName})` 74 + ); 75 + return pyodideReturn; 76 + }; 77 + 78 + export const requestChannelInfo = async () => 79 + window.pyodide.runPython( 80 + `[ch for ch in clean_epochs.ch_names if ch != 'Marker']` 81 + ); 82 + 83 + // ----------------------------- 84 + // Plot functions 85 + 86 + export const cleanEpochsPlot = async () => { 87 + // TODO: Figure out how to get image results from pyodide 88 + window.pyodide.runPython( 89 + `raw_epochs.plot(scalings='auto', n_epochs=6, title="Clean Data", events=None)` 90 + ); 91 + }; 92 + 93 + export const plotPSD = async () => { 94 + // TODO: Figure out how to get image results from pyodide 95 + window.pyodide.runPython(`raw.plot_psd(fmin=1, fmax=30)`); 96 + }; 97 + 98 + export const plotTopoMap = async () => { 99 + // TODO: Figure out how to get image results from pyodide 100 + window.pyodide.runPython(`plot_topo(clean_epochs, conditions)`); 101 + }; 102 + 103 + export const plotERP = (channelIndex: number) => 104 + `X, y = plot_conditions(clean_epochs, ch_ind=${channelIndex}, conditions=conditions, 105 + ci=97.5, n_boot=1000, title='', diff_waveform=None)`; 106 + 107 + export const saveEpochs = (workspaceDir: string, subject: string) => 108 + window.pyodide.runPython( 109 + `raw_epochs.save(${formatFilePath( 110 + path.join( 111 + workspaceDir, 112 + 'Data', 113 + subject, 114 + 'EEG', 115 + `${subject}-cleaned-epo.fif` 116 + ) 117 + )}` 118 + );

+84

app/utils/pyodide/pythonStrings.js

··· 1 + // DEPRECATED 2 + 3 + // import * as path from "path"; 4 + // import { readFileSync } from "fs"; 5 + 6 + // // The output of the functions contained in this file are python commands encoded as strings 7 + // // that would be run in a notebook environment in order to perform the experimental analyses underlying BrainWaves 8 + 9 + // export const utils = () => 10 + // readFileSync(path.join(__dirname, "/utils/pyodide/utils.py"), "utf8"); 11 + 12 + // // export const loadCSV = (filePathArray: Array<string>) => 13 + // // [ 14 + // // `files = [${filePathArray.map(filePath => formatFilePath(filePath))}]`, 15 + // // `replace_ch_names = None`, 16 + // // `raw = load_data(files, replace_ch_names)` 17 + // // ].join("\n"); 18 + 19 + // // export const loadCleanedEpochs = (filePathArray: Array<string>) => 20 + // // [ 21 + // // `files = [${filePathArray.map(filePath => formatFilePath(filePath))}]`, 22 + // // `clean_epochs = concatenate_epochs([read_epochs(file) for file in files])`, 23 + // // `conditions = OrderedDict({key: [value] for (key, value) in clean_epochs.event_id.items()})` 24 + // // ].join("\n"); 25 + 26 + // // NOTE: this command includes a ';' to prevent returning data 27 + // export const filterIIR = (lowCutoff: number, highCutoff: number) => 28 + // `raw.filter(${lowCutoff}, ${highCutoff}, method='iir');`; 29 + 30 + // export const plotPSD = () => 31 + // [`%matplotlib inline`, `raw.plot_psd(fmin=1, fmax=30)`].join("\n"); 32 + 33 + // export const epochEvents = ( 34 + // eventIDs: { [string]: number }, 35 + // tmin: number, 36 + // tmax: number, 37 + // reject?: Array<string> | string = "None" 38 + // ) => 39 + // [ 40 + // `event_id = ${JSON.stringify(eventIDs)}`, 41 + // `tmin=${tmin}`, 42 + // `tmax=${tmax}`, 43 + // `baseline= (tmin, tmax)`, 44 + // `picks = None`, 45 + // `reject = ${reject}`, 46 + // "events = find_events(raw)", 47 + // `raw_epochs = Epochs(raw, events=events, event_id=event_id, 48 + // tmin=tmin, tmax=tmax, baseline=baseline, reject=reject, preload=True, 49 + // verbose=False, picks=picks)`, 50 + // `conditions = OrderedDict({key: [value] for (key, value) in raw_epochs.event_id.items()})` 51 + // ].join("\n"); 52 + 53 + // export const requestEpochsInfo = (variableName: string) => 54 + // `get_epochs_info(${variableName})`; 55 + 56 + // export const requestChannelInfo = () => 57 + // `[ch for ch in clean_epochs.ch_names if ch != 'Marker']`; 58 + 59 + // export const cleanEpochsPlot = () => 60 + // [ 61 + // `%matplotlib`, 62 + // `raw_epochs.plot(scalings='auto', n_epochs=6, title="Clean Data", events=None)` 63 + // ].join("\n"); 64 + 65 + // export const plotTopoMap = () => 66 + // [`%matplotlib inline`, `plot_topo(clean_epochs, conditions)`].join("\n"); 67 + 68 + // export const plotERP = (channelIndex: number) => 69 + // [ 70 + // `%matplotlib inline`, 71 + // `X, y = plot_conditions(clean_epochs, ch_ind=${channelIndex}, conditions=conditions, 72 + // ci=97.5, n_boot=1000, title='', diff_waveform=None)` 73 + // ].join("\n"); 74 + 75 + // export const saveEpochs = (workspaceDir: string, subject: string) => 76 + // `raw_epochs.save(${formatFilePath( 77 + // path.join( 78 + // workspaceDir, 79 + // "Data", 80 + // subject, 81 + // "EEG", 82 + // `${subject}-cleaned-epo.fif` 83 + // ) 84 + // )})`;

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