rename files from jupyter to pyodide · teonbrooks.com/BrainWaves@61a9349

+52

app/actions/pyodideActions.js

··· 1 + // ------------------------------------------------------------------------- 2 + // Action Types 3 + 4 + export const LAUNCH_KERNEL = 'LAUNCH_KERNEL'; 5 + export const REQUEST_KERNEL_INFO = 'REQUEST_KERNEL_INFO'; 6 + export const SEND_EXECUTE_REQUEST = 'SEND_EXECUTE_REQUEST'; 7 + export const LOAD_EPOCHS = 'LOAD_EPOCHS'; 8 + export const LOAD_CLEANED_EPOCHS = 'LOAD_CLEANED_EPOCHS'; 9 + export const LOAD_PSD = 'LOAD_PSD'; 10 + export const LOAD_ERP = 'LOAD_ERP'; 11 + export const LOAD_TOPO = 'LOAD_TOPO'; 12 + export const CLEAN_EPOCHS = 'CLEAN_EPOCHS'; 13 + export const CLOSE_KERNEL = 'CLOSE_KERNEL'; 14 + 15 + // ------------------------------------------------------------------------- 16 + // Actions 17 + 18 + export const launchKernel = () => ({ type: LAUNCH_KERNEL }); 19 + 20 + export const requestKernelInfo = () => ({ type: REQUEST_KERNEL_INFO }); 21 + 22 + export const sendExecuteRequest = (payload: string) => ({ 23 + payload, 24 + type: SEND_EXECUTE_REQUEST, 25 + }); 26 + 27 + export const loadEpochs = (payload: Array<string>) => ({ 28 + payload, 29 + type: LOAD_EPOCHS, 30 + }); 31 + 32 + export const loadCleanedEpochs = (payload: Array<string>) => ({ 33 + payload, 34 + type: LOAD_CLEANED_EPOCHS, 35 + }); 36 + 37 + export const loadPSD = () => ({ 38 + type: LOAD_PSD, 39 + }); 40 + 41 + export const loadERP = (payload: ?string) => ({ 42 + payload, 43 + type: LOAD_ERP, 44 + }); 45 + 46 + export const loadTopo = () => ({ 47 + type: LOAD_TOPO, 48 + }); 49 + 50 + export const cleanEpochs = () => ({ type: CLEAN_EPOCHS }); 51 + 52 + export const closeKernel = () => ({ type: CLOSE_KERNEL });

+412

app/epics/pyodideEpics.js

··· 1 + import { combineEpics } from 'redux-observable'; 2 + import { from, of } from 'rxjs'; 3 + import { map, mergeMap, tap, pluck, ignoreElements, filter, take } from 'rxjs/operators'; 4 + import { find } from 'kernelspecs'; 5 + import { launchSpec } from 'spawnteract'; 6 + import { createMainChannel } from 'enchannel-zmq-backend'; 7 + import { isNil } from 'lodash'; 8 + import { kernelInfoRequest, executeRequest } from '@nteract/messaging'; 9 + import { toast } from 'react-toastify'; 10 + import { getWorkspaceDir } from '../utils/filesystem/storage'; 11 + import { 12 + LAUNCH_KERNEL, 13 + REQUEST_KERNEL_INFO, 14 + LOAD_EPOCHS, 15 + LOAD_CLEANED_EPOCHS, 16 + LOAD_PSD, 17 + LOAD_ERP, 18 + LOAD_TOPO, 19 + CLEAN_EPOCHS, 20 + CLOSE_KERNEL, 21 + loadTopo, 22 + loadERP 23 + } from '../actions/pyodideActions'; 24 + import { 25 + imports, 26 + utils, 27 + loadCSV, 28 + loadCleanedEpochs, 29 + filterIIR, 30 + epochEvents, 31 + requestEpochsInfo, 32 + requestChannelInfo, 33 + cleanEpochsPlot, 34 + plotPSD, 35 + plotERP, 36 + plotTopoMap, 37 + saveEpochs 38 + } from '../utils/pyodide/commands'; 39 + import { 40 + EMOTIV_CHANNELS, 41 + EVENTS, 42 + DEVICES, 43 + MUSE_CHANNELS, 44 + JUPYTER_VARIABLE_NAMES, 45 + } from '../constants/constants'; 46 + import { 47 + parseSingleQuoteJSON, 48 + parseKernelStatus, 49 + debugParseMessage 50 + } from '../utils/pyodide/functions'; 51 + 52 + export const GET_EPOCHS_INFO = 'GET_EPOCHS_INFO'; 53 + export const GET_CHANNEL_INFO = 'GET_CHANNEL_INFO'; 54 + export const SET_KERNEL = 'SET_KERNEL'; 55 + export const SET_KERNEL_STATUS = 'SET_KERNEL_STATUS'; 56 + export const SET_KERNEL_INFO = 'SET_KERNEL_INFO'; 57 + export const SET_MAIN_CHANNEL = 'SET_MAIN_CHANNEL'; 58 + export const SET_EPOCH_INFO = 'SET_EPOCH_INFO'; 59 + export const SET_CHANNEL_INFO = 'SET_CHANNEL_INFO'; 60 + export const SET_PSD_PLOT = 'SET_PSD_PLOT'; 61 + export const SET_ERP_PLOT = 'SET_ERP_PLOT'; 62 + export const SET_TOPO_PLOT = 'SET_TOPO_PLOT'; 63 + export const RECEIVE_EXECUTE_REPLY = 'RECEIVE_EXECUTE_REPLY'; 64 + export const RECEIVE_EXECUTE_RESULT = 'RECEIVE_EXECUTE_RESULT'; 65 + export const RECEIVE_STREAM = 'RECEIVE_STREAM'; 66 + export const RECEIVE_DISPLAY_DATA = 'RECEIVE_DISPLAY_DATA'; 67 + 68 + // ------------------------------------------------------------------------- 69 + // Action Creators 70 + 71 + const getEpochsInfo = (payload) => ({ payload, type: GET_EPOCHS_INFO }); 72 + 73 + const getChannelInfo = () => ({ type: GET_CHANNEL_INFO }); 74 + 75 + const setKernel = (payload) => ({ 76 + payload, 77 + type: SET_KERNEL, 78 + }); 79 + 80 + const setKernelStatus = (payload) => ({ 81 + payload, 82 + type: SET_KERNEL_STATUS, 83 + }); 84 + 85 + const setKernelInfo = (payload) => ({ 86 + payload, 87 + type: SET_KERNEL_INFO, 88 + }); 89 + 90 + const setMainChannel = (payload) => ({ 91 + payload, 92 + type: SET_MAIN_CHANNEL, 93 + }); 94 + 95 + const setEpochInfo = (payload) => ({ 96 + payload, 97 + type: SET_EPOCH_INFO, 98 + }); 99 + 100 + const setChannelInfo = (payload) => ({ 101 + payload, 102 + type: SET_CHANNEL_INFO, 103 + }); 104 + 105 + const setPSDPlot = (payload) => ({ 106 + payload, 107 + type: SET_PSD_PLOT, 108 + }); 109 + 110 + const setTopoPlot = (payload) => ({ 111 + payload, 112 + type: SET_TOPO_PLOT, 113 + }); 114 + 115 + const setERPPlot = (payload) => ({ 116 + payload, 117 + type: SET_ERP_PLOT, 118 + }); 119 + 120 + const receiveExecuteReply = (payload) => ({ 121 + payload, 122 + type: RECEIVE_EXECUTE_REPLY, 123 + }); 124 + 125 + const receiveExecuteResult = (payload) => ({ 126 + payload, 127 + type: RECEIVE_EXECUTE_RESULT, 128 + }); 129 + 130 + const receiveDisplayData = (payload) => ({ 131 + payload, 132 + type: RECEIVE_DISPLAY_DATA, 133 + }); 134 + 135 + const receiveStream = (payload) => ({ 136 + payload, 137 + type: RECEIVE_STREAM, 138 + }); 139 + 140 + // ------------------------------------------------------------------------- 141 + // Epics 142 + 143 + const launchEpic = (action$) => 144 + action$.ofType(LAUNCH_KERNEL).pipe( 145 + mergeMap(() => from(find('brainwaves'))), 146 + tap((kernelInfo) => { 147 + if (isNil(kernelInfo)) { 148 + toast.error("Could not find 'brainwaves' jupyter kernel. Have you installed Python?"); 149 + } 150 + }), 151 + filter((kernelInfo) => !isNil(kernelInfo)), 152 + mergeMap((kernelInfo) => 153 + from( 154 + launchSpec(kernelInfo.spec, { 155 + // No STDIN, opt in to STDOUT and STDERR as node streams 156 + stdio: ['ignore', 'pipe', 'pipe'], 157 + }) 158 + ) 159 + ), 160 + tap((kernel) => { 161 + // Route everything that we won't get in messages to our own stdout 162 + kernel.spawn.stdout.on('data', (data) => { 163 + const text = data.toString(); 164 + console.log('KERNEL STDOUT: ', text); 165 + }); 166 + kernel.spawn.stderr.on('data', (data) => { 167 + const text = data.toString(); 168 + console.log('KERNEL STDERR: ', text); 169 + toast.error('Jupyter: ', text); 170 + }); 171 + 172 + kernel.spawn.on('close', () => { 173 + console.log('Kernel closed'); 174 + }); 175 + }), 176 + map(setKernel) 177 + ); 178 + 179 + const setUpChannelEpic = (action$) => 180 + action$.ofType(SET_KERNEL).pipe( 181 + pluck('payload'), 182 + mergeMap((kernel) => from(createMainChannel(kernel.config))), 183 + tap((mainChannel) => mainChannel.next(executeRequest(imports()))), 184 + tap((mainChannel) => mainChannel.next(executeRequest(utils()))), 185 + map(setMainChannel) 186 + ); 187 + 188 + const receiveChannelMessageEpic = (action$, state$) => 189 + action$.ofType(SET_MAIN_CHANNEL).pipe( 190 + mergeMap(() => 191 + state$.value.jupyter.mainChannel.pipe( 192 + map((msg) => { 193 + console.log(debugParseMessage(msg)); 194 + switch (msg['header']['msg_type']) { 195 + case 'kernel_info_reply': 196 + return setKernelInfo(msg); 197 + case 'status': 198 + return setKernelStatus(parseKernelStatus(msg)); 199 + case 'stream': 200 + return receiveStream(msg); 201 + case 'execute_reply': 202 + return receiveExecuteReply(msg); 203 + case 'execute_result': 204 + return receiveExecuteResult(msg); 205 + case 'display_data': 206 + return receiveDisplayData(msg); 207 + default: 208 + } 209 + }), 210 + filter((action) => !isNil(action)) 211 + ) 212 + ) 213 + ); 214 + 215 + const requestKernelInfoEpic = (action$, state$) => 216 + action$.ofType(REQUEST_KERNEL_INFO).pipe( 217 + filter(() => state$.value.jupyter.mainChannel), 218 + map(() => state$.value.jupyter.mainChannel.next(kernelInfoRequest())), 219 + ignoreElements() 220 + ); 221 + 222 + const loadEpochsEpic = (action$, state$) => 223 + action$.ofType(LOAD_EPOCHS).pipe( 224 + pluck('payload'), 225 + filter((filePathsArray) => filePathsArray.length >= 1), 226 + map((filePathsArray) => 227 + state$.value.jupyter.mainChannel.next(executeRequest(loadCSV(filePathsArray))) 228 + ), 229 + awaitOkMessage(action$), 230 + execute(filterIIR(1, 30), state$), 231 + awaitOkMessage(action$), 232 + map(() => 233 + epochEvents( 234 + { 235 + [state$.value.experiment.params.stimulus1.title]: EVENTS.STIMULUS_1, 236 + [state$.value.experiment.params.stimulus2.title]: EVENTS.STIMULUS_2, 237 + [state$.value.experiment.params.stimulus3.title]: EVENTS.STIMULUS_3, 238 + [state$.value.experiment.params.stimulus4.title]: EVENTS.STIMULUS_4, 239 + }, 240 + -0.1, 241 + 0.8 242 + ) 243 + ), 244 + tap((e)=> {console.log('e', e)}), 245 + map((epochEventsCommand) => 246 + state$.value.jupyter.mainChannel.next(executeRequest(epochEventsCommand)) 247 + ), 248 + awaitOkMessage(action$), 249 + map(() => getEpochsInfo(JUPYTER_VARIABLE_NAMES.RAW_EPOCHS)) 250 + ); 251 + 252 + const loadCleanedEpochsEpic = (action$, state$) => 253 + action$.ofType(LOAD_CLEANED_EPOCHS).pipe( 254 + pluck('payload'), 255 + filter((filePathsArray) => filePathsArray.length >= 1), 256 + map((filePathsArray) => 257 + state$.value.jupyter.mainChannel.next(executeRequest(loadCleanedEpochs(filePathsArray))) 258 + ), 259 + awaitOkMessage(action$), 260 + mergeMap(() => 261 + of(getEpochsInfo(JUPYTER_VARIABLE_NAMES.CLEAN_EPOCHS), getChannelInfo(), loadTopo()) 262 + ) 263 + ); 264 + 265 + const cleanEpochsEpic = (action$, state$) => 266 + action$.ofType(CLEAN_EPOCHS).pipe( 267 + execute(cleanEpochsPlot(), state$), 268 + mergeMap(() => 269 + action$.ofType(RECEIVE_STREAM).pipe( 270 + pluck('payload'), 271 + filter( 272 + (msg) => msg.channel === 'iopub' && msg.content.text.includes('Channels marked as bad') 273 + ), 274 + take(1) 275 + ) 276 + ), 277 + map(() => 278 + state$.value.jupyter.mainChannel.next( 279 + executeRequest( 280 + saveEpochs( 281 + getWorkspaceDir(state$.value.experiment.title), 282 + state$.value.experiment.subject 283 + ) 284 + ) 285 + ) 286 + ), 287 + awaitOkMessage(action$), 288 + map(() => getEpochsInfo(JUPYTER_VARIABLE_NAMES.RAW_EPOCHS)) 289 + ); 290 + 291 + const getEpochsInfoEpic = (action$, state$) => 292 + action$.ofType(GET_EPOCHS_INFO).pipe( 293 + pluck('payload'), 294 + map((variableName) => 295 + state$.value.jupyter.mainChannel.next(executeRequest(requestEpochsInfo(variableName))) 296 + ), 297 + mergeMap(() => 298 + action$.ofType(RECEIVE_EXECUTE_RESULT).pipe( 299 + pluck('payload'), 300 + filter((msg) => msg.channel === 'iopub' && !isNil(msg.content.data)), 301 + pluck('content', 'data', 'text/plain'), 302 + filter((msg) => msg.includes('Drop Percentage')), 303 + take(1) 304 + ) 305 + ), 306 + map((epochInfoString) => 307 + parseSingleQuoteJSON(epochInfoString).map((infoObj) => ({ 308 + name: Object.keys(infoObj)[0], 309 + value: infoObj[Object.keys(infoObj)[0]], 310 + })) 311 + ), 312 + map(setEpochInfo) 313 + ); 314 + 315 + const getChannelInfoEpic = (action$, state$) => 316 + action$.ofType(GET_CHANNEL_INFO).pipe( 317 + execute(requestChannelInfo(), state$), 318 + mergeMap(() => 319 + action$.ofType(RECEIVE_EXECUTE_RESULT).pipe( 320 + pluck('payload'), 321 + filter((msg) => msg.channel === 'iopub' && !isNil(msg.content.data)), 322 + pluck('content', 'data', 'text/plain'), 323 + // Filter to prevent this from reading requestEpochsInfo returns 324 + filter((msg) => !msg.includes('Drop Percentage')), 325 + take(1) 326 + ) 327 + ), 328 + map((channelInfoString) => setChannelInfo(parseSingleQuoteJSON(channelInfoString))) 329 + ); 330 + 331 + const loadPSDEpic = (action$, state$) => 332 + action$.ofType(LOAD_PSD).pipe( 333 + execute(plotPSD(), state$), 334 + mergeMap(() => 335 + action$.ofType(RECEIVE_DISPLAY_DATA).pipe( 336 + pluck('payload'), 337 + // PSD graphs should have two axes 338 + filter((msg) => msg.content.data['text/plain'].includes('2 Axes')), 339 + pluck('content', 'data'), 340 + take(1) 341 + ) 342 + ), 343 + map(setPSDPlot) 344 + ); 345 + 346 + const loadTopoEpic = (action$, state$) => 347 + action$.ofType(LOAD_TOPO).pipe( 348 + execute(plotTopoMap(), state$), 349 + mergeMap(() => 350 + action$.ofType(RECEIVE_DISPLAY_DATA).pipe(pluck('payload'), pluck('content', 'data'), take(1)) 351 + ), 352 + mergeMap((topoPlot) => 353 + of( 354 + setTopoPlot(topoPlot), 355 + loadERP( 356 + state$.value.device.deviceType === DEVICES.EMOTIV ? EMOTIV_CHANNELS[0] : MUSE_CHANNELS[0] 357 + ) 358 + ) 359 + ) 360 + ); 361 + 362 + const loadERPEpic = (action$, state$) => 363 + action$.ofType(LOAD_ERP).pipe( 364 + pluck('payload'), 365 + map((channelName) => { 366 + if (MUSE_CHANNELS.includes(channelName)) { 367 + return MUSE_CHANNELS.indexOf(channelName); 368 + } else if (EMOTIV_CHANNELS.includes(channelName)) { 369 + return EMOTIV_CHANNELS.indexOf(channelName); 370 + } 371 + console.warn('channel name supplied to loadERPEpic does not belong to either device'); 372 + return EMOTIV_CHANNELS[0]; 373 + }), 374 + map((channelIndex) => 375 + state$.value.jupyter.mainChannel.next(executeRequest(plotERP(channelIndex))) 376 + ), 377 + mergeMap(() => 378 + action$.ofType(RECEIVE_DISPLAY_DATA).pipe( 379 + pluck('payload'), 380 + // ERP graphs should have 1 axis according to MNE 381 + filter((msg) => msg.content.data['text/plain'].includes('1 Axes')), 382 + pluck('content', 'data'), 383 + take(1) 384 + ) 385 + ), 386 + map(setERPPlot) 387 + ); 388 + 389 + const closeKernelEpic = (action$, state$) => 390 + action$.ofType(CLOSE_KERNEL).pipe( 391 + map(() => { 392 + state$.value.jupyter.kernel.spawn.kill(); 393 + state$.value.jupyter.mainChannel.complete(); 394 + }), 395 + ignoreElements() 396 + ); 397 + 398 + export default combineEpics( 399 + launchEpic, 400 + setUpChannelEpic, 401 + requestKernelInfoEpic, 402 + receiveChannelMessageEpic, 403 + loadEpochsEpic, 404 + loadCleanedEpochsEpic, 405 + cleanEpochsEpic, 406 + getEpochsInfoEpic, 407 + getChannelInfoEpic, 408 + loadPSDEpic, 409 + loadTopoEpic, 410 + loadERPEpic, 411 + closeKernelEpic 412 + );

+107

app/reducers/pyodideReducer.js

··· 1 + // @flow 2 + import { 3 + SET_KERNEL, 4 + SET_KERNEL_STATUS, 5 + SET_MAIN_CHANNEL, 6 + SET_KERNEL_INFO, 7 + SET_EPOCH_INFO, 8 + SET_CHANNEL_INFO, 9 + SET_PSD_PLOT, 10 + SET_TOPO_PLOT, 11 + SET_ERP_PLOT, 12 + RECEIVE_EXECUTE_RETURN 13 + } from '../epics/pyodideEpics'; 14 + import { ActionType, Kernel } from '../constants/interfaces'; 15 + import { KERNEL_STATUS } from '../constants/constants'; 16 + import { EXPERIMENT_CLEANUP } from '../epics/experimentEpics'; 17 + 18 + export interface JupyterStateType { 19 + +kernel: ?Kernel; 20 + +kernelStatus: KERNEL_STATUS; 21 + +mainChannel: ?any; 22 + +epochsInfo: ?Array<{ [string]: number | string }>; 23 + +channelInfo: ?Array<string>; 24 + +psdPlot: ?{ [string]: string }; 25 + +topoPlot: ?{ [string]: string }; 26 + +erpPlot: ?{ [string]: string }; 27 + } 28 + 29 + const initialState = { 30 + kernel: null, 31 + kernelStatus: KERNEL_STATUS.OFFLINE, 32 + mainChannel: null, 33 + epochsInfo: null, 34 + channelInfo: [], 35 + psdPlot: null, 36 + topoPlot: null, 37 + erpPlot: null, 38 + }; 39 + 40 + export default function jupyter(state: JupyterStateType = initialState, action: ActionType) { 41 + switch (action.type) { 42 + case SET_KERNEL: 43 + return { 44 + ...state, 45 + kernel: action.payload, 46 + }; 47 + 48 + case SET_KERNEL_STATUS: 49 + return { 50 + ...state, 51 + kernelStatus: action.payload, 52 + }; 53 + 54 + case SET_MAIN_CHANNEL: 55 + return { 56 + ...state, 57 + mainChannel: action.payload, 58 + }; 59 + 60 + case SET_KERNEL_INFO: 61 + return state; 62 + 63 + case SET_EPOCH_INFO: 64 + return { 65 + ...state, 66 + epochsInfo: action.payload, 67 + }; 68 + 69 + case SET_CHANNEL_INFO: 70 + return { 71 + ...state, 72 + channelInfo: action.payload, 73 + }; 74 + 75 + case SET_PSD_PLOT: 76 + return { 77 + ...state, 78 + psdPlot: action.payload, 79 + }; 80 + 81 + case SET_TOPO_PLOT: 82 + return { 83 + ...state, 84 + topoPlot: action.payload, 85 + }; 86 + 87 + case SET_ERP_PLOT: 88 + return { 89 + ...state, 90 + erpPlot: action.payload, 91 + }; 92 + 93 + case EXPERIMENT_CLEANUP: 94 + return { 95 + ...state, 96 + epochsInfo: null, 97 + psdPlot: null, 98 + erpPlot: null, 99 + }; 100 + 101 + case RECEIVE_EXECUTE_RETURN: 102 + return state; 103 + 104 + default: 105 + return state; 106 + } 107 + }

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