Rename eeg2bids -> set2bids

laemtl · laemtl · commit 98e691ddfd36 · 2023-11-24T14:54:25.000-05:00
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-![EEG2BIDS Wizard](wiki/images/logo/EEG2bIDS_Wizard_(converter_tool).jpg)
+![SET2BIDS Wizard](wiki/images/logo/EEG2bIDS_Wizard_(converter_tool).jpg)
 
-EEG2BIDS Wizard is a GUI interface for iEEG to BIDS format and used with LORIS (Longitudinal Online Research and Imaging System). Users can use their LORIS credentials with a LORIS URL and automatically retrieve LORIS data for the EEG to BIDS format. Becareful to remove your login credentials after using EEG2BIDS on a shared computer!
+SET2BIDS Wizard is a GUI interface for iEEG to BIDS format and used with LORIS (Longitudinal Online Research and Imaging System). Users can use their LORIS credentials with a LORIS URL and automatically retrieve LORIS data for the EEG to BIDS format. Becareful to remove your login credentials after using SET2BIDS on a shared computer!
 
 ## Installation
 
diff --git a/build.ps1 b/build.ps1
@@ -1,6 +1,6 @@
 .\Scripts\activate
-pyinstaller --paths=python python/eeg2bids.py -D `
---name eeg2bids-service-windows `
+pyinstaller --paths=python python/set2bids.py -D `
+--name set2bids-service-windows `
 --add-data 'python/libs/bids_validator/rules/top_level_rules.json;./bids_validator/rules' `
 --add-data 'python/libs/bids_validator/rules/associated_data_rules.json;./bids_validator/rules' `
 --add-data 'python/libs/bids_validator/rules/file_level_rules.json;./bids_validator/rules' `
diff --git a/build.sh b/build.sh
@@ -1,6 +1,6 @@
 source bin/activate
-pyi-makespec --paths=python python/eeg2bids.py -w -D \
---name eeg2bids-service \
+pyi-makespec --paths=python python/set2bids.py -w -D \
+--name set2bids-service \
 --add-data 'python/libs/bids_validator/rules/top_level_rules.json:bids_validator/rules' \
 --add-data 'python/libs/bids_validator/rules/associated_data_rules.json:bids_validator/rules' \
 --add-data 'python/libs/bids_validator/rules/file_level_rules.json:bids_validator/rules' \
diff --git a/package.json b/package.json
@@ -1,7 +1,7 @@
 {
-  "name": "eeg2bids",
+  "name": "set2bids",
   "description": "EEG/iEEG to BIDS format Wizard",
-  "version": "1.0.17",
+  "version": "1.0.0",
   "dependencies": {
     "@electron/remote": "^1.1.0",
     "@fortawesome/fontawesome-free": "^5.15.4",
@@ -90,7 +90,7 @@
   },
   "build": {
     "appId": "mni.aces.eeg2bids",
-    "productName": "eeg2bids",
+    "productName": "set2bids",
     "copyright": "Open Source",
     "asar": false,
     "linux": {
@@ -143,11 +143,11 @@
             ]
           }
         ],
-        "NSDesktopFolderUsageDescription": "EEG2BIDS Wizard wants to access the Desktop folder.",
-        "NSDocumentsFolderUsageDescription": "EEG2BIDS Wizard wants to access the Documents folder.",
-        "NSDownloadsFolderUsageDescription": "EEG2BIDS Wizard wants to access the Downloads folder.",
-        "NSFileProviderDomainUsageDescription": "EEG2BIDS Wizard wants to access files managed by a file provider.",
-        "NSSystemAdministrationUsageDescription": "The operation being performed by EEG2BIDS Wizard requires elevated permission."
+        "NSDesktopFolderUsageDescription": "SET2BIDS Wizard wants to access the Desktop folder.",
+        "NSDocumentsFolderUsageDescription": "SET2BIDS Wizard wants to access the Documents folder.",
+        "NSDownloadsFolderUsageDescription": "SET2BIDS Wizard wants to access the Downloads folder.",
+        "NSFileProviderDomainUsageDescription": "SET2BIDS Wizard wants to access files managed by a file provider.",
+        "NSSystemAdministrationUsageDescription": "The operation being performed by SET2BIDS Wizard requires elevated permission."
       }
     },
     "nsis": {
@@ -164,7 +164,7 @@
       "python/**/*",
       "python/tools/mff_to_set.exe",
       "dist",
-      "dist/eeg2bids-service.app",
+      "dist/set2bids-service.app",
       "public/*",
       "package.json"
     ],
diff --git a/public/electron.js b/public/electron.js
@@ -26,17 +26,17 @@ const {app} = electron;
 const {BrowserWindow} = electron;
 const nativeImage = electron.nativeImage;
 
-const EEG2BIDSService = process.env.DEV ?
-  require('./eeg2bidsService') :
-  require(path.join(__dirname, '../build/eeg2bidsService'));
+const SET2BIDSService = process.env.DEV ?
+  require('./set2bidsService') :
+  require(path.join(__dirname, '../build/set2bidsService'));
 
 // Launch python service.
-const eeg2bidsService = new EEG2BIDSService();
-eeg2bidsService.startup().then((error) => {
+const set2bidsService = new SET2BIDSService();
+set2bidsService.startup().then((error) => {
   if (error) {
-    console.info('[SERVICE] eeg2bids-service failed');
+    console.info('[SERVICE] set2bids-service failed');
   } else {
-    console.info('[SERVICE] eeg2bids-service success');
+    console.info('[SERVICE] set2bids-service success');
   }
 });
 
@@ -123,7 +123,7 @@ app.on('window-all-closed', () => {
   // Wait for shutdown to stop
   // the service and quit the app
   if (process.platform !== 'darwin') {
-    eeg2bidsService.shutdown(() => app.quit());
+    set2bidsService.shutdown(() => app.quit());
   }
 });
 
diff --git a/public/index.html b/public/index.html
@@ -24,7 +24,7 @@
       work correctly both with client-side routing and a non-root public URL.
       Learn how to configure a non-root public URL by running `npm run build`.
     -->
-    <title>EEG2BIDS Wizard</title>
+    <title>SET2BIDS Wizard</title>
   </head>
   <body>
     <noscript>You need to enable JavaScript to run this app.</noscript>
diff --git a/public/manifest.json b/public/manifest.json
@@ -1,6 +1,6 @@
 {
-  "short_name": "eeg2bids",
-  "name": "eeg2bids",
+  "short_name": "set2bids",
+  "name": "set2bids",
   "icons": [
     {
       "src": "favicon.ico",
diff --git a/public/mffToSetService.js b/public/mffToSetService.js
@@ -4,7 +4,7 @@ const fs = require('fs');
 const os = require('os');
 
 /**
- * EEG2BIDS Wizard Service
+ * SET2BIDS Wizard Service
  */
 module.exports = class MFFToSETService {
   /**
diff --git a/public/preload.js b/public/preload.js
@@ -32,7 +32,7 @@ contextBridge.exposeInMainWorld('myAPI', {
     shell.openExternal('https://mcin.ca');
   },
   visitTemplates: () => {
-    shell.openExternal('https://github.com/aces/EEG2BIDS/tree/main/templates');
+    shell.openExternal('https://github.com/aces/eeg2bids/tree/main/templates');
   },
   getLorisAuthenticationCredentials: async () => {
     const credentials = await ipcRenderer.invoke(
diff --git a/public/set2bidsService.js b/public/set2bidsService.js
@@ -8,9 +8,9 @@ pythonLog.transports.file.fileName = 'python.log';
 pythonLog.transports.file.archiveLog = archiveLog;
 
 /**
- * EEG2BIDS Wizard Service
+ * SET2BIDS Wizard Service
  */
-module.exports = class EEG2BIDSService {
+module.exports = class SET2BIDSService {
   /**
    * constructor
    */
@@ -47,8 +47,8 @@ module.exports = class EEG2BIDSService {
         __dirname,
         '..',
       this.platform === 'win32' ?
-        'dist/eeg2bids-service-windows/eeg2bids-service-windows.exe' :
-        'dist/eeg2bids-service.app/Contents/MacOS/eeg2bids-service',
+        'dist/set2bids-service-windows/set2bids-service-windows.exe' :
+        'dist/set2bids-service.app/Contents/MacOS/set2bids-service',
       );
       this.process = spawn(pathToService, []);
     }
@@ -71,7 +71,7 @@ module.exports = class EEG2BIDSService {
    */
   shutdown(callback) {
     if (this.process) {
-      pythonLog.info('[SHUTDOWN of eeg2bidsService]');
+      pythonLog.info('[SHUTDOWN of set2bidsService]');
 
       if(os.platform() === 'win32'){
         exec('taskkill /pid ' + this.process.pid + ' /T /F', (error, stdout, stderr) => {
diff --git a/python/libs/Modifier.py b/python/libs/Modifier.py
@@ -73,7 +73,7 @@ def clean_dataset_files(self):
 
 
     def modify_dataset_description_json(self):
-        # EEG2BIDS Wizard version
+        # SET2BIDS Wizard version
         appVersion = 'unknown'
         
         try:
@@ -93,7 +93,7 @@ def modify_dataset_description_json(self):
             with open(file_path, "r") as fp:
                 file_data = json.load(fp)
                 file_data['PreparedBy'] = self.data['preparedBy']
-                file_data['Eeg2bidsVersion'] = appVersion
+                file_data['Set2bidsVersion'] = appVersion
                 file_data['Name'] = self.data['participantID'] + '_' + self.data['session']
 
                 with open(file_path, "w") as fp:
diff --git a/python/libs/mne/eeglab.py b/python/libs/mne/eeglab.py
@@ -1,6 +1,6 @@
 
 import numpy as np
-
+import mne.io.eeglab.eeglab as eeglab
 from mne.utils import (
     logger,
     verbose,
@@ -9,13 +9,11 @@
     _check_fname
 )
 from mne.annotations import read_annotations
-from mne.io.eeglab.eeglab import RawEEGLAB, _check_load_mat, _handle_montage_units, _get_info, _check_eeglab_fname, _check_boundary, _set_dig_montage_in_init, _check_latencies
 
 # just fix the scaling for now, EEGLAB doesn't seem to provide this info
 CAL = 1e-6
 
-@fill_doc
-class RawEEGLABOveride(RawEEGLAB):
+class RawEEGLABOveride(eeglab.RawEEGLAB):
     r"""Raw object from EEGLAB .set file.
 
     Parameters
@@ -55,17 +53,17 @@ def __init__(
         verbose=None,
     ):  # noqa: D102
         input_fname = str(_check_fname(input_fname, "read", True, "input_fname"))
-        eeg = _check_load_mat(input_fname, uint16_codec)
+        eeg = eeglab._check_load_mat(input_fname, uint16_codec)
         last_samps = [eeg.pnts - 1]
-        scale_units = _handle_montage_units(montage_units)
-        info, eeg_montage, _ = _get_info(eeg, eog=eog, scale_units=scale_units)
+        scale_units = eeglab._handle_montage_units(montage_units)
+        info, eeg_montage, _ = eeglab._get_info(eeg, eog=eog, scale_units=scale_units)
 
         # read the data
         if isinstance(eeg.data, str):
-            data_fname = _check_eeglab_fname(input_fname, eeg.data)
+            data_fname = eeglab._check_eeglab_fname(input_fname, eeg.data)
             logger.info("Reading %s" % data_fname)
 
-            super(RawEEGLAB, self).__init__(
+            super(eeglab.RawEEGLAB, self).__init__(
                 info,
                 preload,
                 filenames=[data_fname],
@@ -94,7 +92,7 @@ def __init__(
                 data = np.empty((n_chan, n_times), dtype=float)
             data[:n_chan] = eeg.data
             data *= CAL
-            super(RawEEGLAB, self).__init__(
+            super(eeglab.RawEEGLAB, self).__init__(
                 info,
                 data,
                 filenames=[input_fname],
@@ -106,9 +104,9 @@ def __init__(
         # create event_ch from annotations
         annot = read_annotations(input_fname)
         self.set_annotations(annot)
-        _check_boundary(annot, None)
+        eeglab._check_boundary(annot, None)
 
-        _set_dig_montage_in_init(self, eeg_montage)
+        eeglab._set_dig_montage_in_init(self, eeg_montage)
 
         latencies = np.round(annot.onset * self.info["sfreq"])
-        _check_latencies(latencies)
+        eeglab._check_latencies(latencies)
diff --git a/python/set2bids.py b/python/set2bids.py
diff --git a/set2bids-service-windows.spec b/set2bids-service-windows.spec
@@ -1,14 +1,12 @@
-import sys
-sys.setrecursionlimit(sys.getrecursionlimit() * 5)
-
+import sys ; sys.setrecursionlimit(sys.getrecursionlimit() * 5)
 # -*- mode: python ; coding: utf-8 -*-
 
 
 block_cipher = None
 
 
 a = Analysis(
-    ['python\\eeg2bids.py'],
+    ['python\\set2bids.py'],
     pathex=['python'],
     binaries=[],
     datas=[('python/libs/bids_validator/rules/top_level_rules.json', './bids_validator/rules'), ('python/libs/bids_validator/rules/associated_data_rules.json', './bids_validator/rules'), ('python/libs/bids_validator/rules/file_level_rules.json', './bids_validator/rules'), ('python/libs/bids_validator/rules/phenotypic_rules.json', './bids_validator/rules'), ('python/libs/bids_validator/rules/session_level_rules.json', './bids_validator/rules'), ('python/libs/bids_validator/rules/subject_level_rules.json', './bids_validator/rules'), ('python/libs/bids_validator/tsv/non_custom_columns.json', './bids_validator/tsv'), ('python/libs/mne/channels/data/montages/EGI_256.csd', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/GSN-HydroCel-128.sfp', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/GSN-HydroCel-129.sfp', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/GSN-HydroCel-256.sfp', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/GSN-HydroCel-257.sfp', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/GSN-HydroCel-32.sfp', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/GSN-HydroCel-64_1.0.sfp', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/GSN-HydroCel-65_1.0.sfp', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/artinis-brite23.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/artinis-octamon.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/biosemi128.txt', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/biosemi16.txt', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/biosemi160.txt', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/biosemi256.txt', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/biosemi32.txt', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/biosemi64.txt', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/easycap-M1.txt', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/easycap-M10.txt', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/mgh60.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/mgh70.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/standard_1005.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/standard_1020.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/standard_alphabetic.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/standard_postfixed.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/standard_prefixed.elc', './mne/channels/data/montages'), ('python/libs/mne/channels/data/montages/standard_primed.elc', './mne/channels/data/montages'), ('Lib/site-packages/mne', 'mne'), ('Lib/site-packages/mne_bids', 'mne_bids')],
@@ -29,7 +27,7 @@ exe = EXE(
     a.scripts,
     [],
     exclude_binaries=True,
-    name='eeg2bids-service-windows',
+    name='set2bids-service-windows',
     debug=False,
     bootloader_ignore_signals=False,
     strip=False,
@@ -49,5 +47,5 @@ coll = COLLECT(
     strip=False,
     upx=True,
     upx_exclude=[],
-    name='eeg2bids-service-windows',
+    name='set2bids-service-windows',
 )
diff --git a/set2bids-service.spec b/set2bids-service.spec
@@ -8,7 +8,7 @@ block_cipher = None
 
 
 a = Analysis(
-    ['python/eeg2bids.py'],
+    ['python/set2bids.py'],
     pathex=['python'],
     binaries=[],
     datas=[('python/libs/bids_validator/rules/top_level_rules.json', 'bids_validator/rules'), ('python/libs/bids_validator/rules/associated_data_rules.json', 'bids_validator/rules'), ('python/libs/bids_validator/rules/file_level_rules.json', 'bids_validator/rules'), ('python/libs/bids_validator/rules/phenotypic_rules.json', 'bids_validator/rules'), ('python/libs/bids_validator/rules/session_level_rules.json', 'bids_validator/rules'), ('python/libs/bids_validator/rules/subject_level_rules.json', 'bids_validator/rules'), ('python/libs/bids_validator/tsv/non_custom_columns.json', 'bids_validator/tsv'), ('python/lib/python3.8/site-packages/mne/', 'mne'), ('python/lib/python3.8/site-packages/mne_bids/', 'mne_bids')],
@@ -31,7 +31,7 @@ exe = EXE(
     a.zipfiles,
     a.datas,
     [('u', None, 'OPTION')],
-    name='eeg2bids-service',
+    name='set2bids-service',
     debug=False,
     bootloader_ignore_signals=False,
     strip=False,
@@ -47,7 +47,7 @@ exe = EXE(
 )
 app = BUNDLE(
     exe,
-    name='eeg2bids-service.app',
+    name='set2bids-service.app',
     icon=None,
     bundle_identifier=None,
 )
diff --git a/src/jsx/Configuration/RecordingMetadata.js b/src/jsx/Configuration/RecordingMetadata.js
@@ -36,7 +36,7 @@ const RecordingMetadata = () => {
   const socketContext = useContext(SocketContext);
 
   /**
-   * openGitHub - Navigate browser to EEG2BIDS Wizard.
+   * openGitHub - Navigate browser to SET2BIDS Wizard.
    */
   const openTemplates = () => {
     const myAPI = window['myAPI'];
diff --git a/src/jsx/SplashScreen.js b/src/jsx/SplashScreen.js
@@ -19,7 +19,7 @@ const SplashScreen = (props) => {
   return props.visible ? (
     <>
       <p className='loader-font'>
-        EEG2BIDS Wizard is loading ...
+        SET2BIDS Wizard is loading ...
       </p>
       <span
         className='loader centered'
diff --git a/src/jsx/Welcome.js b/src/jsx/Welcome.js
@@ -11,21 +11,21 @@ import {name, version} from '../../package.json';
  */
 const Welcome = (props) => {
   /**
-   * openBIDS - Navigate browser to EEG2BIDS Wizard.
+   * openBIDS - Navigate browser to SET2BIDS Wizard.
    */
   const openBIDS = () => {
     const myAPI = window['myAPI'];
     myAPI.visitBIDS();
   };
   /**
-   * openGitHub - Navigate browser to EEG2BIDS Wizard.
+   * openGitHub - Navigate browser to SET2BIDS Wizard.
    */
   const openGitHub = () => {
     const myAPI = window['myAPI'];
     myAPI.visitGitHub();
   };
   /**
-   * openGitHub - Navigate browser to EEG2BIDS Wizard.
+   * openGitHub - Navigate browser to SET2BIDS Wizard.
    */
   const openIssues = () => {
     const myAPI = window['myAPI'];
@@ -51,15 +51,15 @@ const Welcome = (props) => {
       display: props.visible ? 'block' : 'none',
     }}>
       <span className='title'>
-        Welcome to <b>EEG2BIDS Wizard</b>
+        Welcome to <b>SET2BIDS Wizard</b>
       </span>
       <div className='info' style={{display: 'flex'}}>
         <div className='info' style={{
           justifyContent: 'center',
           margin: '0 auto',
         }}>
           <p>
-            <b>EEG2BIDS Wizard</b> is a tool for de-identification of EEG data
+            <b>SET2BIDS Wizard</b> is a tool for de-identification of EEG data
             and conversion to BIDS format for data sharing.
           </p>
           <p>This software is designed to run on EEGLAB files
diff --git a/src/jsx/elements/help.js b/src/jsx/elements/help.js
@@ -84,7 +84,7 @@ const Help = (props) => {
       <h3>2) Configuration</h3>
       The LORIS login is optional and allows the following:
       <ul>
-        <li>Safely store LORIS credentials in EEG2BIDS</li>
+        <li>Safely store LORIS credentials in SET2BIDS</li>
         <li>Automatically retrieve LORIS data in Configuration</li>
         <li>
           LORIS credentials are deleted by clearing the username and password!
diff --git a/start-server.ps1 b/start-server.ps1
@@ -4,4 +4,4 @@ py -m venv .
 Scripts\activate
 python -m pip install numpy
 python -m pip install -r .\requirements.txt
-python -m python.eeg2bids
+python -m python.set2bids
diff --git a/start-server.sh b/start-server.sh
diff --git a/wiki/dev_notes/README.md b/wiki/dev_notes/README.md
diff --git a/wiki/dev_notes/react/README.md b/wiki/dev_notes/react/README.md
diff --git a/wiki/macOS/README.md b/wiki/macOS/README.md
diff --git a/wiki/ubuntu/README.md b/wiki/ubuntu/README.md
diff --git a/wiki/windows/README.md b/wiki/windows/README.md
diff --git a/wiki/windows/intellij/README.md b/wiki/windows/intellij/README.md

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`		`- "short_name": "eeg2bids",`
`3`		`- "name": "eeg2bids",`
	`2`	`+ "short_name": "set2bids",`
	`3`	`+ "name": "set2bids",`
`4`	`4`	`"icons": [`
`5`	`5`	`{`
`6`	`6`	`"src": "favicon.ico",`