Updates and bugfixes

python/eeg2bids.py

@@ -38,18 +38,17 @@ def connect(sid, environ):
         return False  # extra precaution.
 
 
-def tarfile_bids_thread(data):
-    iEEG.TarFile(data)
+def tarfile_bids_thread(bids_directory):
+    iEEG.TarFile(bids_directory)
     response = {
         'compression_time': 'example_5mins'
     }
     return eventlet.tpool.Proxy(response)
 
 
 @sio.event
-def tarfile_bids(sid, data):
-    # data = { bids_directory: '../path/to/bids/output', output_time: 'bids output time' }
-    response = eventlet.tpool.execute(tarfile_bids_thread, data)
+def tarfile_bids(sid, bids_directory):
+    response = eventlet.tpool.execute(tarfile_bids_thread, bids_directory)
     send = {
         'compression_time': response['compression_time']
     }
@@ -288,16 +287,14 @@ def edf_to_bids(sid, data):
 
 
 @sio.event
-def validate_bids(sid, data):
-    # data = { bids_directory: '../path/to/bids/output', output_time: 'bids output time' }
-    print('validate_bids: ', data)
+def validate_bids(sid, bids_directory):
+    print('validate_bids: ', bids_directory)
     error_messages = []
-    if 'bids_directory' not in data or not data['bids_directory']:
+    if not bids_directory:
         error_messages.append('The BIDS output directory is missing.')
-    if 'output_time' not in data or not data['output_time']:
-        error_messages.append('The BIDS format is missing.')
+
     if not error_messages:
-        BIDS.Validate(data)
+        BIDS.Validate(bids_directory)
         response = {
             'file_paths': BIDS.Validate.file_paths,
             'result': BIDS.Validate.result

python/libs/BIDS.py

@@ -6,14 +6,12 @@ class Validate:
     file_paths = []
     result = []
 
-    def __init__(self, data):
+    def __init__(self, bids_directory):
         print('- Validate: init started.')
-        sep = os.path.sep
-        start_path = data['bids_directory'] + sep + data['output_time']  # current directory
         file_paths = []
         result = []
         validator = BIDSValidator()
-        for path, dirs, files in os.walk(start_path):
+        for path, dirs, files in os.walk(bids_directory):
             for filename in files:
                 if filename == '.bidsignore':
                     continue
@@ -25,9 +23,9 @@ def __init__(self, data):
                     continue
 
                 temp = os.path.join(path, filename)
-                file_paths.append(temp[len(start_path):len(temp)])
-                result.append(validator.is_bids(temp[len(start_path):len(temp)]))
-                # print(validator.is_bids(temp[len(start_path):len(temp)]))
+                file_paths.append(temp[len(bids_directory):len(temp)])
+                result.append(validator.is_bids(temp[len(bids_directory):len(temp)]))
+                # print(validator.is_bids(temp[len(bids_directory):len(temp)]))
 
         self.set_file_paths(file_paths)
         self.set_result(result)

python/libs/Modifier.py

@@ -29,7 +29,7 @@ def get_bids_root_path(self):
 
     def get_eeg_path(self):
         directory_path = 'sub-' + self.data['participantID'].replace('_', '').replace('-', '').replace(' ', '')
-        
+
         return os.path.join(
             self.get_bids_root_path(),
             directory_path,
@@ -40,29 +40,29 @@ def get_eeg_path(self):
 
     def clean_dataset_files(self):
         if len(self.data['edfData']['files']) > 0:
-            # for split recording, clean the duplicates _eeg.json and _channels.tsv
+            # for multiple run recording, clean the duplicates _eeg.json and _channels.tsv
             channels_files = [f for f in os.listdir(self.get_eeg_path()) if f.endswith('_channels.tsv')]
             for i in range(1, len(channels_files)):
                 filename = os.path.join(self.get_eeg_path(), channels_files[i])
-                os.remove(filename) 
-                
+                os.remove(filename)
+
             sidecar_files = [f for f in os.listdir(self.get_eeg_path()) if f.endswith('eeg.json')]
             for i in range(1, len(sidecar_files)):
                 filename = os.path.join(self.get_eeg_path(), sidecar_files[i])
-                os.remove(filename) 
-            
-            # remove the split suffix in the file names
+                os.remove(filename)
+
+            # remove the run suffix in the file names
             fileOrig = os.path.join(self.get_eeg_path(), channels_files[0])
             fileDest = os.path.join(
                 self.get_eeg_path(),
-                re.sub(r"_split-[0-9]+", '', channels_files[0])
+                re.sub(r"_run-[0-9]+", '', channels_files[0])
             )
             os.rename(fileOrig, fileDest)
 
             fileOrig = os.path.join(self.get_eeg_path(), sidecar_files[0])
             fileDest = os.path.join(
                 self.get_eeg_path(),
-                re.sub(r"_split-[0-9]+", '', sidecar_files[0])
+                re.sub(r"_run-[0-9]+", '', sidecar_files[0])
             )
             os.rename(fileOrig, fileDest)
 
@@ -84,7 +84,7 @@ def modify_dataset_description_json(self):
         except IOError:
             print("Could not read or write dataset_description.json file")
 
-        
+
     def modify_participants_tsv(self):
         file_path = os.path.join(
             self.get_bids_root_path(),
@@ -180,13 +180,13 @@ def copy_annotation_files(self):
         for eegRun in self.data.get('eegRuns'):
             edf_file = eegRun['edfBIDSBasename']
             filename = os.path.join(self.get_eeg_path(), edf_file + '_annotations')
-            
+
             if eegRun['annotationsTSV']:
                 shutil.copyfile(
                     eegRun['annotationsTSV'],
                     os.path.join(self.get_eeg_path(), filename + '.tsv')
                 )
-            
+
             if eegRun['annotationsJSON']:
                 shutil.copyfile(
                     eegRun['annotationsJSON'],
@@ -198,7 +198,7 @@ def copy_event_files(self):
         for eegRun in self.data.get('eegRuns'):
             edf_file = eegRun['edfBIDSBasename']
             filename = os.path.join(self.get_eeg_path(), edf_file + '_annotations')
-            
+
             if eegRun['eventFile']:
                 # events.tsv data collected:
                 output = []
@@ -228,7 +228,7 @@ def copy_event_files(self):
                         temp = os.path.join(path, filename)
                         if temp.endswith(eegRun['edfBIDSBasename'] + '_events.tsv'):
                             path_event_files = temp
-                        
+
                 # We now open BIDS events.tsv file if it exists
                 if path_event_files:
                     try:
@@ -272,7 +272,7 @@ def modify_eeg_json(self):
             raise ValueError('Found more than one eeg.json file')
 
         file_path = os.path.join(self.get_eeg_path(), eeg_json[0])
-        
+
         try:
             with open(file_path, "r") as fp:
                 file_data = json.load(fp)
@@ -284,12 +284,12 @@ def modify_eeg_json(self):
                     referenceField = 'EGGReference'
 
                 file_data[referenceField] = self.data['reference']
-                
+
                 if 'metadata' in self.data['bidsMetadata'] and 'invalid_keys' in self.data['bidsMetadata']:
                     for key in self.data['bidsMetadata']['metadata']:
-                        if key not in self.data['bidsMetadata']['invalid_keys']:    
+                        if key not in self.data['bidsMetadata']['invalid_keys']:
                             file_data[key] = self.data['bidsMetadata']['metadata'][key]
-                  
+
                 with open(file_path, "w") as fp:
                     json.dump(file_data, fp, indent=4)
 

python/libs/iEEG.py

@@ -91,23 +91,20 @@ class WriteError(PermissionError):
 
 # TarFile - tarfile the BIDS data.
 class TarFile:
-    # data = { bids_directory: '../path/to/bids/output', output_time: 'bids output time' }
-    def __init__(self, data):
+    def __init__(self, bids_directory):
         import tarfile
-        import os.path
-        sep = os.path.sep
-        source_dir = data['bids_directory'] + sep + data['output_time']  # current directory
-        output_filename = data['bids_directory'] + sep + data['output_time'] + '.tar.gz'
+        output_filename = bids_directory + '.tar.gz'
         with tarfile.open(output_filename, "w:gz") as tar:
-            tar.add(source_dir, arcname=os.path.basename(source_dir))
-        import platform
-        import subprocess
-        if platform.system() == 'Windows':
-            os.startfile(data['bids_directory'])
-        elif platform.system() == 'Darwin':
-            subprocess.Popen(['open', data['bids_directory']])
-        else:
-            subprocess.Popen(['xdg-open', data['bids_directory']])
+            tar.add(bids_directory, arcname=os.path.basename(bids_directory))
+
+        #import platform
+        #import subprocess
+        #if platform.system() == 'Windows':
+        #    os.startfile(data['bids_directory'])
+        #elif platform.system() == 'Darwin':
+        #    subprocess.Popen(['open', data['bids_directory']])
+        #else:
+        #    subprocess.Popen(['xdg-open', data['bids_directory']])
 
 
 # Anonymize - scrubs edf header data.
@@ -257,7 +254,7 @@ def to_bids(self,
                 bids_basename.update(session=session)
 
                 try:
-                    write_raw_bids(raw, bids_basename, anonymize=dict(daysback=33630), overwrite=False, verbose=False)
+                    write_raw_bids(raw, bids_basename, overwrite=False, verbose=False)
                     with open(bids_basename, 'r+b') as f:
                         f.seek(8)  # id_info field starts 8 bytes in
                         f.write(bytes("X X X X".ljust(80), 'ascii'))

requirements.txt

@@ -1,12 +1,10 @@
-eventlet>=0.31.0
+eventlet~=0.31.0
 mne~=0.23.0
-# MNE-BIDS 0.8 will support the .EDF extension   
-# Before its release we need to use the dev version        
-git+git://github.com/mne-tools/mne-bids@main#egg=mne-bids
+mne-bids~=0.8
 mne-features~=0.1
 numpy~=1.19.5
 python-socketio~=5.0.4
 python-engineio~=4.0.0
 bids-validator~=1.6.0
-pybv>=0.4
-requests>=2.25.0
+pybv~=0.4
+requests~=2.25.0

src/App.js

@@ -84,7 +84,7 @@ const App = () => {
                 },
               },
               {
-                title: '4) Validator',
+                title: '4) Validate and package',
                 onClick: (e) => {
                   e.preventDefault();
                   setActiveMenuTab(3);

src/css/Authentication.module.css

@@ -6,6 +6,7 @@
     cursor: default;
     font-size: 12px;
     background-color: #e9eaee;
+    width: 50%;
 }
 .loginMessage {
     font-size: 14px;

src/css/Configuration.css

@@ -22,4 +22,9 @@ input[type="button"].primary-btn:disabled {
 textarea {
     vertical-align: top;
     font-family: Arial;
-}
+}
+.resetBtn {
+    text-align: right;
+    width: 50%;
+    background-color: #e9eaee;
+}