created utils.py with data loading

Author: kylemath

utils.py

@@ -0,0 +1,145 @@
+#find the factors of a number |to add extra dimension for CNN|
+def factors(n):
+      return [i for i in range(1, n + 1) if not n%i]
+  
+##Setup TensorFlow
+def SetupTensorFlow():
+  
+  #run tensorboard
+  LOG_DIR = './log'
+  get_ipython().system_raw(
+      'tensorboard --logdir {} --host 0.0.0.0 --port 6007 &'
+      .format(LOG_DIR)
+  )
+
+  #run ngork
+  get_ipython().system_raw('./ngrok http 6007 &')
+
+  #get url
+  ! curl -s http://localhost:4040/api/tunnels | python3 -c \
+      "import sys, json; print(json.load(sys.stdin)['tunnels'][0]['public_url'])"
+
+
+#load in recorder data files
+def load_data(filename,data_type='muse',plot_sensors=True,plot_raw=True,plot_raw_psd=True,stim_channel=False, ):  
+ 
+  
+    #load .vhdr files from brain vision recorder
+    raw = io.read_raw_brainvision(filename, 
+                            montage='standard_1020', 
+                            eog=('HEOG', 'VEOG'), 
+                            preload=True,stim_channel=stim_channel)
+
+    #set sampling rate
+    sfreq = raw.info['sfreq']
+    print('Sampling Rate = ' + str(sfreq))
+
+    #load channel locations
+    print('Loading Channel Locations')
+    if plot_sensors:
+      raw.plot_sensors(show_names='True')
+
+    ##Plot raw data
+    if plot_raw:
+      raw.plot(n_channels=16, block=True)
+
+     #plot raw psd 
+    if plot_raw_psd:
+      raw.plot_psd(fmin=.1, fmax=100 ) 
+  
+    return raw, sfreq
+
+
+#from eeg-notebooks
+def load_muse_csv_as_raw(filename, sfreq=256., ch_ind=[0, 1, 2, 3],
+                         stim_ind=5, replace_ch_names=None, verbose=1):
+    """Load CSV files into a Raw object.
+
+    Args:
+        filename (str or list): path or paths to CSV files to load
+
+    Keyword Args:
+        subject_nb (int or str): subject number. If 'all', load all
+            subjects.
+        session_nb (int or str): session number. If 'all', load all
+            sessions.
+        sfreq (float): EEG sampling frequency
+        ch_ind (list): indices of the EEG channels to keep
+        stim_ind (int): index of the stim channel
+        replace_ch_names (dict or None): dictionary containing a mapping to
+            rename channels. Useful when an external electrode was used.
+
+    Returns:
+        (mne.io.array.array.RawArray): loaded EEG
+    """
+    n_channel = len(ch_ind)
+
+    raw = []
+    for fname in filename:
+        # read the file
+        data = pd.read_csv(fname, index_col=0)
+
+        # name of each channels
+        ch_names = list(data.columns)[0:n_channel] + ['Stim']
+
+        if replace_ch_names is not None:
+            ch_names = [c if c not in replace_ch_names.keys()
+                        else replace_ch_names[c] for c in ch_names]
+
+        # type of each channels
+        ch_types = ['eeg'] * n_channel + ['stim']
+        montage = read_montage('standard_1005')
+
+        # get data and exclude Aux channel
+        data = data.values[:, ch_ind + [stim_ind]].T
+
+        # convert in Volts (from uVolts)
+        data[:-1] *= 1e-6
+
+        # create MNE object
+        info = create_info(ch_names=ch_names, ch_types=ch_types,
+                           sfreq=sfreq, montage=montage, verbose=verbose)
+        raw.append(RawArray(data=data, info=info, verbose=verbose))
+
+    # concatenate all raw objects
+    raws = concatenate_raws(raw, verbose=verbose)
+
+    return raws
+  
+#from eeg-notebooks load_data
+def muse_load_data(data_dir, subject_nb=1, session_nb=1, sfreq=256.,
+              ch_ind=[0, 1, 2, 3], stim_ind=5, replace_ch_names=None, verbose=1):
+    """Load CSV files from the /data directory into a Raw object.
+
+    Args:
+        data_dir (str): directory inside /data that contains the
+            CSV files to load, e.g., 'auditory/P300'
+
+    Keyword Args:
+        subject_nb (int or str): subject number. If 'all', load all
+            subjects.
+        session_nb (int or str): session number. If 'all', load all
+            sessions.
+        sfreq (float): EEG sampling frequency
+        ch_ind (list): indices of the EEG channels to keep
+        stim_ind (int): index of the stim channel
+        replace_ch_names (dict or None): dictionary containing a mapping to
+            rename channels. Useful when an external electrode was used.
+
+    Returns:
+        (mne.io.array.array.RawArray): loaded EEG
+    """
+    if subject_nb == 'all':
+        subject_nb = '*'
+    if session_nb == 'all':
+        session_nb = '*'
+
+    data_path = os.path.join(
+            'eeg-notebooks/data', data_dir,
+            'subject{}/session{}/*.csv'.format(subject_nb, session_nb))
+    fnames = glob(data_path)
+
+    return load_muse_csv_as_raw(fnames, sfreq=sfreq, ch_ind=ch_ind,
+                                stim_ind=stim_ind,
+                                replace_ch_names=replace_ch_names, verbose=verbose)
+