updates to eeg analysis

devices/Bitalino.py

@@ -74,7 +74,7 @@ def read(self):
         for i, c in enumerate(self.channels):
             samples[c] = in_samples[:, -len(self.channels) + i].tolist()
             if c == 'eeg': #eeg supports multiple electrodes
-                samples[c] = [samples[c]]
+                samples[c] = [ [ s ] for s in samples[c] ]
         return samples
 
     #stop streaming

devices/OpenBCI.py

@@ -7,6 +7,7 @@
 
 import glob
 import serial
+import serial.tools.list_ports
 import struct
 import time
 import sys
@@ -32,10 +33,23 @@ def __init__(self, dev_i = 0):
 
         print("Serial established...")
 
+
+
+
     #find all devices
     #return as array of device id strings
     def list_devices(self):
-        return glob.glob('/dev/tty.usb*')
+
+        def serial_ports():
+            """ Lists serial port names
+
+                :raises EnvironmentError:
+                    On unsupported or unknown platforms
+                :returns:
+                    A list of the serial ports available on the system
+            """
+        return [comport.device for comport in serial.tools.list_ports.comports()]
+        #return glob.glob('/dev/tty.usb*')
 
     #start streaming
     def start(self, fs, channels):

examples/receive_eeg_to_pd.pd

@@ -1,15 +1,67 @@
-#N canvas 400 90 540 405 10;
+#N canvas 50 150 1212 620 10;
 #X obj 37 48 mrpeach/unpackOSC;
 #X floatatom 45 134 10 0 0 0 - - -;
-#X obj 37 73 route /rtbio/eeg/alpha /rtbio/eeg/beta /rtbio/eeg/gamma
-/rtbio/eeg/delta;
 #X floatatom 125 132 10 0 0 0 - - -;
-#X floatatom 227 164 10 0 0 0 - - -;
+#X floatatom 200 132 10 0 0 0 - - -;
 #X floatatom 291 132 10 0 0 0 - - -;
 #X obj 37 23 mrpeach/udpreceive 4810;
-#X connect 0 0 2 0;
+#X obj 37 73 route /rtbio/eeg/alpha /rtbio/eeg/beta /rtbio/eeg/theta
+/rtbio/eeg/delta /rtbio/eeg/raw;
+#N canvas 0 50 1377 540 graph 0;
+#N canvas 350 172 1009 430 (subpatch) 0;
+#X array \$0_array 500 float 1;
+#A 0 12 85 7 61 81 -58 103 8 71 -12 -9 31 -55 31 62 96 61 -101 -27
+-91 48 83 44 -28 21 84 3 93 -38 4 27 9 -111 -72 -170 -152 -81 -15 23
+88 -116 -117 -103 -77 -30 95 26 71 87 5 -40 27 -21 66 -29 78 131 118
+164 116 -52 -182 -124 -24 123 -44 135 -131 -322 -205 -125 14 63 -30
+-62 85 -165 -48 -89 -23 48 -70 -57 -30 -30 7 -121 -148 -90 -5 -112
+-143 -126 -95 -136 -38 143 153 36 103 120 61 19 53 240 98 264 224 62
+141 49 102 204 96 299 215 150 186 220 45 -43 -94 -61 -14 95 -78 -13
+4 138 158 -9 -153 -92 -139 -129 -126 -69 -159 -111 106 87 85 70 62
+0 -125 -26 65 225 -1 95 -71 -182 -265 -246 -213 -167 -12 -125 3 107
+-59 -35 -4 -153 -216 -109 -23 21 -25 -116 -204 -112 1 -9 12 56 -8 31
+56 2 15 -4 -30 -2 -49 -130 -60 -57 -36 -55 -35 39 13 50 16 -67 -70
+77 176 178 211 151 110 97 -119 -109 -45 26 -28 -39 39 102 124 -20 -10
+-29 71 -80 -194 -334 -320 -266 -193 -254 -194 -512 -512 -512 -512 -512
+-512 -512 -512 -512 -512 -65 307 506 506 506 506 506 506 506 506 506
+506 506 506 506 506 506 506 506 506 506 463 336 275 310 411 366 332
+385 403 113 -2 -41 55 100 169 198 299 121 40 -185 -153 -175 4 37 11
+172 88 103 -89 -330 -292 -212 -121 39 179 56 57 -77 -106 -335 -231
+-266 -111 -118 -48 -91 -143 -119 -89 -64 24 38 64 -36 -69 -166 -96
+-97 -57 -48 -32 -199 -236 -269 -149 -143 -13 -270 -260 -136 -35 -137
+-37 -49 93 32 -84 -86 165 -85 -73 -32 130 -121 -153 -76 -315 -321 -251
+-302 -209 -63 -30 -21 163 363 506 506 506 506 476 350 365 506 321 261
+278 218 260 271 236 132 178 127 277 103 141 -29 121 3 116 0 139 25
+71 34 38 71 1 3 112 14 -8 -25 25 21 47 -11 52 45 17 -160 13 -73 -1
+-55 28 -50 -4 -8 -63 -60 4 -84 17 96 -38 -38 -45 -51 110 -3 122 102
+44 23 -37 -230 -84 -79 7 -148 77 10 -25 -89 -217 -157 -512 -512 -512
+-512 -512 -512 -512 -512 -512 -512 -356 -27 108 355 483 502 506 391
+371 337 478 506 506 506 506 506 506 435 506 383 319 308 379 271 248
+285 329 164 119 128 146 139 240 33 241 140 77 -100 -123 31 -142 -97
+-144 -50 -26 334 198 142 8 41 71 34 39 72 -83;
+#X coords 0 400 499 -400 500 100 1 0 0;
+#X restore 304 124 graph;
+#X obj 172 301 + 1;
+#X obj 155 258 0;
+#X obj 72 234 t f b;
+#X obj 213 259 % 500;
+#X obj 52 296 tabwrite \$0_array;
+#X obj 61 31 inlet;
+#X obj 75 161 - 512;
+#X connect 1 0 4 0;
 #X connect 2 0 1 0;
-#X connect 2 1 3 0;
-#X connect 2 2 4 0;
-#X connect 2 3 5 0;
-#X connect 6 0 0 0;
+#X connect 2 0 5 1;
+#X connect 3 0 5 0;
+#X connect 3 1 2 0;
+#X connect 4 0 2 1;
+#X connect 6 0 7 0;
+#X connect 7 0 3 0;
+#X coords 0 -1 1 1 510 130 1 300 100;
+#X restore 665 180 pd graph;
+#X connect 0 0 6 0;
+#X connect 5 0 0 0;
+#X connect 6 0 1 0;
+#X connect 6 1 2 0;
+#X connect 6 2 3 0;
+#X connect 6 3 4 0;
+#X connect 6 4 7 0;

examples/visualize.html

@@ -45,12 +45,14 @@
                     var time_data = event.data.split('|');
                     var time = time_data[0] * 1000;
                     var data = time_data[1].split('/');
+                    console.log(data[3]);
                     if(data[2] == 'raw') {
                         ts_index = channels[data[1]];
                         if(ts_index !== undefined) {
                             var samples = data[3].replace('[', '').replace(']', '').replace('[', '').replace(']', '').split(', ');
+                            console.log(samples);
                             for(var i=0; i<samples.length; i++) {
-                                var sample = samples[i];
+                                var sample = samples[i].replace('[', '').replace(']', '');
                                 if(data[1] == 'eda') {
                                     sample = prev_eda !== undefined ? 0.995 * prev_eda + 0.005 * sample : sample;
                                     prev_eda = sample;

init_sources.py

@@ -20,12 +20,12 @@ def init_sources(connections, fs):
                 #have to get eeg chan numbers from somewhere
                 num_chans = 1 if fs == 100 else 8
                 print('number of chans {}'.format(num_chans))
-                sources[source] = Oscillations(fs, num_chans, 500, 0.75, 
+                sources[source] = Oscillations(fs, num_chans, 256, 0.8, 
                     {
                         'theta': [4.0, 8.0],
                         'alpha': [8.0, 13.0],
                         'beta': [13.0, 30.0],
-                        'delta': [3.0, 4.0],
+                        'delta': [1.0, 4.0],
                     }
                 )
             else:

physiology/Oscillations.py

@@ -19,7 +19,8 @@ def add_data(self, samples):
             #for c in samples:
             #    out.append(c[i])
             #freqs = self.add_samples(out)
-            freqs = self.add_samples(samples[i])
+            freqs_in = self.add_samples(samples[i])
+            freqs = freqs_in if freqs_in != None else freqs
         return freqs
 
     def add_samples(self, samples):
@@ -45,8 +46,8 @@ def add_samples(self, samples):
                 for f in self.freqs:
                     freq = self.freqs[f]
                     start = np.where((freqC <= freq[0]) & (freqC >= 0))[0][-1]
-                    stop = np.where((freqC >= freq[1]) & (freqC >= 0))[0][-1]
-                    freqpower[f][i] = sum(powerspect[start:stop])            
+                    stop = np.where((freqC >= freq[1]) & (freqC >= 0))[0][0]
+                    freqpower[f][i] = np.mean(powerspect[start:stop]) + np.mean(powerspect[-stop-1:-start-1])
 
                 self.idx = int(self.fft_size * self.overlap)
                 raw_electrodes[i] = [float(electrode_data[a]) for a in range(self.idx, len(electrode_data))]

router.py

@@ -49,7 +49,8 @@ def route_data(self, source, connections, features, raw_data):
             for destination in connections['r' + source]: 
                 osc_dest = '/{}/raw'.format(source)
                 if destination == 'osc':
-                    self.osc_client.send_message(self.osc_prefix + osc_dest, raw_data)
+                    for data in raw_data:
+                        self.osc_client.send_message(self.osc_prefix + osc_dest, data)
                 elif destination == 'file':
                     self.file_handle.write('{} {}: {}\n'.format(current_time, osc_dest, str(raw_data)))
                 elif destination == 'ws':
@@ -61,15 +62,16 @@ def route_data(self, source, connections, features, raw_data):
             for destination in source_connections:
                 for feature in features.keys():
                     osc_dest = '/{}/{}'.format(source, feature)
-                    for data in features[feature]:
-                        if destination == 'osc':
-                            self.osc_client.send_message(self.osc_prefix + osc_dest, data)
-                        elif destination == 'file':
-                            self.file_handle.write('{} {}: {}\n'.format(current_time, osc_dest, str(data)))
-                        elif destination == 'ws':
-                            self.ws_server.add_message('{}|{}/{}'.format(current_time, osc_dest, str(raw_data)))
-                        elif destination == 'digital':
-                            if self.digital_out_func:
-                                self.digital_out_func()
+                    #for data in features[feature]:
+                    data = features[feature]
+                    if destination == 'osc':
+                        self.osc_client.send_message(self.osc_prefix + osc_dest, data)
+                    elif destination == 'file':
+                        self.file_handle.write('{} {}: {}\n'.format(current_time, osc_dest, str(data)))
+                    elif destination == 'ws':
+                        self.ws_server.add_message('{}|{}/{}'.format(current_time, osc_dest, str(raw_data)))
+                    elif destination == 'digital':
+                        if self.digital_out_func:
+                            self.digital_out_func()
 
 

tests/test_Oscillations.py

@@ -5,9 +5,41 @@ def test_Oscillations():
         'alpha': [8, 13]
     })
 
-    res = eeg.add_data([[0, 0, 0, 0, 0, 0]])
+    res = eeg.add_data([[0], [0], [0], [0], [0], [0]])
     assert res == None
 
-    more_data = [[1 for _ in range(250)]]
+    more_data = [[1] for _ in range(250)]
     res = eeg.add_data(more_data)
     assert res['alpha'] == [-10650.084320520564]
+
+
+def test_Oscillations_10Hz():
+    sin_10 = [[50], [79] ,[98] ,[98] ,[79] ,[50] ,[21] ,[2] ,[2] ,[21] ]
+    wave = []
+    for _ in range(30):
+        wave += sin_10
+
+    eeg = Oscillations(100, 1, 256, 0.5, {
+        'alpha': [8, 13],
+        'beta': [13, 30]
+    })
+    res = eeg.add_data(wave)
+    print(res)
+
+import numpy as np
+
+def test_Oscillations_5Hz():
+    sin_5 = [[50], [98] ,[79] ,[21] ,[2] ]
+    wave = []
+    for _ in range(60):
+        wave += sin_5
+    wave = np.array(wave) * 100
+
+    eeg = Oscillations(100, 1, 256, 0.5, {
+        'all': [1, 40],
+        'alpha': [8, 13],
+        'beta': [4.9, 5.1]
+    })
+    res = eeg.add_data(wave)
+    print(res)
+