HTML and BAT files for running the graphical interface (Biosignals Plux)

.gitignore

@@ -3,4 +3,4 @@ build/
 .pytest_cache/
 .DS_Store
 temp.txt
-*.pyc
+*.pyc

README.md

@@ -35,3 +35,9 @@
         [prefix (default: /rtbio)]
     --filename [filename]
         [filename (default: temp.txt)]
+
+
+To run from Python:
+- You can use the `art-bio.yaml` file to intitialize the Anaconda environment with the necessary packages
+- Run from terminal with for example the command `python art-bio.py -d biosignalsplux -c recg ws` to try the banana demo
+- The biosignalsplux library files for Win64/Python 3.8 are included by default, for other platforms copy the files from the corresponding folder at [https://github.com/biosignalsplux/python-samples/tree/master/PLUX-API-Python3](https://github.com/biosignalsplux/python-samples/tree/master/PLUX-API-Python3) to the `devices/pluxlib` folder.

argparser.py

@@ -46,13 +46,21 @@ def getSamplingFrequency(args):
 
 def getFilename(args):
     if '--filename' in args:
-        index = next(i for i, arg in enumerate(args) if arg == '--filename' or arg == '-f')
+        index = next(i for i, arg in enumerate(args) if arg == '--filename')
         try:
             return args[index+1]
         except IndexError:
             raise ValueError('filename is empty')
     return None
 
+def getPort(args):
+    if '--port' in args:
+        index = next(i for i, arg in enumerate(args) if arg == '--port')
+        try:
+            return args[index+1]
+        except IndexError:
+            raise ValueError('port is empty')
+    return None
 
 
 source_types = ['ecg', 'eda', 'eeg', 'emg']

art-bio.py

@@ -1,3 +1,4 @@
+# coding=UTF-8
 readme = '''
  🐍 rt-bio : A Real-Time BIOsignal feature extraction tool 🦆 
     https://github.com/vatte/rt-bio
@@ -42,6 +43,7 @@
 
 import argparser as parser
 from devices import *
+from devices.Biosignalsplux import Biosignalsplux
 from init_sources import init_sources
 from router import Router
 
@@ -58,6 +60,7 @@
 router.osc_address = '127.0.0.1:4810'
 router.osc_prefix = '/rtbio'
 router.filename = 'temp.txt'
+router.ws_port = 5678
 
 args = sys.argv
 
@@ -82,6 +85,10 @@
         device_list = OpenBCI.list_devices(None)
         for i, dev in enumerate(device_list):
             print('[{}] {}'.format(i, dev))
+    elif(device_name == 'biosignalsplux'):
+        device_list = Biosignalsplux.list_devices(None)
+        for i, dev in enumerate(device_list):
+            print('[{}] {}'.format(i, dev))
     else:
         raise ValueError('No such device: ' + device_name)
     print('exiting...')
@@ -102,6 +109,11 @@
 if filename_arg:
     router.filename = filename_arg
 
+#get ws port from args
+port_arg = parser.getPort(args)
+if port_arg:
+    router.ws_port = port_arg
+
 
 #get sampling_frequency from args
 sampling_frequency_arg = parser.getSamplingFrequency(args)
@@ -134,6 +146,14 @@
     def noDigital():
         raise ValueError('openbci has no digital output defined')
     router.digital_out_func = noDigital
+elif device_name == 'biosignalsplux':
+    device = Biosignalsplux(device_index)
+    if 'biosignalsplux' in config:
+        channels = {}
+        for k in config['biosignalsplux']:
+            channels[k] = [ int(c) for c in config['biosignalsplux'][k].split(',') ]
+        device.channel_map = channels
+
 else:
     raise ValueError('No such device: ' + device_name)
 
@@ -145,15 +165,34 @@ def noDigital():
 #start streaming
 device.start(sampling_frequency, sources.keys())
 
+## filter experiment here for powerline
+# from scipy import signal
+
+# b,a = signal.iirnotch(50, 25, 100)
+
+# print("B: " + str(b) + "A: " + str(a))
+
+# z = [0, 0, 0, 0, 0, 0, 0, 0]
+# for i, zz in enumerate(z):
+#     z[i] = signal.lfilter_zi(b, a)
+
 try:
     while True:
         # Read samples
         samples = device.read()
+        #print(samples)
         for source in samples.keys():
             features = []
             for i, channel in enumerate(samples[source]):
-                features.append(sources[source][i].add_data(channel))
+                #for j, s in enumerate(channel):
+                    #y, z[i] = signal.lfilter(b,a,[s], zi = z[i])
+                    #channel[j] = y[0]
+                if source != 'unknown' and source in sources:
+                    features.append(sources[source][i].add_data(channel))
             router.route_data(source, connections, features, samples[source])
 
-except KeyboardInterrupt:
+except (Exception, KeyboardInterrupt) as e:
     device.close()
+    if router.ws_server:
+        router.ws_server.stop()
+    raise(e)

art-bio.yaml

@@ -0,0 +1,31 @@
+name: art-bio
+channels:
+  - defaults
+dependencies:
+  - blas=1.0=mkl
+  - ca-certificates=2021.10.26=haa95532_2
+  - certifi=2021.10.8=py38haa95532_0
+  - icc_rt=2019.0.0=h0cc432a_1
+  - intel-openmp=2021.4.0=haa95532_3556
+  - mkl=2021.4.0=haa95532_640
+  - mkl-service=2.4.0=py38h2bbff1b_0
+  - mkl_fft=1.3.1=py38h277e83a_0
+  - mkl_random=1.2.2=py38hf11a4ad_0
+  - numpy=1.21.2=py38hfca59bb_0
+  - numpy-base=1.21.2=py38h0829f74_0
+  - openssl=1.1.1l=h2bbff1b_0
+  - pip=21.0.1=py38haa95532_0
+  - pyserial=3.5=py38haa95532_0
+  - python=3.8.12=h6244533_0
+  - scipy=1.7.1=py38hbe87c03_2
+  - six=1.16.0=pyhd3eb1b0_0
+  - sqlite=3.36.0=h2bbff1b_0
+  - vc=14.2=h21ff451_1
+  - vs2015_runtime=14.27.29016=h5e58377_2
+  - wheel=0.37.0=pyhd3eb1b0_1
+  - wincertstore=0.2=py38haa95532_2
+  - pip:
+    - bitalino==1.2.1
+    - python-osc==1.8.0
+    - setuptools==57.5.0
+    - websockets==10.1

biosignals.bat

@@ -0,0 +1,5 @@
+@ECHO on
+call C:\Users\MTG-user\anaconda3\Scripts\activate.bat activate art-bio
+cd C:\Users\MTG-user\Desktop\art-bio-biosignalsplux
+python art-bio.py -d biosignalsplux -c reeg ws -c recg ws -c reda ws -c reeg file -c recg file -c reda file --filename readings.txt
+PAUSE

config.ini

@@ -1,7 +1,12 @@
 #bitalino channel configuration for custom setups
 #analog inputs are starting with index 0
 [bitalino]
-emg: 0
+emg: 0,4
 ecg: 1
 eda: 2
-eeg: 3
+eeg: 3
+
+[biosignalsplux]
+eeg: 0,1
+ecg: 2
+eda: 3

devices/Biosignalsplux.py

@@ -0,0 +1,133 @@
+# biosignalsplux
+
+import glob
+import sys
+import platform
+import time
+
+from threading import Thread
+
+sys.path.append('devices/pluxlib') #add the plux library for your platform to this folder
+import plux
+
+from .Device import Device
+
+class Biosignalsplux(Device):
+
+    def __init__(self, dev_i = 0):
+
+        #default channel numbers for biosignalsplux
+        self.channel_map = {
+            'emg': [0],
+            'ecg': [1],
+            'eda': [2],
+            'eeg': [3]
+        }
+
+        # find device
+        print('Looking for biosignalsplux device')
+        retries = 0
+        self.device_list = []
+
+        while retries < 3 and len(self.device_list) == 0:
+            self.device_list = self.list_devices()
+
+        if len(self.device_list) == 0:
+            raise Exception('No biosignalsplux device found')
+
+        try:
+            device_address = self.device_list[dev_i]
+        except IndexError:
+            raise Exception('No biosignalsplux found with index ' + str(dev_i))
+
+        print("Connecting to " + device_address)
+
+        class PluxDevice(plux.SignalsDev):
+            def __init__(self, address):
+                plux.MemoryDev.__init__(address)
+                self.started = True
+                self.in_samples = []
+
+            def onRawFrame(self, nSeq, data):  # onRawFrame takes three arguments
+                self.in_samples.append(data)
+                if not self.started:
+                    return True
+                return False
+
+        # Connect to biosignalsplux
+        self.device = PluxDevice(device_address)
+
+    #find all devices
+    def list_devices(self):
+        devices = []
+        for mac in plux.BaseDev.findDevices():
+            devices.append(mac[0])
+        return devices
+
+    #start streaming
+    def start(self, fs, channels):
+        self.fs = fs
+        self.channels = []
+        chans = []
+        #order channels for biosignalsplux 
+        for c in self.channel_map.keys():
+            if c in channels:
+                for index in self.channel_map[c]:
+                    chans.append(index)
+        chans.sort()
+        self.n_chans = chans[-1] + 1
+        for c in range(self.n_chans):
+            found = False
+            for k in self.channel_map:
+                if c in self.channel_map[k]:
+                    self.channels.append(k)
+                    found = True
+                    break
+            if not found:
+                self.channels.append('unknown')
+        print(self.channels)
+
+        codes = [ 0x01, 0x03, 0x07, 0x0F, 0x1F, 0x3F, 0x7F, 0xFF] #codes for biosignalsplux device for different n_chans
+
+        # Start Acquisition
+        self.started = True
+        self.device.started = True
+        self.device.start(fs, codes[self.n_chans-1], 16)
+
+        def myfunc():
+            self.device.loop()
+
+        t = Thread(target=myfunc)
+        t.start()
+
+
+
+    #read samples (blocking)
+    def read(self):
+        samples = {}
+
+        while len(self.device.in_samples) == 0:
+            time.sleep(0.01)
+
+        for i, c in enumerate(self.channels):
+            if not c in samples:
+                samples[c] = []
+            samples[c].append([s[i] for s in self.device.in_samples])
+        #if 'eeg' in samples:
+        #    samples['eeg'] = [ [ [samples['eeg'][i][j] for i in range(len(samples['eeg'])) ] for j in range(len(samples['eeg'][0]))] ]
+        #print(samples)
+        self.device.in_samples = [] # clear the sample buffer
+        return samples
+
+    #stop streaming
+    def stop(self):
+        # Stop acquisition
+        self.started = False
+        self.device.started = False
+
+    #close connection
+    def close(self):
+        if self.started:
+            self.started = False
+            self.device.started = False
+