Merge pull request #962 from OpenBCI/development

GUI 5.0.4

Author: retiutut

.github/workflows/mergenovadev.yml

@@ -25,3 +25,4 @@ libBoardController.so
 libDataHandler.so
 libGanglionLib.so
 libGanglionScan.so
+libunicorn.so

.gitignore

@@ -13,7 +13,6 @@ jobs:
 branches:
   only:
   - master
-  - novaxr-dev
 
 before_install:
 - if [ "$TRAVIS_OS_NAME" = osx ] && [ "$TRAVIS_PULL_REQUEST" == "false" ]; then openssl aes-256-cbc -K $encrypted_2f5d2771e3cb_key -iv $encrypted_2f5d2771e3cb_iv -in release_script/mac_only/Certificates.p12.enc -out release_script/mac_only/Certificates.p12 -d; fi

.travis.yml

@@ -1,3 +1,20 @@
+# v5.0.4
+
+### Improvements
+* Add Copy/Paste for all textfields on all OS #940
+* Update BrainFlow library to version that includes a marker channel
+* Handle paths with spaces on Linux Standalone GUI #916
+* Allow Expert Ganglion Users to send square wave commands via keyboard #950
+* Show Send Custom Hardware Command UI for Cyton Expert Mode in Hardware Settings
+* Improve Hardware Setting UX/UI for ADS1299 boards #954
+
+### Bug Fixes
+* Clean up GUI code to fix Processing/JVM memory issue causing crash #955
+* Avoid playback history file not found exception #959
+* Fix issue with Spectrogram Widget data image default height
+* Fix issue with Accelerometer Widget graph default vertical scale
+* Fix text drawing in wrong spot in Session Data box in Control Panel
+
 # v5.0.3
 
 ### Improvements

CHANGELOG.md

@@ -0,0 +1,147 @@
+#############################################################################       
+##                           BrainFlow + LSL                               ##
+##      Use BrainFlow to read data from board send it as an LSL stream     ##
+#############################################################################
+
+# Install dependencies with:
+# pip install --upgrade numpy brainflow pylsl
+
+# Here are example commands using Cyton and get_exg_channels()from BrainFlow. This has only been tested with Cyton + Dongle, for now.
+
+# Mac:
+# python3 Networking-Test-Kit/LSL/brainflow_lsl.py --board-id 2 --serial-port /dev/cu.usbserial-DM00D7TW --name test --data-type EXG --channel-names 1,2,3,4,5,6,7,8 --uid brainflow
+
+# Windows:
+# python3 Networking-Test-Kit/LSL/brainflow_lsl.py --board-id 2 --serial-port COM3 --name test --data-type EXG --channel-names 1,2,3,4,5,6,7,8 --uid brainflow
+
+import argparse
+import time
+import numpy as np
+
+from queue import Queue
+
+import brainflow
+from brainflow.board_shim import BoardShim, BrainFlowInputParams
+from brainflow.data_filter import DataFilter, FilterTypes, AggOperations
+
+from pylsl import StreamInfo, StreamOutlet, local_clock
+
+def channel_select(board, board_id, data_type): 
+    switcher = { 
+        'EXG': board.get_exg_channels(board_id),
+        # can add more
+    } 
+ 
+    return switcher.get(data_type, "error") 
+
+def main():
+    BoardShim.enable_dev_board_logger()
+
+    parser = argparse.ArgumentParser()
+
+    # brainflow params - use docs to check which parameters are required for specific board, e.g. for Cyton set serial port
+    parser.add_argument('--timeout', type=int, help='timeout for device discovery or connection', required=False, default=0)
+    parser.add_argument('--ip-address', type=str, help='ip address', required=False, default='')
+    parser.add_argument('--board-id', type=int, help='board id, check docs to get a list of supported boards', required=True)
+    parser.add_argument('--serial-port', type=str, help='serial port', required=False, default='')
+    parser.add_argument('--streamer-params', type=str, help='streamer params', required=False, default='')
+
+    # LSL params 
+    parser.add_argument('--name', type=str, help='name', required=True)
+    parser.add_argument('--data-type', type=str, help='data type', required=True)
+    parser.add_argument('--channel-names', type=str, help='channel names', required=True)
+    parser.add_argument('--uid', type=str, help='uid', required=True)
+
+    args = parser.parse_args()
+
+    # brainflow initialization
+    params = BrainFlowInputParams()
+    params.serial_port = args.serial_port
+    params.ip_address = args.ip_address
+    board = BoardShim(args.board_id, params)
+
+    # LSL initialization  
+    channel_names = args.channel_names.split(',')
+    n_channels = len(channel_names)
+    srate = board.get_sampling_rate(args.board_id)
+    info = StreamInfo(args.name, args.data_type, n_channels, srate, 'double64', args.uid)
+    outlet = StreamOutlet(info)
+    fw_delay = 0
+
+    # prepare session
+    board.prepare_session()
+
+    # send commands to the board for every channel. Cyton has 8 Channels. Here, we turn off every channel except for 1 and 8.
+    # This is here for testing purposes.
+    #board.config_board("x1000110X") #Lower the gain to 1x on channel 1
+    #board.config_board("x1061000X")
+    #board.config_board("x2161000X")
+    #board.config_board("x3161000X")
+    #board.config_board("x4161000X")
+    #board.config_board("x5161000X")
+    #board.config_board("x6161000X")
+    #board.config_board("x7161000X")
+    #board.config_board("x8060110X")
+
+    # start stream
+    board.start_stream(45000, args.streamer_params)
+    time.sleep(1)
+    start_time = local_clock()
+    sent_samples = 0
+    queue = Queue(maxsize = 5*srate)
+    chans = channel_select(board, args.board_id, args.data_type)
+
+    # Vars for filters
+    applyBandStop = True
+    applyBandPass = True
+    bandStopFrequency = 60.0
+    bp_lowerBound = 5.0
+    bp_upperBound = 50.0
+    bp_centerFreq = (bp_upperBound + bp_lowerBound) / 2.0;
+    bp_bandWidth = bp_upperBound - bp_lowerBound
+
+
+    # read data with brainflow and send it via LSL
+    print("Now sending data...")
+    while True:
+        data = board.get_board_data()[chans]
+
+        # It's best to apply filters on the receiving end, but this is here just for testing purposes.
+        """
+        for chan in range(len(chans)):
+            if applyBandStop:
+                DataFilter.perform_bandstop(data[chan],
+                    BoardShim.get_sampling_rate(args.board_id), 
+                    bandStopFrequency,
+                    4.0,
+                    2,
+                    FilterTypes.BUTTERWORTH.value, 
+                    0);
+            if applyBandPass:
+                DataFilter.perform_bandpass(
+                    data[chan], 
+                    BoardShim.get_sampling_rate(args.board_id), 
+                    bp_centerFreq, 
+                    bp_bandWidth, 
+                    2, 
+                    FilterTypes.BUTTERWORTH.value, 
+                    0);
+        """
+
+        for i in range(len(data[0])):
+            queue.put(data[:,i].tolist())
+        elapsed_time = local_clock() - start_time
+        required_samples = int(srate * elapsed_time) - sent_samples
+        if required_samples > 0 and queue.qsize() >= required_samples:    
+            mychunk = []
+
+            for i in range(required_samples):
+                mychunk.append(queue.get())
+            stamp = local_clock() - fw_delay 
+            outlet.push_chunk(mychunk, stamp)
+            sent_samples += required_samples
+        time.sleep(1)
+
+
+if __name__ == "__main__":
+    main()

Networking-Test-Kit/LSL/brainflow_lsl.py

@@ -15,20 +15,25 @@
 
 def testLSLSamplingRate():
     start = time.time()
-    numSamples = 0
+    totalNumSamples = 0
+    validSamples = 0
     numChunks = 0
 
     while time.time() <= start + duration:
         # get chunks of samples
         samples, timestamp = inlet.pull_chunk()
-        if timestamp:
+        if samples:
             numChunks += 1
             print( len(samples) )
-            numSamples += len(samples)
+            totalNumSamples += len(samples)
             # print(samples);
+            for sample in samples:
+                print(sample)
+                validSamples += 1
 
-    print( "Number of Chunks == {}".format(numChunks) )
-    print( "Avg Sampling Rate == {}".format(numSamples / duration) )
+    print( "Number of Chunks and Samples == {} , {}".format(numChunks, totalNumSamples) )
+    print( "Valid Samples and Duration == {} / {}".format(validSamples, duration) )
+    print( "Avg Sampling Rate == {}".format(validSamples / duration) )
 
 
 testLSLSamplingRate()

Networking-Test-Kit/LSL/lslStreamTest.py

@@ -0,0 +1,58 @@
+"""Example program to show how to read a multi-channel time series from LSL."""
+import time
+from pylsl import StreamInlet, resolve_stream
+from time import sleep
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib import style
+from collections import deque
+
+# first resolve an EEG stream on the lab network
+print("looking for an EEG stream...")
+streams = resolve_stream('type', 'EXG')
+
+# create a new inlet to read from the stream
+inlet = StreamInlet(streams[0])
+duration = 10
+
+sleep(0)
+
+def testLSLSamplingRate():
+    start = time.time()
+    numSamples = 0
+    numChunks = 0
+
+    while time.time() <= start + duration:
+        # get chunks of samples
+        chunk, timestamp = inlet.pull_chunk()
+        if timestamp:
+            numChunks += 1
+            for sample in chunk:
+                numSamples += 1
+
+    print( "Number of Chunks == {}".format(numChunks) )
+    print( "Avg Sampling Rate == {}".format(numSamples / duration) )
+
+
+# testLSLSamplingRate()
+
+print("gathering data to plot...")
+
+def testLSLPulseData():
+    start = time.time()
+    raw_pulse_signal = []
+
+    while time.time() <= start + duration:
+        chunk, timestamp = inlet.pull_chunk()
+        if timestamp:
+            for sample in chunk:
+                print(sample)
+                raw_pulse_signal.append(sample[0])
+
+    # print(raw_pulse_signal)
+    print( "Avg Sampling Rate == {}".format(len(raw_pulse_signal) / duration) )
+    plt.plot(raw_pulse_signal)
+    plt.ylabel('raw analog signal')
+    plt.show()
+
+testLSLPulseData()