open-ephys-plugins · no-bo · Sep 2, 2022 · Sep 2, 2022 · Sep 2, 2022 · Sep 2, 2022
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@ if (NOT DEFINED GUI_BASE_DIR)
 	if (DEFINED ENV{GUI_BASE_DIR})
 		set(GUI_BASE_DIR $ENV{GUI_BASE_DIR})
 	else()
-		set(GUI_BASE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../../plugin-GUI)
+		set(GUI_BASE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../../plugin-GUI-main)
 	endif()
 endif()
 

diff --git a/README.md b/README.md
@@ -2,16 +2,19 @@
 
 ![matlab-interface-screenshot](Resources/matlab-interface.png)
 
-Streams one channel of continuous data from the Open Ephys GUI to a live Matlab session. A Matlab API allows seamless processing of the incoming data in real time.
+Streams channel and spike_id information of all sorted spikes from open-ephys to matlab. The major application of the present plugin is my custom-made matlab-based close-loop BCI algorithm. It may also help with spike-oriented live processing.
 
 
 ## Installation
 
-This plugin can be added via the Open Ephys GUI Plugin Installer. To access the Plugin Installer, press **ctrl-P** or **⌘P** from inside the GUI. Once the installer is loaded, browse to the "Matlab Interface" plugin and click "Install."
+(Coming soon)
+
 
 ## Usage
 
-Once installed, the plugin will appear as 'Matlab Interface' in the 'Filters' section of the 'Processor List' of the Open Ephys GUI. The plugin can be placed after any source, filter, or sink in the signal chain and will stream the data output by the preceding processor into your Matlab session. 
+Once installed, the plugin will appear as 'Matlab Interface' in the 'Filters' section of the 'Processor List' of the Open Ephys GUI. The plugin can be placed after any source, filter, or sink in the signal chain and will stream the data output by the preceding processor into your Matlab session. A 'Spike Sorter' must be upstream of 'Matlab Interface', otherwise fatal errors shall arise. Signal chain like below shall work properly:
+
+![matlab-interface-screenshot](Resources/chain.png)
 
 Before starting data acquisition, you will need to press the 'Connect' button in the editor to initiate a connection between the plugin and your Matlab session. The plugin will open a socket using the IP and Port address listed in the Matlab Interface editor.
 
@@ -51,149 +54,62 @@ classdef MyClass < GenericProcessor
 end
 ```
 
-Here's an example of a simple peak detection algorithm:
-
-```matlab
-classdef PeakDetector < GenericProcessor
-
-    properties
-        peaks;
-    end
-
-    methods 
-        function self = PeakDetector(host, port)
-            self = self@GenericProcessor(host, port);
-            self.process();
-        end
-    end
-
-    methods (Access = protected)
-        function process(self)
-            while (true)
-                process@GenericProcessor(self); 
-                yd = diff(self.dataIn.continuous)./diff(1:self.dataIn.numSamplesFetched);
-                self.peaks = find(~yd);
-            end
-        end
-    end
-end
-```
+Once you have designed your class, you can call it from the Matlab command window using `MyClass(host,port)`, where host and port need to match the entries specified in the MatlabEngine editor in the OpenEphys GUI. 
 
-And a simple threshold detector... 
+However, for those who are not familiar with object-oriented programming of matlab, simple scripts are available using the API provided. Here is an example that prints information of every spike every 50ms:
 
 ```matlab
-classdef ThresholdDetector < GenericProcessor
-
-    properties
-        thresholdValue;
-    end
-
-    methods 
-        function self = ThresholdDetector(host, port)
-            self = self@GenericProcessor(host, port);
-            self.thresholdValue = 3.2; %V
-            self.process();
-        end
-    end
-
-    methods (Access = protected)
-        function process(self)
-            while (true)
-                process@GenericProcessor(self); 
-                k = find(self.dataIn.continuous > self.thresholdValue);
+host='127.0.0.1'
+port=1234
+processor=GenericProcessor(host, port);
+
+cycle_duration=0.05 %50ms cycle
+
+timeall=tic();
+while 1
+    timet=tic();
+
+    data=[];	
+    t=processor.process();
+    if ~isempty(t)
+        t=split(t,' ');
+        for i=1:length(t)-1
+            % For some unknown reason, there are some garbled codes in the data received for the first time
+            % If your system language is CHINESE, such codes are presented in the form of '屯'
+            % For users of other languages, you may experiment yourself
+            % For formal use, simply discard the data obtained the first time
+            if ~isempty(t{i}) && t{i}(1)~='屯' 
+                tt=split(t{i},'+');
+                data=[data;str2double(tt(1)),str2double(tt(2))];
             end
         end
     end
+
+    if ~isempty(data)
+        data
+    end
+
+    while toc(timet)<cycle_duration;   end
+
+    toc(timeall)
 end
 ```
 
-And here's an example of a Plotter that plots the incoming data to a figure in real-time. 
-
-```matlab
-classdef Plotter < GenericProcessor
-
-    properties
-        hPlot;
-    end
-
-    properties
-        xAxisRange;
-        yAxisRange;
-    end
-
-    methods 
-
-        function self = Plotter(host, port)
-
-            self = self@GenericProcessor(host, port);
-
-            self.xAxisRange = [0,80000];
-            self.yAxisRange = [-1000 1000];
-
-            plotTitle = 'Open Ephys Data Stream';
-            xLabel = 'Sample Count';
-            yLabel = 'Voltage [uV]';
-
-            clf; cla; 
-            self.hPlot = plot(0,0); drawnow; hold on;
-            title(plotTitle);
-            xlabel(xLabel); ylabel(yLabel);
-            xlim(self.xAxisRange); ylim(self.yAxisRange);
-
-            self.process();
-        end
-    end
-
-    methods (Access = protected)
-
-        function process(self)
-
-            lastSample = 0;
-            xAxisSize = self.xAxisRange(2);
-
-            while ishandle(self.hPlot) 
-
-                process@GenericProcessor(self); 
-
-                numSamples = self.dataIn.numSamplesFetched;
 
-                if lastSample + numSamples > xAxisSize
-                    xData = (lastSample+1):xAxisSize;
-                    yData = self.dataIn.continuous(1:(xAxisSize-lastSample));
-                else
-                    xData = (lastSample+1):(lastSample+numSamples);
-                    yData = self.dataIn.continuous;
-                end
-
-                self.hPlot = plot(xData,yData); drawnow;
-                set(self.hPlot, 'XData', xData, 'YData', yData); 
-
-                %TODO: Currently ignores (doesn't plot) samples that overshoot x-axis range
-                lastSample = lastSample + numSamples;
-                if lastSample > xAxisSize
-                    lastSample = 0;
-                    cla; self.hPlot = plot(0,0); drawnow; 
-                end
-            end
-        end
-    end
-end
-```
 
-Once you have designed your class, you can call it from the Matlab command window using `MyClass(host,port)`, where host and port need to match the entries specified in the MatlabEngine editor in the OpenEphys GUI. 
 
 
 ## Building from source
 
 First, follow the instructions on [this page](https://open-ephys.github.io/gui-docs/Developer-Guide/Compiling-the-GUI.html) to build the Open Ephys GUI.
 
-**Important:** This plugin is intended for use with the latest version of the GUI (0.6.0 and higher). The GUI should be compiled from the [`main`](https://github.com/open-ephys/plugin-gui/tree/main) branch, rather than the former `master` branch.
+**Important:** This plugin is intended for the latest version of open-ephys GUI (**0.6.0**). 
 
 Then, clone this repository into a directory at the same level as the `plugin-GUI`, e.g.:
 
 ```
 Code
-├── plugin-GUI
+├── plugin-GUI-master
 │   ├── Build
 │   ├── Source
 │   └── ...
@@ -218,6 +134,7 @@ Next, launch Visual Studio and open the `OE_PLUGIN_matlab-interface.sln` file th
 
 Selecting the `INSTALL` project and manually building it will copy the `.dll` and any other required files into the GUI's `plugins` directory. The next time you launch the GUI from Visual Studio, the Matlab Interface plugin should be available.
 
+**Warning:** Linux and macOS are not tested yet
 
 ### Linux
 
@@ -232,7 +149,7 @@ make -j
 make install
 ```
 
-This will build the plugin and copy the `.so` file into the GUI's `plugins` directory. The next time you launch the compiled version of the GUI, the Matlab Interface plugin should be available.
+This will build the plugin and copy the `.so` file into the GUI's `plugins` directory. The next time you launch the GUI compiled version of the GUI, the Matlab Interface plugin should be available.
 
 
 ### macOS
@@ -251,4 +168,4 @@ Running the `ALL_BUILD` scheme will compile the plugin; running the `INSTALL` sc
 
 ### Questions and Troubleshooting
 
-If you have any questions and/or issues regarding this plugin, please open an Issue in this repository or reach out to [email protected].
+If you have any questions and/or issues regarding this plugin, please open an Issue in this repository.
diff --git a/Resources/API/GenericProcessor.m b/Resources/API/GenericProcessor.m
@@ -15,7 +15,7 @@
 
 			self.client = OEClient(host, port);
 			self.dataIn = DataBuffer(self.client);
-            self.dataOut = ['Test!' blanks(self.client.WRITE_MSG_SIZE_IN_BYTES/2-5)];
+            self.dataOut = ['Fetch' blanks(self.client.WRITE_MSG_SIZE_IN_BYTES/2-5)];
             self.timer = tic;
             self.dataRate = 0;
             self.packetsFetched = 0;
@@ -24,16 +24,23 @@
 
 	end
 
-	methods (Access = protected)
+	methods (Access = public)
 
-		function process(self)
+		function data=process(self)
             self.client.write(self.dataOut);
-			self.dataIn.continuous = str2num(self.client.read()); %#ok<*ST2NM>
-            self.packetsFetched = self.packetsFetched + 1;
-			self.dataIn.numSamplesFetched = length(self.dataIn.continuous);
-            lastFetch = self.dataIn.numSamplesFetched/toc(self.timer);
-            self.dataRate = (lastFetch + self.packetsFetched * self.dataRate ) / (self.packetsFetched + 1);
-            fprintf("Data rate: %1.2f\n", self.dataRate);
+            t=tic();
+            while toc(t)<0.002
+            end
+            data=self.client.read();
+            data=char(data);
+%             fprintf("%s;\n",t);
+
+% 			self.dataIn.continuous = t; %#ok<*ST2NM>
+%             self.packetsFetched = self.packetsFetched + 1;
+% 			self.dataIn.numSamplesFetched = length(self.dataIn.continuous);
+%             lastFetch = self.dataIn.numSamplesFetched/toc(self.timer);
+%             self.dataRate = (lastFetch + self.packetsFetched * self.dataRate ) / (self.packetsFetched + 1);
+%             fprintf("Data rate: %1.2f\n", self.dataRate);
             self.timer = tic;
 		end
 

diff --git a/Resources/API/OEClient.m b/Resources/API/OEClient.m
@@ -1,9 +1,9 @@
 classdef OEClient < handle
 
-    %OECLIENT A client socket for receiving data streams from the Open-Ephys GUI. 
+    %OECLIENT A client socket for receiving data streams from the Open-Ephys GUI.
     %   This class encapsulates a socket on a dedicated, local port in order to
-    %   receive continous data stream from Open Ephys. 
-
+    %   receive continous data stream from Open Ephys.
+    
     properties (Access = public)
         header;
     end
@@ -19,13 +19,13 @@
         stream_reader;
         buffered_reader;
     end
-
+    
     properties (Constant)
         END_OF_MESSAGE = '~';
-        MAX_CONNECT_ATTEMPTS = 5;
+        MAX_CONNECT_ATTEMPTS = 50;
         WRITE_MSG_SIZE_IN_BYTES = 1024;
     end
-
+    
     methods
 
         function self = OEClient(host, port)
@@ -41,23 +41,32 @@
                 attempts = attempts + 1;
             end
 
-            if ~self.connected 
+            if ~self.connected
                 fprintf("Failed to connect to Open Ephys!\n");
             end
 
         end
-
+        
         function line = read(self)
-
-            line = self.buffered_reader.readLine;
-
+%             line=[];
+%             t=self.buffered_reader.read()
+%             while t~=-1
+%                 line=[line t];
+%                 t=self.buffered_reader.read()
+%             end
+%             line=[line t];
+if self.buffered_reader.ready()
+    line = self.buffered_reader.readLine();
+else
+    line=[];
+end
         end
-
+        
         function self = write(self, message)
 
-            fprintf("Size of msg: %d\n", length(message));
-            fprintf("Message: %s\n", message);
-
+            %             fprintf("Size of msg: %d\n", length(message));
+            %             fprintf("Message: %s\n", message);
+            
             if (length(message)/2 == self.WRITE_MSG_SIZE_IN_BYTES)
                 self.stream_writer.writeBytes(message);
                 self.stream_writer.flush;
@@ -66,7 +75,7 @@
                 self.stream_writer.writeBytes([message msg_pad]);
                 self.stream_writer.flush;
             end
-
+            
         end
 
         function self = connect(self, host, port)
@@ -87,12 +96,12 @@
                 fprintf("Created output stream writer...\n");
                 self.stream_reader = InputStreamReader(self.in_stream);
                 fprintf("Created input stream reader...\n");
-                self.buffered_reader = BufferedReader(self.stream_reader);
+                self.buffered_reader = BufferedReader(self.stream_reader,65536);
                 fprintf("Created buffered reader...\n");
-            catch 
-                fprintf("Connecting...\n");
+            catch
+                fprintf("Connecting openEphys...\n");
             end
-
+            
         end
 
     end

diff --git a/Resources/chain.png b/Resources/chain.png