Dev 133 create plotand write ecg example for matlab

Resources/newWriteHeadersToFile.m

@@ -0,0 +1,27 @@
+function firstTime = newWriteHeadersToFile(fileName, signalNameArray, signalFormatArray, signalUnitArray)
+
+    if iscell(signalNameArray)
+        signalNames = cellfun(@char, signalNameArray, 'UniformOutput', false);
+    end
+
+    if iscell(signalFormatArray)
+        signalFormats = cellfun(@char, signalFormatArray, 'UniformOutput', false);
+    end
+
+    if iscell(signalUnitArray)
+        signalUnits = cellfun(@char, signalUnitArray, 'UniformOutput', false);
+    end
+
+    signalNamesString = strjoin(signalNames, '\t');
+    signalFormatsString = strjoin(signalFormats, '\t');
+    signalUnitsString = strjoin(signalUnits, '\t');
+
+    fid = fopen(fileName, 'wt');
+    if fid == -1
+        error('Cannot open file: %s', fileName);
+    end
+    fprintf(fid, '%s\n%s\n%s\n', signalNamesString, signalFormatsString, signalUnitsString);
+    fclose(fid);
+
+    firstTime = false;
+end

ShimmerDeviceHandler.m

@@ -0,0 +1,52 @@
+classdef ShimmerDeviceHandler
+    properties
+        obj
+        shimmer
+        comPort
+        sensorClass
+    end
+
+    methods
+        function this = ShimmerDeviceHandler(comPort)
+            javaaddpath('ShimmerBiophysicalProcessingLibrary_Rev_0_10.jar');
+            javaaddpath('libs/ShimmerJavaClass.jar');
+            javaaddpath('libs/jssc-2.9.6.jar');
+            javaaddpath('libs/vecmath-1.3.1.jar');
+            javaaddpath('libs/commons-lang3-3.8.1.jar');
+
+            this.sensorClass = javaObjectEDT('com.shimmerresearch.driver.Configuration$Shimmer3$SENSOR_ID');
+            this.comPort = comPort;
+            this.obj = com.shimmerresearch.tools.matlab.ShimmerJavaClass();
+        end
+
+        function [success, this] = connect(this)
+            this.obj.mBluetoothManager.connectShimmerThroughCommPort(this.comPort);
+
+            timeout = 15;
+            startTime = tic;
+            this.shimmer = [];
+
+            while isempty(this.shimmer) && toc(startTime) < timeout
+                pause(1);
+                this.shimmer = this.obj.mBluetoothManager.getShimmerDeviceBtConnected(this.comPort);
+
+                if ~isempty(this.shimmer)
+                    disp(['Device connected... Elapsed time: ', num2str(toc(startTime)), ' seconds']);
+                    success = true;
+                    pause(10);
+                    return;
+                end
+            end
+            success = false;
+        end
+
+        function success = start(this)
+            this.shimmer = this.obj.mBluetoothManager.getShimmerDeviceBtConnected(this.comPort);
+            if isempty(this.shimmer)
+                error('Shimmer device is not connected.');
+            end
+            this.shimmer.startStreaming();
+            success = true;
+        end
+    end
+end

javaclasspath.txt

@@ -1,4 +1,4 @@
 <before>
 
-C:\Users\AbdullahHarithJamadi\Documents\MATLAB\libs\commons-math-2.2.jar
-C:\Users\AbdullahHarithJamadi\Documents\MATLAB\libs\commons-math3-3.6.jar
+C:\Users\AbdullahHarithJamadi\Documents\GitHub\Shimmer-MATLAB-ID\libs\commons-math-2.2.jar
+C:\Users\AbdullahHarithJamadi\Documents\GitHub\Shimmer-MATLAB-ID\libs\commons-math3-3.6.jar

newplotandwriteecgexample.m

@@ -0,0 +1,254 @@
+function shimmer = newplotandwriteecgexample(comPort, captureDuration, fileName)
+%NEWPLOTANDWRITEECGEXAMPLE - Plotting ecg signal and write to file
+%  INPUT: comPort  - String value defining the COM port number for Shimmer
+%   
+%  INPUT: captureDuration  - Numerical value defining the capture duration
+%
+%  INPUT: fileName - String value defining the name of the data file
+%
+%  OUTPUT: shimmer  - Object of the ShimmerDeviceHandler
+%
+%  EXAMPLE: newplotandwriteecgexample('COM5', 30, 'testdata.dat')
+%
+%  See also newplotandwriteexample ShimmerDeviceHandler
+%
+% Example for Shimmer3
+
+%% definitions
+shimmer = ShimmerDeviceHandler(comPort);                                     % Define shimmer as a ShimmerHandle Class instance with comPort1
+
+    fs = 512;                                                                  % sample rate in [Hz]
+    firsttime = true;
+
+    % Note: these constants are only relevant to this examplescript and are not used
+    % by the ShimmerHandle Class
+    NO_SAMPLES_IN_PLOT = 5000;                                                 % Number of samples in the plot 
+    DELAY_PERIOD = 0.2;                                                        % Delay (in seconds) between data read operations
+    numSamples = 0;
+
+    addpath('./Resources/')   
+%% settings
+
+    % filtering settings
+    fm = 50;                                                                   % mains frequency [Hz]
+    fchp = 0.5;                                                                % corner frequency highpassfilter [Hz]; Shimmer recommends 0.5Hz for monitoring applications, 0.05Hz for diagnostic settings
+    nPoles = 4;                                                                % number of poles (HPF, LPF)
+    pbRipple = 0.5;                                                            % pass band ripple (%)
+
+    HPF = true;                                                                % enable (true) or disable (false) highpass filter
+    LPF = true;                                                                % enable (true) or disable (false) lowpass filter
+    BSF = true;                                                                % enable (true) or disable (false) bandstop filter
+
+    % highpass filters for ExG channels
+    if (HPF)
+        hpfexg1ch1 = FilterClass(FilterClass.HPF,fs,fchp,nPoles,pbRipple);
+        hpfexg1ch2 = FilterClass(FilterClass.HPF,fs,fchp,nPoles,pbRipple);
+        hpfexg2ch1 = FilterClass(FilterClass.HPF,fs,fchp,nPoles,pbRipple);
+        hpfexg2ch2 = FilterClass(FilterClass.HPF,fs,fchp,nPoles,pbRipple);
+    end
+    % lowpass filters for ExG channels
+    if (LPF)
+        lpfexg1ch1 = FilterClass(FilterClass.LPF,fs,fs/2-1,nPoles,pbRipple);
+        lpfexg1ch2 = FilterClass(FilterClass.LPF,fs,fs/2-1,nPoles,pbRipple);
+        lpfexg2ch1 = FilterClass(FilterClass.LPF,fs,fs/2-1,nPoles,pbRipple);
+        lpfexg2ch2 = FilterClass(FilterClass.LPF,fs,fs/2-1,nPoles,pbRipple);
+    end
+    % bandstop filters for ExG channels;
+    % cornerfrequencies at +1Hz and -1Hz from mains frequency
+    if (BSF)
+        bsfexg1ch1 = FilterClass(FilterClass.LPF,fs,[fm-1,fm+1],nPoles,pbRipple);
+        bsfexg1ch2 = FilterClass(FilterClass.LPF,fs,[fm-1,fm+1],nPoles,pbRipple);
+        bsfexg2ch1 = FilterClass(FilterClass.LPF,fs,[fm-1,fm+1],nPoles,pbRipple);
+        bsfexg2ch2 = FilterClass(FilterClass.LPF,fs,[fm-1,fm+1],nPoles,pbRipple);
+    end
+
+%%
+
+[success, obj] = shimmer.connect();
+
+if success
+
+    shimmerClone = obj.shimmer.deepClone();
+    shimmerClone.setSamplingRateShimmer(fs);
+
+    shimmerClone.disableAllSensors();                                      % Disables all currently enabled sensors
+    shimmerClone.setEnabledAndDerivedSensorsAndUpdateMaps(0, 0);           % Resets configuration on enabled and derived sensors
+
+    sensorIds = javaArray('java.lang.Integer', 1);
+    sensorIds(1) = java.lang.Integer(obj.sensorClass.HOST_ECG);
+
+    shimmerClone.setSensorIdsEnabled(sensorIds);
+
+    commType = javaMethod('valueOf', 'com.shimmerresearch.driver.Configuration$COMMUNICATION_TYPE', 'BLUETOOTH');
+    com.shimmerresearch.driverUtilities.AssembleShimmerConfig.generateSingleShimmerConfig(shimmerClone, commType);
+    obj.shimmer.configureFromClone(shimmerClone);
+
+    pause(20);
+
+    if shimmer.start()
+
+        plotData = [];                                               
+            timeStamp = [];
+            filteredplotData = [];
+
+            h.figure1=figure('Name','Shimmer ECG signals');                    % Create a handle to figure for plotting data from shimmer
+            set(h.figure1, 'Position', [100, 500, 800, 400]);
+            h.figure2=figure('Name','Shimmer ECG signals');                    % Create a handle to figure for plotting data from shimmer
+            set(h.figure2, 'Position', [950, 500, 800, 400]);
+
+            elapsedTime = 0;                                                   % Reset to 0    
+            tic;                                                               % Start timer
+
+            while (elapsedTime < captureDuration)       
+
+                pause(DELAY_PERIOD);                                           % Pause for this period of time on each iteration to allow data to arrive in the buffer
+                data = obj.obj.receiveData();                                  % Read the latest data from shimmer data buffer, signalFormatArray defines the format of the data and signalUnitArray the unit
+                newData = data(1);
+                signalNameArray = data(2);
+                signalFormatArray = data(3);
+                signalUnitArray = data(4); 
+
+                signalNameCellArray = cell(numel(signalNameArray), 1);     
+                for i = 1:numel(signalNameArray)
+                    signalNameCellArray{i} = char(signalNameArray(i));     % Convert each Java string to a MATLAB char array
+                end
+
+                signalFormatCellArray = cell(numel(signalFormatArray), 1);     
+                for i = 1:numel(signalFormatArray)
+                    signalFormatCellArray{i} = char(signalFormatArray(i));     % Convert each Java string to a MATLAB char array
+                end
+
+                signalUnitCellArray = cell(numel(signalUnitArray), 1);     
+                for i = 1:numel(signalUnitArray)
+                    signalUnitCellArray{i} = char(signalUnitArray(i));         % Convert each Java string to a MATLAB char array
+                end
+
+                if(~isempty(signalNameCellArray))
+                    chIndex(1) = find(ismember(signalNameCellArray, 'ECG_LL-RA_24BIT'));
+                    chIndex(2) = find(ismember(signalNameCellArray, 'ECG_LA-RA_24BIT'));
+                    chIndex(3) = find(ismember(signalNameCellArray, 'ECG_Vx-RL_24BIT'));
+                    chIndex(4) = find(ismember(signalNameCellArray, 'ECG_LL-LA_24BIT'));
+                end   
+
+                if (firsttime==true && isempty(newData)~=1)
+                    firsttime = newWriteHeadersToFile(fileName,signalNameCellArray(chIndex),signalFormatCellArray(chIndex),signalUnitCellArray(chIndex));
+                end
+
+                if ~isempty(newData)                                           % TRUE if new data has arrived
+
+                    ECGData = newData(:,chIndex);
+                    ECGDataFiltered = ECGData;
+                    % filter the data
+                    if HPF % filter newData with highpassfilter to remove DC-offset
+                        ECGDataFiltered(:,1) = hpfexg1ch1.filterData(ECGDataFiltered(:,1));
+                        ECGDataFiltered(:,2) = hpfexg1ch2.filterData(ECGDataFiltered(:,2));
+                        ECGDataFiltered(:,3) = hpfexg2ch1.filterData(ECGDataFiltered(:,3));
+                        ECGDataFiltered(:,4) = hpfexg2ch2.filterData(ECGDataFiltered(:,4));
+                    end
+
+                    if BSF % filter highpassfiltered data with bandstopfilter to suppress mains interference
+                        ECGDataFiltered(:,1) = bsfexg1ch1.filterData(ECGDataFiltered(:,1));
+                        ECGDataFiltered(:,2) = bsfexg1ch2.filterData(ECGDataFiltered(:,2));
+                        ECGDataFiltered(:,3) = bsfexg2ch1.filterData(ECGDataFiltered(:,3));
+                        ECGDataFiltered(:,4) = bsfexg2ch2.filterData(ECGDataFiltered(:,4));
+                    end
+
+                    if LPF % filter bandstopfiltered data with lowpassfilter to avoid aliasing
+                        ECGDataFiltered(:,1) = lpfexg1ch1.filterData(ECGDataFiltered(:,1));
+                        ECGDataFiltered(:,2) = lpfexg1ch2.filterData(ECGDataFiltered(:,2));
+                        ECGDataFiltered(:,3) = lpfexg2ch1.filterData(ECGDataFiltered(:,3));
+                        ECGDataFiltered(:,4) = lpfexg2ch2.filterData(ECGDataFiltered(:,4));
+                    end
+
+                    dlmwrite(fileName, double(ECGDataFiltered), '-append', 'delimiter', '\t','precision',16); % Append the new data to the file in a tab delimited format
+
+                    plotData = [plotData; ECGData];                            % Update the plotData buffer with the new ECG data
+                    filteredplotData = [filteredplotData; ECGDataFiltered];    % Update the filteredplotData buffer with the new filtered ECG data
+                    numPlotSamples = size(plotData,1);
+                    numSamples = numSamples + size(newData,1);
+                    timeStampNew = newData(:,1);                                   % get timestamps
+                    timeStamp = [timeStamp; timeStampNew];
+                    if numSamples > NO_SAMPLES_IN_PLOT
+                        plotData = plotData(numPlotSamples-NO_SAMPLES_IN_PLOT+1:end,:);
+                        filteredplotData = filteredplotData(numPlotSamples-NO_SAMPLES_IN_PLOT+1:end,:);
+                    end
+                    sampleNumber = max(numSamples-NO_SAMPLES_IN_PLOT+1,1):numSamples;
+
+                    set(0,'CurrentFigure',h.figure1);   
+                    subplot(2,2,1);                                        % Create subplot
+                    signalIndex = chIndex(1);
+                    plot(sampleNumber,plotData(:,1));                      % Plot the ecg for channel 1 of SENSOR_EXG1
+                    legendName1 = [char(signalFormatArray(signalIndex)) ' ' char(signalNameArray(signalIndex)) ' (' char(signalUnitArray(signalIndex)) ')']; 
+                    legend(legendName1);                                   % Add legend to plot
+                    xlim([sampleNumber(1) sampleNumber(end)]);
+
+                    subplot(2,2,2);                                        % Create subplot
+                    signalIndex = chIndex(2);
+                    plot(sampleNumber,plotData(:,2));                      % Plot the ecg for channel 2 of SENSOR_EXG1
+                    legendName1 = [char(signalFormatArray(signalIndex)) ' ' char(signalNameArray(signalIndex)) ' (' char(signalUnitArray(signalIndex)) ')'];   
+                    legend(legendName1);                                   % Add legend to plot
+                    xlim([sampleNumber(1) sampleNumber(end)]);
+
+                    subplot(2,2,3);                                        % Create subplot
+                    signalIndex = chIndex(1);
+                    plot(sampleNumber,filteredplotData(:,1));              % Plot the filtered ecg for channel 1 of SENSOR_EXG1
+                    legendName1 = [char(signalFormatArray(signalIndex)) ' ' char(signalNameArray(signalIndex)) ' (' char(signalUnitArray(signalIndex)) ')'];  
+                    legend(legendName1);                                   % Add legend to plot
+                    xlim([sampleNumber(1) sampleNumber(end)]);
+
+                    subplot(2,2,4);                                        % Create subplot
+                    signalIndex = chIndex(2);
+                    plot(sampleNumber,filteredplotData(:,2));              % Plot the filtered ecg for channel 2 of SENSOR_EXG1
+                    legendName1 = [char(signalFormatArray(signalIndex)) ' ' char(signalNameArray(signalIndex)) ' (' char(signalUnitArray(signalIndex)) ')'];  
+                    legend(legendName1);                                   % Add legend to plot
+                    xlim([sampleNumber(1) sampleNumber(end)]);
+
+
+                    set(0,'CurrentFigure',h.figure2);   
+                    subplot(2,2,1);                                        % Create subplot
+                    signalIndex = chIndex(3);
+                    plot(sampleNumber,plotData(:,3));                      % Plot the ecg for channel 1 of SENSOR_EXG1
+                    legendName1 = [char(signalFormatArray(signalIndex)) ' ' char(signalNameArray(signalIndex)) ' (' char(signalUnitArray(signalIndex)) ')']; 
+                    legend(legendName1);                                   % Add legend to plot
+                    xlim([sampleNumber(1) sampleNumber(end)]);
+
+                    subplot(2,2,2);                                        % Create subplot
+                    signalIndex = chIndex(4);
+                    plot(sampleNumber,plotData(:,4));                      % Plot the ecg for channel 2 of SENSOR_EXG1
+                    legendName1 = [char(signalFormatArray(signalIndex)) ' ' char(signalNameArray(signalIndex)) ' (' char(signalUnitArray(signalIndex)) ')'];   
+                    legend(legendName1);                                   % Add legend to plot
+                    xlim([sampleNumber(1) sampleNumber(end)]);
+
+                    subplot(2,2,3);                                        % Create subplot
+                    signalIndex = chIndex(3);
+                    plot(sampleNumber,filteredplotData(:,3));              % Plot the filtered ecg for channel 1 of SENSOR_EXG1
+                    legendName1 = [char(signalFormatArray(signalIndex)) ' ' char(signalNameArray(signalIndex)) ' (' char(signalUnitArray(signalIndex)) ')'];   
+                    legend(legendName1);                                   % Add legend to plot
+                    xlim([sampleNumber(1) sampleNumber(end)]);
+
+                    subplot(2,2,4);                                        % Create subplot
+                    signalIndex = chIndex(4);
+                    plot(sampleNumber,filteredplotData(:,4));              % Plot the filtered ecg for channel 2 of SENSOR_EXG1
+                    legendName1 = [char(signalFormatArray(signalIndex)) ' ' char(signalNameArray(signalIndex)) ' (' char(signalUnitArray(signalIndex)) ')'];  
+                    legend(legendName1);                                   % Add legend to plot
+                    xlim([sampleNumber(1) sampleNumber(end)]);
+
+                end
+
+                elapsedTime = elapsedTime + toc;                           % Update elapsedTime with the time that elapsed since starting the timer
+                tic;                                                       % Start timer           
+
+            end  
+
+            elapsedTime = elapsedTime + toc;                               % Update elapsedTime with the time that elapsed since starting the timer
+            fprintf('The percentage of received packets: %d \n',obj.shimmer.getPacketReceptionRateCurrent()); % Detect loss packets
+            obj.shimmer.stopStreaming();                                                  % Stop data streaming                                                    
+
+        end 
+
+    end
+
+    obj.shimmer.disconnect();
+
+end
+