Dev 131 create ecgtohr matlab example

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

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+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

newecgtoheartrateexample.m

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+function void = newecgtoheartrateexample(comPort, captureDuration, fileName)
+%NEWECGTOHEARTRATEEXAMPLE - Heart Rate from electrocardiogram signal
+%
+%  NEWECGTOHEARTRATEEXAMPLE(COMPORT, CAPTUREDURATION, FILENAME)
+%  plots ECG and estimated Heart Rate from the Shimmer
+%  paired with COMPORT. The function will stream data for a fixed duration
+%  of time defined by the constant CAPTUREDURATION. The function also
+%  writes the data in a tab delimited format to the file defined in
+%  FILENAME.
+%
+%  SYNOPSIS: newecgtoheartrateexample(comPort, captureDuration, fileName)
+%
+%  INPUT: comPort - String value defining the COM port number for Shimmer
+%
+%  INPUT: captureDuration - Numerical value defining the period of time
+%                           (in seconds) for which the function will stream
+%                           data from  the Shimmers.
+%  INPUT : fileName - String value defining the name of the file that data
+%                     is written to in a comma delimited format.
+%  OUTPUT: none
+%
+%  EXAMPLE: newecgtoheartrateexample('COM5', 30, 'testdata.dat')
+%
+%  See also plotandwriteexample ShimmerDeviceHandler
+%  newppgtoheartrateexample
+%
+% NOTE: To use the Java Shimmer Biophysical Processing Library in   
+% conjunction with the MATLAB ID:
+% Save the ShimmerBiophysicalProcessingLibrary_Rev_X_Y.jar  file to
+% C:\Program\Files\MATLAB\R2013b\java\jar (or the equivalent) on your PC and
+% add the location of the ShimmerBiophysicalProcessingLibrary_Rev_X_Y.jar file
+% to the JAVA dynamic class path:
+%
+% javaclasspath('C:\Program Files\MATLAB\R2013b\java\jar\ShimmerBiophysicalProcessingLibrary_Rev_X_Y.jar')
+%
+% NOTE: In this example the ECG data is pre-filtered using a second order
+% Chebyshev HPF with corner freq 0.5Hz by using FilterClass.m
+
+%% definitions
+shimmer = ShimmerDeviceHandler(comPort);                                     % Define shimmer as a ShimmerHandle Class instance with comPort1
+SensorMacros = SetEnabledSensorsMacrosClass;                               % assign user friendly macros for setenabledsensors
+
+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 = 2500;                                                 % Number of samples that will be displayed in the plot at any one time
+DELAY_PERIOD = 0.2;                                                        % A delay period of time in seconds between data read operations
+numSamples = 0;
+
+%% filter 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
+
+
+%% ECG2HR settings
+ECG2HR = com.shimmerresearch.biophysicalprocessing.ECGtoHRAdaptive(fs);  % create ECG to Heart Rate object
+
+%%
+
+[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 = [];
+        heartRate = [];
+        storeData = [];
+
+        h.figure1=figure('Name','Shimmer ECG and Heart Rate signals');     % create a handle to figure for plotting data from shimmer
+        set(h.figure1, 'Position', [100, 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();
+            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
+
+            if (firsttime==true && isempty(newData)~=1) 
+                tab = char(9);
+                cal = 'CAL';
+                signalNamesString =[char('Time Stamp'), tab, char('ECG LL-RA'), tab, char('ECG LL-RA Filtered'), tab, char('Heart Rate')]; % create a single string, signalNamesString    
+                signalFormatsString =[cal, tab, cal, tab, cal, tab, cal, tab];
+                signalUnitsString = ['milliseconds',tab,'mV',tab,'mV',tab,'BPM'];
+
+                % write headers to file
+                headerLines = {signalNamesString; signalFormatsString; signalUnitsString};
+                fid = fopen(fileName, 'wt');
+                for l = 1:numel(headerLines)
+                    fprintf(fid, '%s\n',headerLines{l});
+                end
+                fclose(fid);
+            end
+
+
+            if ~isempty(newData)                                                            % TRUE if new data has arrived
+
+                % get signal indices
+                chIndex(1) = find(ismember(signalNameCellArray, 'Timestamp'));
+                chIndex(2) = find(ismember(signalNameCellArray, 'ECG_LL-RA_24BIT'));                  % ECG output 'LL-RA'
+                ECGData = newData(:,chIndex(2));
+                ECGDataFiltered = ECGData;
+                if (HPF)
+                    ECGDataFiltered = hpfexg1ch1.filterData(ECGDataFiltered);               % filter with high pass filter
+                end
+                if (LPF)
+                    ECGDataFiltered = lpfexg1ch1.filterData(ECGDataFiltered);               % filter with low pass filter
+                end
+                if (BSF)
+                    ECGDataFiltered = bsfexg1ch1.filterData(ECGDataFiltered);               % filter with band stop filter
+                end
+
+                newheartRate = ECG2HR.ecgToHrConversion(ECGDataFiltered, newData(:,chIndex(1)));  % compute Heart Rate from ECG data
+
+
+                plotData = [plotData; ECGData];                                             % update the plotDataBuffer with the new PPG data
+                filteredplotData = [filteredplotData; ECGDataFiltered];                     % update the filteredplotData buffer with the new filtered PPG data
+                heartRate = [heartRate; newheartRate];                                      % update the filteredHRData buffer with the new filtered Heart Rate data
+                numPlotSamples = size(plotData,1);                          
+                numSamples = numSamples + size(newData,1);
+                timeStampNew = newData(:,chIndex(1));                                       % get timestamps
+                timeStamp = [timeStamp; timeStampNew];
+
+                newstoreData = [timeStampNew ECGData ECGDataFiltered newheartRate];
+                storeData = [storeData; newstoreData];
+
+                dlmwrite(fileName, storeData, '-append', 'delimiter', '\t', 'precision',16);                % append the new data to the file in a tab delimited format
+
+
+                 if numSamples > NO_SAMPLES_IN_PLOT
+
+                        plotData = plotData(numPlotSamples-NO_SAMPLES_IN_PLOT+1:end,:);
+                        filteredplotData = filteredplotData(numPlotSamples-NO_SAMPLES_IN_PLOT+1:end,:);
+                        heartRate = heartRate(numPlotSamples-NO_SAMPLES_IN_PLOT+1:end,:);
+
+                 end
+                 sampleNumber = max(numSamples-NO_SAMPLES_IN_PLOT+1,1):numSamples;
+
+
+                % plotting the data
+                set(0,'CurrentFigure',h.figure1);         
+                subplot(3,1,1)
+                plot(sampleNumber, plotData(:,1));                         % plot the PPG data
+                legend('ECG LL-RA (mV)', 'Location', 'West'); 
+                xlim([sampleNumber(1) sampleNumber(end)]);
+                ylim('auto');                                          
+
+                subplot(3,1,2)
+                plot(sampleNumber, filteredplotData(:,1));                 % plot the filtered PPG data
+                legend('Filtered ECG LL-RA (mV)', 'Location', 'West'); 
+                xlim([sampleNumber(1) sampleNumber(end)]);
+                ylim('auto');                                          
+
+                subplot(3,1,3)
+                plot(sampleNumber, heartRate);                             % plot the Heart Rate data
+                legend('Heart Rate (BPM', 'Location', 'West');   
+                xlim([sampleNumber(1) sampleNumber(end)]);
+                ylim('auto');           
+
+            end
+
+            elapsedTime = elapsedTime + toc;                               % stop timer and add to elapsed time
+            tic;                                                           % start timer           
+
+        end  
+
+        elapsedTime = elapsedTime + toc;                                   % stop timer
+        fprintf('The percentage of received packets: %d \n',obj.shimmer.getPacketReceptionRateCurrent()); % Detect loss packets
+        obj.shimmer.stopStreaming();                                                      % stop data streaming                                                    
+
+    end 
+
+    obj.shimmer.disconnect();                                                    % disconnect from shimmer
+
+end
+
+
+end