Merge branch 'master' into CON_v2_1

Author: jyong15

ShimmerBluetoothManager/build.gradle

@@ -12,6 +12,8 @@ Rev0.2
 
 sourceCompatibility = 1.11
 targetCompatibility = 1.11
+//sourceCompatibility = '1.8'  // Ensure code is compiled with Java 8 when compiling ShimmerJavaClass for Matlab see ShimmerDriverPC (build.gradle)
+//targetCompatibility = '1.8'  // Ensure bytecode is compatible with Java 8 when compiling ShimmerJavaClass for Matlab see ShimmerDriverPC (build.gradle)
 
 repositories {
     mavenCentral()

ShimmerDriver/build.gradle

@@ -15,6 +15,8 @@ Rev0.2
 apply plugin: 'java-library'
 sourceCompatibility = 1.11
 targetCompatibility = 1.11
+//sourceCompatibility = '1.8'  // Ensure code is compiled with Java 8 when compiling ShimmerJavaClass for Matlab see ShimmerDriverPC (build.gradle)
+//targetCompatibility = '1.8'  // Ensure bytecode is compatible with Java 8 when compiling ShimmerJavaClass for Matlab see ShimmerDriverPC (build.gradle)
 
 repositories {
     mavenCentral()

ShimmerDriver/src/main/java/com/shimmerresearch/driver/Configuration.java

@@ -677,7 +677,7 @@ public class SensorBitmap{
 		 * data packets. The firmware also uses the IMU IDs as Sensor IDs in the
 		 * IMU/BMP calibration bytes. 
 		 */
-		public class SENSOR_ID{
+		public static class SENSOR_ID{
 			public static final int RESERVED_ANY_SENSOR = -1;
 
 			public static final int HOST_SHIMMER_STREAMING_PROPERTIES = -100;

ShimmerDriver/src/main/java/com/shimmerresearch/driver/ObjectCluster.java

@@ -88,6 +88,7 @@ final public class ObjectCluster implements Cloneable,Serializable{
 
 	private String mMyName;
 	private String mBluetoothAddress;
+	private String mComPort;
 
 	// ------- Old Array approach - Start -----------
 	public byte[] mRawData;
@@ -220,6 +221,13 @@ public void setMacAddress(String macAddress){
 		mBluetoothAddress = macAddress;
 	}
 
+	public  void setComPort(String comport) {
+		mComPort = comport;
+	}
+	
+	public String getComPort() {
+		return mComPort;
+	}
 	/**
 	 * Takes in a collection of Format Clusters and returns the Format Cluster specified by the string format
 	 * @param collectionFormatCluster
@@ -247,6 +255,15 @@ public double getFormatClusterValue(ChannelDetails channelDetails, CHANNEL_TYPE
 		return getFormatClusterValue(channelDetails.mObjectClusterName, channelType.toString());
 	}
 
+	public FormatCluster getFormatCluster(String channelName, String format) 
+	{
+		FormatCluster formatCluster = getLastFormatCluster(channelName, format);
+		if(formatCluster!=null){
+			return formatCluster;
+		}
+		return null;
+	}
+	
 //	public double getFormatClusterValue(ChannelDetails channelDetails, String format){
 //		return getFormatClusterValue(channelDetails.mObjectClusterName, format);
 //	}

ShimmerDriver/src/main/java/com/shimmerresearch/driver/ShimmerDevice.java

@@ -4502,6 +4502,13 @@ public String getComPort() {
 		return mComPort;
 	}
 
+	/**This method will only return the comport name
+	 * @return
+	 */
+	public String getComPortName() {
+		return mComPort;
+	}
+	
 	public boolean isReadyToConnect() {
 		if (mCommsProtocolRadio==null 
 				||mCommsProtocolRadio.mRadioHal==null

ShimmerDriver/src/main/java/com/shimmerresearch/driver/ShimmerObject.java

@@ -812,6 +812,7 @@ public ObjectCluster buildMsg(byte[] newPacket, COMMUNICATION_TYPE fwType, boole
 
 		objectCluster.setShimmerName(mShimmerUserAssignedName);
 		objectCluster.setMacAddress(mMyBluetoothAddress);
+		objectCluster.setComPort(getComPortName());
 		objectCluster.mRawData = newPacket;
 
 		if(fwType!=COMMUNICATION_TYPE.BLUETOOTH && fwType!=COMMUNICATION_TYPE.SD){
@@ -4845,7 +4846,8 @@ public void setDefaultShimmerConfiguration() {
 			clearExgConfig(); // this currently must be called before sensorAndConfigMapsCreate() as it controls ExG booleans which affect EnabledSensors
 			sensorAndConfigMapsCreate();
 
-			if (getHardwareVersion() == HW_ID.SHIMMER_3){
+			int hwVersion = getHardwareVersion();
+			if (hwVersion == HW_ID.SHIMMER_3){
 				if(getExpansionBoardId()==HW_ID_SR_CODES.SHIMMER_ECG_MD){
 					setSensorEnabledState(Configuration.Shimmer3.SENSOR_ID.HOST_ECG, true);
 				} else {
@@ -4856,6 +4858,13 @@ public void setDefaultShimmerConfiguration() {
 
 					setIsAlgorithmEnabled(GyroOnTheFlyCalModule.GENERAL_ALGORITHM_NAME, true);
 				}
+			} else if (hwVersion == HW_ID.SHIMMER_3R) {
+				setSensorEnabledState(Configuration.Shimmer3.SENSOR_ID.SHIMMER_LSM6DSV_ACCEL_LN, true);
+				setSensorEnabledState(Configuration.Shimmer3.SENSOR_ID.SHIMMER_LSM6DSV_GYRO, true);
+				setSensorEnabledState(Configuration.Shimmer3.SENSOR_ID.SHIMMER_LIS2MDL_MAG, true);
+				setSensorEnabledState(Configuration.Shimmer3.SENSOR_ID.SHIMMER_VBATT, true);
+				
+				setIsAlgorithmEnabled(GyroOnTheFlyCalModule.GENERAL_ALGORITHM_NAME, true);
 			}
 
 			mTrialName = DEFAULT_EXPERIMENT_NAME;

ShimmerDriverPC/build.gradle

@@ -8,13 +8,17 @@
  */
 
 // Apply the java plugin to add support for Java
-apply plugin: 'java'
-apply plugin: 'java-library'
-apply plugin: 'eclipse'
-apply plugin: 'maven-publish'
-
+plugins {
+    id 'java'
+    id 'java-library'
+    id 'eclipse'
+    id 'maven-publish'
+    id 'com.github.johnrengelman.shadow' version '7.0.0'  // Apply the Shadow plugin
+}
 sourceCompatibility = 1.11
-
+targetCompatibility = 1.11
+//sourceCompatibility = '1.8'  // Ensure code is compiled with Java 8 when compiling ShimmerJavaClass for Matlab see ShimmerDriverPC (build.gradle)
+//targetCompatibility = '1.8'  // Ensure bytecode is compatible with Java 8 when compiling ShimmerJavaClass for Matlab see ShimmerDriverPC (build.gradle)
 /*
 Rev0.2
 - switch to using jfrog
@@ -102,3 +106,20 @@ dependencies {
     // https://mvnrepository.com/artifact/org.bouncycastle/bcprov-jdk15on
 	implementation("org.bouncycastle:bcprov-jdk15on:1.61")
 }
+
+// Shadow JAR task to create a runnable JAR with dependencies
+/*
+Change to using the following below for ShimmerDriverPC/ShimmerDriver/ShimmerBluetoothManager
+sourceCompatibility = '1.8'  // Ensure code is compiled with Java 8
+targetCompatibility = '1.8'  // Ensure bytecode is compatible with Java 8
+*/
+shadowJar {
+    archiveBaseName.set('ShimmerJavaClass')  // Use archiveBaseName instead of baseName
+    archiveClassifier.set('')  // Remove classifier so it’s named shimmerjavaclass.jar
+    
+    manifest {
+        attributes 'Main-Class': 'com.shimmerresearch.tools.matlab.ShimmerJavaClass'  // Specify the main class
+    }
+
+    mergeServiceFiles()  // Merges service files (if any)
+}