Updates to support ContactCollator plugin (#33)

* Change synchronization on RawDataTransforms soit uses the owner data
holder, not itself for synchronization. Otherwise you get thread locks.

* fix problem in SummaryComand

* Update command line options

* Change synchronization on RawDataTransforms soit uses the owner data
holder, not itself for synchronization. Otherwise you get thread locks.

* Update command line options

* Update DecimatorParams.java

* couple of updates to support new contact collator plugin

* Sorting out sample rate info in clip display to support Contact Collator
plugin

* FLAC Speed

Improve flac speed

* Update .gitignore

* Update .gitignore

* Updates to support new features in Contact Collator

* Small update to RawDatautils to handle null data

.classpath

@@ -6,7 +6,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/Java 17">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

.gitignore

@@ -36,3 +36,5 @@ target/WMM.COF
 
 settings.xml
 .classpath
+.classpath
+.classpath

.settings/org.eclipse.jdt.core.prefs

@@ -1,11 +1,11 @@
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=16
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=11
-org.eclipse.jdt.core.compiler.compliance=16
+org.eclipse.jdt.core.compiler.compliance=11
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
 org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
 org.eclipse.jdt.core.compiler.release=enabled
-org.eclipse.jdt.core.compiler.source=16
+org.eclipse.jdt.core.compiler.source=11

src/PamUtils/PamUtils.java

@@ -397,7 +397,7 @@ public class PamUtils {
 	 /**
 	  * Force an angle to sit within some range. 
 	  * @param angle input angle (radians) 
-	  * @param maxAngle maximum angle in degrees
+	  * @param maxAngle maximum angle in radians
 	  * @return output angle (radians)
 	  */
 	static public double constrainedAngleR(double angle, double maxAngle) {

src/PamguardMVC/RawDataUtils.java

@@ -19,14 +19,23 @@ import java.io.IOException;
 public class RawDataUtils {
 
 	/**
-	 * Write the wave clip in scaled int8 format into a data output stream. 
+	 * Write the wave clip in scaled int8 format into a data output stream. If rawData is null
+	 * or empty, it will still write the header consisting of nChan, nSamp and a scale, but no
+	 * data. 
 	 * @param dos Data output stream
 	 * @param rawData raw data
 	 * @throws IOException 
 	 */
 	public void writeWaveClipInt8(DataOutputStream dos, double[][] rawData) throws IOException {
-		int nChan = rawData.length;
+		int nChan, nSamps;
-		int nSamps = rawData[0].length;
+		if (rawData == null || rawData.length == 0 || rawData[0] == null) {
+			nChan = 0;
+			nSamps = 0;
+		}
+		else {
+			nChan = rawData.length;
+			nSamps = rawData[0].length;
+		}
 		double minVal = 0, maxVal = 0;
 		for (int iC = 0; iC < nChan; iC++) {
 			double[] chanData = rawData[iC];
@@ -36,7 +45,13 @@ public class RawDataUtils {
 			}
 		}
 		maxVal = Math.max(maxVal, -minVal);
-		float scale = (float) (127./maxVal);
+		float scale;
+		if (maxVal == 0) {
+			scale = 1.f;
+		}
+		else {
+			scale = (float) (127./maxVal);
+		}
 		dos.writeShort(nChan);
 		dos.writeInt(nSamps);
 		dos.writeFloat(scale);
@@ -51,13 +66,17 @@ public class RawDataUtils {
 	/**
 	 * Read a waveform clip in scaled int8 format from a data input stream
 	 * @param dis data input stream
-	 * @return waveform double array
+	 * @return waveform double array or null if nChan or nSamps was zero (implying an empty array 
+	 * was written in the fist place)
 	 * @throws IOException
 	 */
 	public double[][] readWavClipInt8(DataInputStream dis) throws IOException {
 		int nChan = dis.readShort();
 		int nSamps = dis.readInt();
 		double scale = 1./dis.readFloat();
+		if (nChan == 0 || nSamps == 0) {
+			return null;
+		}
 		double[][] rawData = new double[nChan][nSamps];
 		for (int iC = 0; iC < nChan; iC++) {
 			double[] chanData = rawData[iC];