From 1d7a9866219f64b5ce3a971086812384be849328 Mon Sep 17 00:00:00 2001
From: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:29:28 +0100
Subject: [PATCH] V2.02.11e fix file start skip

Skipping start of files was causing click detector to not find clicks. Changed code so first seconds are still sent, but with data set to 0, rather than not sending data since that was causing sample counts in different bits of PAMGuard to get out of synch.
---
 pom.xml                                    | 2 +-
 src/Acquisition/FileInputSystem.java       | 7 +++++--
 src/PamController/PamguardVersionInfo.java | 4 ++--
 src/clickDetector/ClickDetector.java       | 4 ++--
 4 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/pom.xml b/pom.xml
index 94956613..d09a31fd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.11d</version>
+  <version>2.02.11e</version>
   <name>Pamguard</name>
   <description>Pamguard using Maven to control dependencies</description>
 	<url>www.pamguard.org</url>
diff --git a/src/Acquisition/FileInputSystem.java b/src/Acquisition/FileInputSystem.java
index 33779534..b4678913 100644
--- a/src/Acquisition/FileInputSystem.java
+++ b/src/Acquisition/FileInputSystem.java
@@ -15,6 +15,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.Serializable;
 import java.text.DateFormat;
+import java.util.Arrays;
 import java.util.Calendar;
 import java.util.List;
 
@@ -1017,9 +1018,11 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 						newDataUnit = new RawDataUnit(ms, 1 << ichan, totalSamples, newSamples);
 						newDataUnit.setRawData(doubleData[ichan]);
 
-						if (1000*(readFileSamples/sampleRate)>=fileInputParameters.skipStartFileTime) {
-							newDataUnits.addNewData(newDataUnit);
+						if (1000*(readFileSamples/sampleRate)<fileInputParameters.skipStartFileTime) {
+							// zero the data. Skipping it causes all the timing to screw up
+							Arrays.fill(doubleData[ichan], 0.);
 						}
+						newDataUnits.addNewData(newDataUnit);
 
 						// GetOutputDataBlock().addPamData(pamDataUnit);
 					}
diff --git a/src/PamController/PamguardVersionInfo.java b/src/PamController/PamguardVersionInfo.java
index b40c4afa..d1cee5f8 100644
--- a/src/PamController/PamguardVersionInfo.java
+++ b/src/PamController/PamguardVersionInfo.java
@@ -31,12 +31,12 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.11d";
+	static public final String version = "2.02.11e";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "30 May 2024";
+	static public final String date = "19 June 2024";
 	
 //	/**
 //	 * Release type - Beta or Core
diff --git a/src/clickDetector/ClickDetector.java b/src/clickDetector/ClickDetector.java
index 56b9481e..2ee4ece2 100644
--- a/src/clickDetector/ClickDetector.java
+++ b/src/clickDetector/ClickDetector.java
@@ -329,7 +329,7 @@ public class ClickDetector extends PamProcess {
 		offlineEventLogging.setSubLogging(getClickDataBlock().getOfflineClickLogging());
 
 		triggerBackgroundHandler = new TriggerBackgroundHandler(this);
-		
+
 		clickBackgroundManager = new ClickBackgroundManager(this);
 
 		setProcessCheck(new BaseProcessCheck(this, RawDataUnit.class, 1, 0.0000001));
@@ -1378,7 +1378,7 @@ public class ClickDetector extends PamProcess {
 		private boolean initialiseFilters;
 
 		private long clickStartSample, clickEndSample;
-		
+
 		private double maxSignalExcess;
 
 		private int clickTriggers;