From 786bfb1ef5e81c1e77435f51b253d25eee3cbf84 Mon Sep 17 00:00:00 2001 From: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon, 1 Apr 2024 17:56:46 +0100 Subject: [PATCH 1/4] Merge from dg branch (#134) * options to modify scroller focus Needed to stop focus of scroller when other components need to use some of the key strokes which would normally be consumed by the scroller. * update lims search in overlay mark. --- src/PamView/paneloverlay/overlaymark/OverlayMark.java | 4 ++-- src/pamScrollSystem/PamScrollSlider.java | 7 +++++++ 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/src/PamView/paneloverlay/overlaymark/OverlayMark.java b/src/PamView/paneloverlay/overlaymark/OverlayMark.java index 2cadab21..5dd1439b 100644 --- a/src/PamView/paneloverlay/overlaymark/OverlayMark.java +++ b/src/PamView/paneloverlay/overlaymark/OverlayMark.java @@ -173,10 +173,10 @@ public class OverlayMark { //now must find the limits of the zoom. Can be complex shapes so a bit difficult; double minX=Double.MAX_VALUE; - double maxX=Double.MIN_VALUE; + double maxX=Double.NEGATIVE_INFINITY; double minY=Double.MAX_VALUE; - double maxY=Double.MIN_VALUE; + double maxY=Double.NEGATIVE_INFINITY; //now find those maximum, and minimum values, for (int i=0; i Date: Fri, 12 Apr 2024 18:39:38 +0100 Subject: [PATCH 2/4] Fix a couple of null pointers And pre release 2.02.10bc --- README.html | 183 +++++++++++------- dependency-reduced-pom.xml | 2 +- pom.xml | 2 +- src/Acquisition/FileInputSystem.java | 4 + src/Acquisition/FolderInputSystem.java | 1 + src/PamController/PamguardVersionInfo.java | 4 +- src/PamView/panel/KeyPanel.java | 5 +- .../lookupTables/LookUpTables.java | 4 +- 8 files changed, 127 insertions(+), 78 deletions(-) diff --git a/README.html b/README.html index d4faac7a..8f8d31ad 100644 --- a/README.html +++ b/README.html @@ -387,8 +387,11 @@ PamguardBeta_ViewerMode.exe):

Latest Version 2.02.10 January 2024

+font-family:"Cambria",serif;font-style:normal'>Latest +Version 2.02.11 April 2024 + +

Version 2.02.10 January 2024

Version 2.02.09 June 2023

@@ -461,14 +464,47 @@ Version 2.00.10 June 2017

Version 2.02.10 January 2024

+name="_Version_2.02.10_January">Version +2.02.11 April 2024 + +

 

+ +

New Features

+ +

Click detector: Remembers locations of displays and doesn’t +continually reset them.

+ +

Help for Matched Click Classifier

+ +

Bug Fixes

+ +

Linking clicks to offline clicks table. We had a database +that had become corrupted so added code to relink offline clicks to their corresponding +clicks from binary data.

+ +

Drawing non-acoustic data: Data that were not associated +with any hydrophones, e.g. visual sightings in Logger forms were not drawing on +the map. This fixed and PAMGuard will use the vessels GPS position as +reference.

+ +

Lookup tables: fix feature which was causing table entries +to repeat.

+ +

Click Train Detector: Add exception handlers to avoid errors +as PAMGuard stops / restarts.

+ +

Group Detection starts and ends: Check data integrity +function fixed and now inserts correct times of start and ends of events into +database.

+ +

Version 2.02.10 January 2024

New Features

Importing modules from other configurations: New options from file menu allowing -import of specific modules, or module settings from other configurations. E.g. -if you had three similar configurations and had set one of them up with a new +lang=EN-US> from other configurations: New options from file menu allowing import +of specific modules, or module settings from other configurations. E.g. if you +had three similar configurations and had set one of them up with a new detector, or got the click classifier settings set up just right in one of those configurations, you can import the additional modules or the click detector settings easily into the other configurations.

@@ -496,9 +532,9 @@ correctly saving updated bearings to the database. Now fixed.

ROCCA Classifier fixes

-

Allow Rocca to run without classifiers: -Fixed bug that threw an error if no classifier files were  specified in -Rocca Params dialog

+

Allow Rocca to run without classifiers: Fixed +bug that threw an error if no classifier files were  specified in Rocca +Params dialog

Fix memory issue with RoccaContourDataBlocks not being released for garbage collection

@@ -596,9 +632,9 @@ angle offsets applied to static hydrophones in viewer mode. This is now fixed. <

Click tool bar: Correctly shows event selection options even if no species classification options are in place.

-

Fixed Landmarks: Earlier versions were ‘losing’ -these every time PAMGuard started or new data were loaded in viewer mode. Now -fixed.

+

Fixed Landmarks: Earlier versions were +‘losing’ these every time PAMGuard started or new data were loaded in viewer +mode. Now fixed.

ROCCA: Fixed (another) memory leak which caused PAMGuard to crash when processing large data sets with the ROCCA @@ -767,8 +803,9 @@ the TF FX display to crash if no data were displayed.

See major release notes for V 2.02.01 below.

-

Bug 495: TD FX display throws NullPointerException -if user has removed all data units and then moves mouse over display area.

+

Bug 495: TD FX display throws +NullPointerException if user has removed all data units and then moves mouse +over display area.

Version 2.02.01 October 2021

@@ -791,11 +828,11 @@ font-family:"Times New Roman",serif'> 

File Format Change

-

Changes have been made to the binary file format to support the -output of additional noise outputs for certain detectors (See below). Binary -files created with this version will not be compatible with earlier versions -2.01.### and below. This version will read and may convert earlier format -binary files.

+

Changes have been made to the binary file format to support +the output of additional noise outputs for certain detectors (See below). +Binary files created with this version will not be compatible with earlier +versions 2.01.### and below. This version will read and may convert earlier +format binary files.

 

@@ -1181,10 +1218,10 @@ lang=EN-US> Add functionality for bluetooth headsets.

2.        Add user-facing option to adjust the startup delay for the -time-correction (Global Time module). This provides a workaround to speed up -analysis of thousands of wav files (i.e. by setting startup delay to 0 instead -of default value of 2000 ms).

+lang=EN-US> Add user-facing option to adjust the startup delay for the time-correction +(Global Time module). This provides a workaround to speed up analysis of +thousands of wav files (i.e. by setting startup delay to 0 instead of default +value of 2000 ms).

3.       

2.        -Java 12 is better at handling Windows scaling issues on high-DPI displays. -Beyond that, users should not notice much of a difference between this version -and previous beta releases.

+Java 12 is better at handling Windows scaling issues on high-DPI displays. Beyond +that, users should not notice much of a difference between this version and +previous beta releases.

@@ -1706,8 +1743,8 @@ with installation and use of this version.

1.        -Bug 338. Problem displaying coastlines and bathymetric contours around the -dateline (+/- 180 longitude) in the map.

+Bug 338. Problem displaying coastlines and bathymetric contours around +the dateline (+/- 180 longitude) in the map.

2.        @@ -2218,8 +2255,8 @@ UID

If old data are opened with the PAMGuard viewer they will automatically be converted. For safety, the original binary files will not be overwritten and the new data will be placed in a new folder -on your computer with the same path as the old data, but suffixed with ‘_WithUID’, -e.g. if your binary data were previously stored in the folder +on your computer with the same path as the old data, but suffixed with +‘_WithUID’, e.g. if your binary data were previously stored in the folder C:\MySurvey\binarydata the new data will be written to C:\MySurvey\binarydata_WithUID.

@@ -2295,8 +2332,8 @@ Hawaii/Temperate Pacific/North Atlantic datasets. This has been corrected.

2.       -Bug 320. Pamguard stopped reading Click Detector Event data from database -when target motion analysis information was encountered. Corrected.

+Bug 320. Pamguard stopped reading Click Detector Event data from +database when target motion analysis information was encountered. Corrected.

3.       @@ -2578,9 +2615,9 @@ main click detector display.

Target Motion Analysis

-

A major piece of work has been undertaken -to improve the Target Motion tracking with PAMGuard. Details are available in -the online help. Users of the Click Detector will notice the following changes:

+

A major piece of work has been undertaken to +improve the Target Motion tracking with PAMGuard. Details are available in the +online help. Users of the Click Detector will notice the following changes:

1.       @@ -2752,8 +2789,8 @@ being imported into the new database. Problem 2 was that indexing of imported click events in the new database was incorrect. Both these issues have now been fixed.

-

Version 1.15.02 March -2016

+

Version 1.15.02 +March 2016

A number of small bug fixes following release of 1.15.00.

@@ -2905,13 +2942,13 @@ for details.

3.       -GPS Loading into PAMGuard Viewer. This has been modified -so that the rules governing GPS data collection and storage also apply when -loading data from the database. For instance, if you've stored all GPS data, -you've probably got a record every second in the database which can create -memory overflows if you try to load a lot of data in the viewer. You can now -tell PAMGuard to only load a data point every n seconds which will reduce the -number of points loaded. Useful when making large scale overview maps of a +GPS Loading into PAMGuard Viewer. This has been +modified so that the rules governing GPS data collection and storage also apply +when loading data from the database. For instance, if you've stored all GPS +data, you've probably got a record every second in the database which can +create memory overflows if you try to load a lot of data in the viewer. You can +now tell PAMGuard to only load a data point every n seconds which will reduce +the number of points loaded. Useful when making large scale overview maps of a survey.

4.9.        -Bug 239. Fixed bug in the DIFAR module that was -incorrectly preventing cross-fixes for some calls.

+Bug 239. Fixed bug in the DIFAR module that was incorrectly +preventing cross-fixes for some calls.

Details of these bugs can be found at https://sourceforge.net/p/pamguard/bugs

@@ -3210,8 +3247,9 @@ to read on a time. Fixed

Menu Layout

-

The PAMGuard menus have been rearranged into a more intuitive -grouping which we believe will help users find functionality more easily.

+

The PAMGuard menus have been rearranged into a more +intuitive grouping which we believe will help users find functionality more +easily.

'Detection' menu has been renamed to 'Settings' since many menu items within this menu were not directly to do with 'Detection'.

@@ -3302,9 +3340,9 @@ of third octave noise bands. See online help for details.

Filtered Noise Measurement (Sound Processing Group)

-

This module, developed by Douglas Gillespie, measures noise levels -in a single frequency band using a variety of filter functions. See online help -for details.

+

This module, developed by Douglas Gillespie, measures noise +levels in a single frequency band using a variety of filter functions. See +online help for details.

Envelope Tracing (Beta Only, Sound Processing Group)

@@ -3340,10 +3378,11 @@ different. Details are available in the online help.

FLAC File Support

Can now read raw audio data direct from FLAC files. FLAC is a lossless compression algorithm -for audio data. Files, or folders of files are accessed in the same way as WAV -and AIFF files in the Sound Acquisition module. In a future release we also -hope to provide support for writing FLAC files from the sound recorder module.

+href="http://en.wikipedia.org/wiki/FLAC">FLAC is a lossless compression +algorithm for audio data. Files, or folders of files are accessed in the same +way as WAV and AIFF files in the Sound Acquisition module. In a future release +we also hope to provide support for writing FLAC files from the sound recorder +module.

Sound Recorder Module

@@ -3476,9 +3515,9 @@ to these menus to provide additional information to users.  

Radar Display

-

Functionality has been added to -the radar display so that bearings can be shown relative to either the vessel -or to true North.

+

Functionality has been added to the +radar display so that bearings can be shown relative to either the vessel or to +true North.

Better control of data in viewer mode, making is easy to scroll through and view data for short time periods.

@@ -4116,8 +4155,8 @@ Symbol'>''         -This results in a major speed up of data exchange between modules and can -lead to a x4 improvement in overall performance.

+This results in a major speed up of data exchange between modules and +can lead to a x4 improvement in overall performance.

'         @@ -4230,9 +4269,9 @@ Symbol'>''         -Channel lists in output data streams of Decimator and other modules fixed, -so that when channel numbers change, downstream modules configurations get the -correct list of available channels.

+Channel lists in output data streams of Decimator and other modules +fixed, so that when channel numbers change, downstream modules configurations +get the correct list of available channels.

'         @@ -4263,11 +4302,11 @@ Symbol'>''         -New menu functionality by right clicking on any of the tabs of the main -tab control will allow the user to copy the tab contents to the system -clipboard from where it can be copied into other programs (e.g. Word, -Powerpoint, etc.).Some modules, such as the map, have this implemented in other -menus (right click) and also allow printing. 

+New menu functionality by right clicking on any of the tabs of the main tab +control will allow the user to copy the tab contents to the system clipboard +from where it can be copied into other programs (e.g. Word, Powerpoint, +etc.).Some modules, such as the map, have this implemented in other menus +(right click) and also allow printing. 

'         @@ -4335,8 +4374,8 @@ online help.

PAMGUARD Mixed Mode operation

-

Analyses data from wav or AIF file and synchronises it with -GPS data reloaded from a database so that detected sounds may be correctly +

Analyses data from wav or AIF file and synchronises it with GPS +data reloaded from a database so that detected sounds may be correctly localised. Multiple display frames - enables PAMGUARD GUI to be split into multiple display windows, displayed on multiple monitors if desired. Enables the operator to simultaneously view the map and the click detector for example, @@ -4855,8 +4894,8 @@ Symbol'>'1.0Beta 22 Jan 2008 - Pamguard -starts two releases, core and beta release,

+class=Heading2Char>1.0Beta 22 Jan 2008 - +Pamguard starts two releases, core and beta release,

this is the beta release

diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml index fd1fe9e4..8b677f99 100644 --- a/dependency-reduced-pom.xml +++ b/dependency-reduced-pom.xml @@ -4,7 +4,7 @@ org.pamguard Pamguard Pamguard Java12+ - 2.02.10bb + 2.02.10bc Pamguard for Java 12+, using Maven to control dependcies www.pamguard.org diff --git a/pom.xml b/pom.xml index e6b66c5f..ec6fde65 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ 4.0.0 org.pamguard Pamguard - 2.02.10bb + 2.02.10bc Pamguard Java12+ Pamguard for Java 12+, using Maven to control dependcies www.pamguard.org diff --git a/src/Acquisition/FileInputSystem.java b/src/Acquisition/FileInputSystem.java index 2727ca05..87f86046 100644 --- a/src/Acquisition/FileInputSystem.java +++ b/src/Acquisition/FileInputSystem.java @@ -810,6 +810,10 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe protected void collectFlacData() { FileInputStream fileStream; try { + File currFile = getCurrentFile(); + if (currFile == null) { + return; + } fileStream = new FileInputStream(getCurrentFile()); } catch (FileNotFoundException e) { e.printStackTrace(); diff --git a/src/Acquisition/FolderInputSystem.java b/src/Acquisition/FolderInputSystem.java index 7b20311e..b8e80f37 100644 --- a/src/Acquisition/FolderInputSystem.java +++ b/src/Acquisition/FolderInputSystem.java @@ -602,6 +602,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D @Override public File getCurrentFile() { //System.out.println("All files: " + allFiles); +// System.out.printf("Folder: getCurrentfile. on %d of %d\n", currentFile, allFiles.size()); if (allFiles != null && allFiles.size() > currentFile) { return allFiles.get(currentFile); } diff --git a/src/PamController/PamguardVersionInfo.java b/src/PamController/PamguardVersionInfo.java index 178b203c..19d07d1f 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 = "2.02.10bb"; + static public final String version = "2.02.10bc"; /** * Release date */ - static public final String date = "29 March 2024"; + static public final String date = "12 April 2024"; // /** // * Release type - Beta or Core diff --git a/src/PamView/panel/KeyPanel.java b/src/PamView/panel/KeyPanel.java index cb6834df..b180a099 100644 --- a/src/PamView/panel/KeyPanel.java +++ b/src/PamView/panel/KeyPanel.java @@ -102,7 +102,10 @@ public class KeyPanel { } private void fillPanel() { - + JPanel panel = this.panel; + if (panel == null) { + return; + } panel.removeAll(); GridBagConstraints c = new GridBagConstraints(); diff --git a/src/generalDatabase/lookupTables/LookUpTables.java b/src/generalDatabase/lookupTables/LookUpTables.java index bd095eba..abea6653 100644 --- a/src/generalDatabase/lookupTables/LookUpTables.java +++ b/src/generalDatabase/lookupTables/LookUpTables.java @@ -141,9 +141,11 @@ public class LookUpTables { // search for repeats. for (int i = 0; i < n-1; i++) { String code = list.get(i).getCode().trim(); + String topic1 = list.get(i).getTopic().trim(); for (int j = i+1; j < n; j++) { String code2 = list.get(j).getCode().trim(); - if (code.equals(code2)) { + String topic2 = list.get(j).getTopic().trim(); + if (code.equals(code2) && topic1.equals(topic2)) { isRepeat[j] = true; nRepeat++; } From 8537a2ddecfd1f495e5139366097d5256fae4ef2 Mon Sep 17 00:00:00 2001 From: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sun, 21 Apr 2024 16:33:56 +0100 Subject: [PATCH 3/4] fix continual restart Stop it not stopping when processing folders of files. --- src/Acquisition/FolderInputSystem.java | 2 +- .../timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java | 2 +- src/PamController/PamController.java | 5 ++++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/src/Acquisition/FolderInputSystem.java b/src/Acquisition/FolderInputSystem.java index b8e80f37..c8c2d872 100644 --- a/src/Acquisition/FolderInputSystem.java +++ b/src/Acquisition/FolderInputSystem.java @@ -690,7 +690,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D } if (currentFile < allFiles.size()) { // only restart if the file ended - not if it stopped - if (getStreamStatus() == STREAM_ENDED) { + if (getStreamStatus() == STREAM_ENDED && PamController.getInstance().isManualStop() == false) { // System.out.println(String.format("Start new file timer (file %d/%d)",currentFile+1,allFiles.size())); newFileTimer.start(); } diff --git a/src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java b/src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java index d6908eca..59c166fd 100644 --- a/src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java +++ b/src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java @@ -214,7 +214,7 @@ public class PairBearingLocaliser implements BearingLocaliser { private boolean resetArray(long timeMillis){ if (this.timeMillis!=timeMillis && currentArray.getHydrophoneLocator().isChangeable()){ - System.out.println("Reset PairBearingLocaliser"); +// System.out.println("Reset PairBearingLocaliser"); prepare(this.arrayElements, timeMillis, this.timingError); return true; } diff --git a/src/PamController/PamController.java b/src/PamController/PamController.java index 54f7735f..c52905fd 100644 --- a/src/PamController/PamController.java +++ b/src/PamController/PamController.java @@ -1099,7 +1099,8 @@ public class PamController implements PamControllerInterface, PamSettings { * later in the AWT event queue. */ public void startLater() { - SwingUtilities.invokeLater(new StartLater(true)); +// SwingUtilities.invokeLater(new StartLater(true)); + startLater(true); } public void startLater(boolean saveSettings) { @@ -1173,6 +1174,7 @@ public class PamController implements PamControllerInterface, PamSettings { @Override public void manualStop() { lastStartStopButton = BUTTON_STOP; + setManualStop(true); pamStop(); } @@ -1186,6 +1188,7 @@ public class PamController implements PamControllerInterface, PamSettings { @Override public boolean pamStart() { // Debug.println("PAMController: pamStart"); + setManualStop(false); return pamStart(true); } From 6db451699fb491ddbdf5e7669e2dc76927833646 Mon Sep 17 00:00:00 2001 From: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue, 23 Apr 2024 17:57:15 +0100 Subject: [PATCH 4/4] Fix data load bug 2.02.10bd Problem in master gps reference hitting a null, which was in turn stopping data matching for sub detections. Fixed in temp release 2.02.10bd --- dependency-reduced-pom.xml | 2 +- pom.xml | 2 +- src/Array/ArrayManager.java | 2 +- src/GPS/GPSControl.java | 3 +++ src/PamController/PamguardVersionInfo.java | 4 ++-- src/PamguardMVC/superdet/SuperDetDataBlock.java | 4 ++-- src/clickTrainDetector/ClickTrainProcess.java | 5 +++-- 7 files changed, 13 insertions(+), 9 deletions(-) diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml index 8b677f99..77d475b0 100644 --- a/dependency-reduced-pom.xml +++ b/dependency-reduced-pom.xml @@ -4,7 +4,7 @@ org.pamguard Pamguard Pamguard Java12+ - 2.02.10bc + 2.02.10bd Pamguard for Java 12+, using Maven to control dependcies www.pamguard.org diff --git a/pom.xml b/pom.xml index ec6fde65..23a2f82a 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ 4.0.0 org.pamguard Pamguard - 2.02.10bc + 2.02.10bd Pamguard Java12+ Pamguard for Java 12+, using Maven to control dependcies www.pamguard.org diff --git a/src/Array/ArrayManager.java b/src/Array/ArrayManager.java index 6a605fff..445688ea 100644 --- a/src/Array/ArrayManager.java +++ b/src/Array/ArrayManager.java @@ -1111,7 +1111,7 @@ public class ArrayManager extends PamControlledUnit implements PamSettings, PamO referencePoint = shipPos.getGpsData(); } } - if (referencePoint == null) { + if (referencePoint == null && MasterReferencePoint.getFixTime() != null && MasterReferencePoint.getLatLong() != null) { // running out of options, so fall back to the master reference point, interpolated (probably has zero speeed) referencePoint = new GpsData(MasterReferencePoint.getFixTime(), MasterReferencePoint.getLatLong()).getPredictedGPSData(timeMillis); } diff --git a/src/GPS/GPSControl.java b/src/GPS/GPSControl.java index a2f9899d..23f1fe8f 100644 --- a/src/GPS/GPSControl.java +++ b/src/GPS/GPSControl.java @@ -267,6 +267,9 @@ public class GPSControl extends PamControlledUnit implements PamSettings, Positi GpsDataUnit pointBefore = null, pointAfter = null; synchronized (getGpsDataBlock().getSynchLock()) { ListIterator iter = getGpsDataBlock().getListIterator(timeMilliseconds, 0, PamDataBlock.MATCH_BEFORE, PamDataBlock.POSITION_BEFORE); + if (iter == null) { + return null; + } if (iter.hasNext()) { pointBefore = iter.next(); } diff --git a/src/PamController/PamguardVersionInfo.java b/src/PamController/PamguardVersionInfo.java index 19d07d1f..d4f9b826 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 = "2.02.10bc"; + static public final String version = "2.02.10bd"; /** * Release date */ - static public final String date = "12 April 2024"; + static public final String date = "23 April 2024"; // /** // * Release type - Beta or Core diff --git a/src/PamguardMVC/superdet/SuperDetDataBlock.java b/src/PamguardMVC/superdet/SuperDetDataBlock.java index b8e5269a..78b5538d 100644 --- a/src/PamguardMVC/superdet/SuperDetDataBlock.java +++ b/src/PamguardMVC/superdet/SuperDetDataBlock.java @@ -450,8 +450,8 @@ public class SuperDetDataBlock