Merge pull request #64 from PAMGuard/main

Merge from main

README.html

@@ -466,9 +466,9 @@ name="_Version_2.02.10_January"></a>Version 2.02.10 January 2024</h1>
 <h2><span lang=EN-US>New Features</span></h2>
 
 <p class=MsoNormal><b><span lang=EN-US>Importing modules</span></b><span
-lang=EN-US> from other configurations: New options from file menu allowing import
+lang=EN-US> from other configurations: New options from file menu allowing
-of specific modules, or module settings from other configurations. E.g. if you
+import of specific modules, or module settings from other configurations. E.g.
-had three similar configurations and had set one of them up with a new
+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. </span></p>
@@ -478,8 +478,9 @@ files) file performance</span></b><span lang=EN-US> when scrolling through
 audio data in Viewer mode. </span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Viewer Launch</span></b><span
-lang=EN-US> by right clicking on sqlite database and selecting <20>open with / Pamguard
+lang=EN-US> by right clicking on sqlite database and selecting “open with /
-ViewerMode launcher<65> menu option.</span></p>
+Pamguard ViewerMode” launcher menu option.</span></p>
+
 <h2><span lang=EN-US>Bug Fixes</span></h2>
 
 <p class=MsoNormal><b><span lang=EN-US>Logger Forms</span></b></p>
@@ -526,10 +527,18 @@ clicks not being correctly reassigned to different events. </span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Screen Position</span></b><span
 lang=EN-US>: When using multiple monitors, if you move a configuration to a
-computer with a different monitor layout, the GUI should work out if it’s
+computer with a different monitor layout, the GUI should work out if it’s
 opening on a screen area which no longer exists and move itself onto the
 primary monitor. </span></p>
 
+<p class=MsoNormal><b><span lang=EN-US>File Folder Processing</span></b><span
+lang=EN-US>: Previous version had a bug which caused files to not always be
+sorted into the correct order for processing. This caused some instability in
+some detectors, causing memory leaks when new data arrived with time stamps
+earlier than already processed data in memory. This is now fixed – files are ow
+correctly sorted alphabetically </span>by file name, i.e. not including the
+name of the folder containing the files.</p>
+
 <h1><span lang=EN-US>Version 2.02.09 June 2023</span></h1>
 
 <h2><span lang=EN-US>Bug Fixes</span></h2>
@@ -548,8 +557,8 @@ were reading local time, even when set to use UTC. </span></p>
 which mostly occurred when processing large datasets of many offline files, has
 been fixed.</span></p>
 
-<p class=MsoNormal><span lang=EN-US>Data Map: “Scroll To Data” pop-up menu,
+<p class=MsoNormal><span lang=EN-US>Data Map: “Scroll To Data” pop-up menu,
-which didn’t always scroll to the correct place, is now fixed. </span></p>
+which didn’t always scroll to the correct place, is now fixed. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Bearing Localiser offline: If reprocessing
 bearings, the localizer was not correctly loading required raw or FFT data to
@@ -572,7 +581,7 @@ files and stores them within the PAMGuard configuration. This does not affect
 processing, but is important for record keeping. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>GPS options to use any valid RMC or GGA
-string. Not all GPS receivers output their RMC data as GPRMC – e.g. some may
+string. Not all GPS receivers output their RMC data as GPRMC – e.g. some may
 output as GNRMC. A new option allows the GPS module to use any string, whatever
 the first two characters of the string name may be. </span></p>
 
@@ -581,15 +590,15 @@ the first two characters of the string name may be. </span></p>
 <h2><span lang=EN-US>Bug Fixes</span></h2>
 
 <p class=MsoNormal><span lang=EN-US>Use of localization sensor and orientation
-data for static hydrophones had a bug whereby it would continually ‘forget’
+data for static hydrophones had a bug whereby it would continually ‘forget’
 angle offsets applied to static hydrophones in viewer mode. This is now fixed. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Click tool bar: Correctly shows event
 selection options even if no species classification options are in place. </span></p>
 
-<p class=MsoNormal><span lang=EN-US>Fixed Landmarks: Earlier versions were
+<p class=MsoNormal><span lang=EN-US>Fixed Landmarks: Earlier versions were ‘losing’
-‘losing’ these every time PAMGuard started or new data were loaded in viewer
+these every time PAMGuard started or new data were loaded in viewer mode. Now
-mode. Now fixed. </span></p>
+fixed. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>ROCCA: Fixed (another) memory leak which
 caused PAMGuard to crash when processing large data sets with the ROCCA
@@ -607,11 +616,11 @@ processing.</span></p>
 
 <p class=MsoNormal><span lang=EN-US>New sound type for simulated sounds which
 generates random chirps between around 200 and 800Hz, roughly the frequency
-you’d expect sound from higher frequency baleen whales, such as humpbacks, to
+you’d expect sound from higher frequency baleen whales, such as humpbacks, to
 vocalise at. &nbsp;&nbsp;</span></p>
 
 <p class=MsoNormal><span lang=EN-US>Hiding tool tips. A menu item to
-permanently turn off all tool tips, or tap the ‘Esc’ key to turn them off for 6
+permanently turn off all tool tips, or tap the ‘Esc’ key to turn them off for 6
 seconds if they are getting in the way, particularly when trying to interact
 with displays using the mouse. </span></p>
 
@@ -632,7 +641,7 @@ whistle classification module.</span></p>
 
 <h2><span lang=EN-US>New Features</span></h2>
 
-<p class=MsoNormal><span lang=EN-US>SoundTrap SUD file reading. If you’re using
+<p class=MsoNormal><span lang=EN-US>SoundTrap SUD file reading. If you’re using
 SoundTrap autonomous recorders from Ocean Instruments, you no longer need to
 decompress the SoundTrap files prior to processing. This will save time and a
 lot of disk space. Extraction of clicks from the inbuilt SoundTrap Click
@@ -696,7 +705,7 @@ audio files. </span></p>
 <h2><span lang=EN-US>Bug Fixes</span></h2>
 
 <p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate
-binary files even if DWV file doesn’t exist (which is correct behavior in
+binary files even if DWV file doesn‚’t exist (which is correct behavior in
 quiet conditions when no clicks were detected). </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Spectrogram. Changes to stop occasional
@@ -731,8 +740,8 @@ running in real time. Added template names based on file names. </p>
 <p class=MsoNormal>#13 Merging files when offline processing file folders: Had
 an error introduced in last release which caused it to fail to recognise gaps
 between files, meaning that some output data (i.e. after a gap) would have an
-incorrect time stamp. This did not affect data if the ‘merge contiguous
+incorrect time stamp. This did not affect data if the ‘merge contiguous files’
-files’ option was not selected. </p>
+option was not selected. </p>
 
 <p class=MsoNormal>#14 Logger forms data were not plotting correctly. This was
 due to the required data selection functions not being fully implemented. This
@@ -758,9 +767,8 @@ the TF FX display to crash if no data were displayed.</span></p>
 <p class=MsoNormal><span lang=EN-US>See major release notes for V 2.02.01
 below. </span></p>
 
-<p class=MsoNormal><span lang=EN-US>Bug 495: TD FX display throws
+<p class=MsoNormal><span lang=EN-US>Bug 495: TD FX display throws NullPointerException
-NullPointerException if user has removed all data units and then moves mouse
+if user has removed all data units and then moves mouse over display area.</span></p>
-over display area.</span></p>
 
 <h1><a name="_Latest_Version_2.02.01"></a><span lang=EN-US>Version 2.02.01
 October 2021</span></h1>
@@ -783,11 +791,11 @@ font-family:"Times New Roman",serif'>&nbsp;</span></p>
 
 <h2>File Format Change</h2>
 
-<p class=MsoNormal>Changes have been made to the binary file format to support
+<p class=MsoNormal>Changes have been made to the binary file format to support the
-the output of additional noise outputs for certain detectors (See below).
+output of additional noise outputs for certain detectors (See below). Binary
-Binary files created with this version will not be compatible with earlier
+files created with this version will not be compatible with earlier versions
-versions 2.01.### and below. This version will read and may convert earlier
+2.01.### and below. This version will read and may convert earlier format
-format binary files.</p>
+binary files.</p>
 
 <p class=MsoNormal style='margin-bottom:0cm'><span style='font-size:12.0pt;
 font-family:"Times New Roman",serif'>&nbsp;</span></p>
@@ -795,19 +803,20 @@ font-family:"Times New Roman",serif'>&nbsp;</span></p>
 <p class=MsoNormal><b><span lang=EN-US>Localisation Modules</span></b><span
 lang=EN-US> </span></p>
 
-<p class=MsoNormal>Bearing and Group 3D localization modules have been thoroughly
+<p class=MsoNormal>Bearing and Group 3D localization modules have been
-tested and a number of bugs rectified. Documentation has been developed and is
+thoroughly tested and a number of bugs rectified. Documentation has been
-available in the online help. Further, a number of example configurations have
+developed and is available in the online help. Further, a number of example
-been generated, configuration files for these are available in the PAMGuard
+configurations have been generated, configuration files for these are available
-downloads area <a href="http://www.pamguard.org/downloads.php?cat_id=3">here</a>.</p>
+in the PAMGuard downloads area <a
+href="http://www.pamguard.org/downloads.php?cat_id=3">here</a>.</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Detection Group Localiser</span></b><span
 lang=EN-US> </span></p>
 
-<p class=MsoNormal>This module has been renamed “Detection Grouper”, so
+<p class=MsoNormal>This module has been renamed “Detection Grouper”, so as to
-as to avoid confusion with the Group 3D localizer. This is because the
+avoid confusion with the Group 3D localizer. This is because the Detection
-Detection Grouper is more for organizing data into groups to be localized than
+Grouper is more for organizing data into groups to be localized than it is for
-it is for doing localization.</p>
+doing localization.</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Minor Bug Fixes</span></b><span
 lang=EN-US> </span></p>
@@ -862,9 +871,9 @@ lang=EN-US> </span>Allow Clip Generator to create both a binary record and a
 wav file </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Implemented a Backup Manager for backing up multiple types of data to multiple
+lang=EN-US> </span>Implemented a Backup Manager for backing up multiple types
-locations] </p>
+of data to multiple locations] </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -905,8 +914,8 @@ lang=EN-US> </span>Extend the Hyperbolic Localiser to handle 2D planar arrays
 (previously limited to 3D volumetric arrays) </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>14. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-new CPOD features </p>
+lang=EN-US> </span>new CPOD features </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>15. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -914,22 +923,23 @@ lang=EN-US> </span>Better interpolation of data by the Decimator when
 decimating/upsampling by a non-integer amount </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>16. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Noise Level Outputs - as an aid to performance diagnosis, some detectors
+lang=EN-US> </span>Noise Level Outputs - as an aid to performance diagnosis,
-(currently the GPL, Click Detector and Whistle and Moan Detector) are
+some detectors (currently the GPL, Click Detector and Whistle and Moan
-outputting additional noise metrics to their binary output files. These can be
+Detector) are outputting additional noise metrics to their binary output files.
-read with the <a href="https://sourceforge.net/projects/pamguard/files/Matlab/">PAMGuard
+These can be read with the <a
-Matlab library</a> and used to diagnose system performance in varying noise
+href="https://sourceforge.net/projects/pamguard/files/Matlab/">PAMGuard Matlab
+library</a> and used to diagnose system performance in varying noise
 conditions. Improved displays within PAMGuard for these noise metrics will be
 included in a future release. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>17. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
 lang=EN-US> </span>An implementation of the Generalized Power Law Detector,
-developed by Tyler Helble ([Helble et al., ‘A generalized power-law
+developed by Tyler Helble ([Helble et al., ‘A generalized power-law detection
-detection algorithm for humpback whale vocalizations’, The Journal of the
+algorithm for humpback whale vocalizations’, The Journal of the Acoustical
-Acoustical Society of America, vol. 131, no. 4, pp. 2682–2699, 2012) is now
+Society of America, vol. 131, no. 4, pp. 2682–2699, 2012) is now available. For
-available. For details, see the online help </p>
+details, see the online help </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -1057,11 +1067,11 @@ understand the notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta
 Version 2.00.10</a> before proceeding with installation and use of this
 version.</b></p>
 
-<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13 (release
+<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13
-13.0.1). PSFX files generated in previous beta releases (2.xx.xx) should be
+(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx)
-compatible with this version, and vice-versa. PSF files generated in core
+should be compatible with this version, and vice-versa. PSF files generated in
-releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
+core releases (1.15.xx) can be loaded in this version, but will be converted to
-files when PAMGuard exits.</p>
+PSFX files when PAMGuard exits.</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Bug Fixes</span></b></p>
 
@@ -1289,8 +1299,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 Bug 440. Measurement Computing Cards not enumerating properly.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>9. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Bug 441. Plot coordinate calculations incorrect in PamAxis.</p>
+lang=EN-US> </span>Bug 441. Plot coordinate calculations incorrect in PamAxis.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -1303,9 +1313,9 @@ lang=EN-US> </span>Bug 443. NI playback crashing immediately if a device is not
 present.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>12. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Bug 444. Bug in data selector which caused it to mess up history of recent psf
+lang=EN-US> </span>Bug 444. Bug in data selector which caused it to mess up
-files.</p>
+history of recent psf files.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>13. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -1445,8 +1455,8 @@ lang=EN-US> </span>Bug 431. Error when trying to mark section of spectrogram to
 send to Bearing Calculator module</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Bug 432. MySQL database interface - connection problems</p>
+lang=EN-US> </span>Bug 432. MySQL database interface - connection problems</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></p>
 
@@ -1696,8 +1706,8 @@ with installation and use of this version.</span></p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 338. Problem displaying coastlines and bathymetric contours around
+</span>Bug 338. Problem displaying coastlines and bathymetric contours around the
-the dateline (+/- 180 longitude) in the map.</p>
+dateline (+/- 180 longitude) in the map.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -1823,9 +1833,9 @@ see new options in main menu.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-lang=EN-US> </span>Added Matched Template Click Classifier. Classifies clicks based
+lang=EN-US> </span>Added Matched Template Click Classifier. Classifies clicks
-on an ideal template to match and a template to reject. An example of this is
+based on an ideal template to match and a template to reject. An example of
-to classify beaked whale clicks in an environment with dolphin clicks.</p>
+this is to classify beaked whale clicks in an environment with dolphin clicks.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@@ -1935,9 +1945,9 @@ interface when importing Soundtrap data. Also changed the default date/time
 format to ISO8601 standard.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-A number of upgrades and fixes to the Localiser algorithms, including expanding
+lang=EN-US> </span>A number of upgrades and fixes to the Localiser algorithms,
-to work with whistles.</p>
+including expanding to work with whistles.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -2097,8 +2107,8 @@ lang=EN-US> </span>User is now able to specify Soundtrap date/time format</p>
 <h1><a name="_Latest_Beta_Version_2.00.11"></a><span lang=EN-US>Beta Version
 2.00.11 October 2017</span></h1>
 
-<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates. You
+<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates.
-should read and understand the notes listed for <a
+You should read and understand the notes listed for <a
 href="#_Latest_Beta_Version_2.00.10">Beta Version 2.00.10</a> before proceeding
 with installation and use of this version.</span></p>
 
@@ -2201,22 +2211,22 @@ file format is the addition of a Unique Data Identifier (UID) to each unit of
 data. This is intended to aid in offline analysis by making it easier for the
 user to link what they are seeing on different PAMGuard displays and also to
 link with any data post processed in Matlab or other custom analysis software.
-UID’s are also added to PAMGuard database tables. </span></p>
+UID’s are also added to PAMGuard database tables. </span></p>
 
 <h4><span lang=EN-US>Converting Old Data</span></h4>
 
 <p class=MsoNormal><span lang=EN-US>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
+on your computer with the same path as the old data, but suffixed with ‘_WithUID’,
-‘_WithUID’, e.g. if your binary data were previously stored in the folder
+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. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>The additional UID column will be added to
 all database tables and populated with unique values. For data which are stored
-in both the binary files and in database tables, the same UID’s will be used
+in both the binary files and in database tables, the same UID’s will be used in
-in both data stores. </span></p>
+both data stores. </span></p>
 
 <h3><span lang=EN-US>New Displays</span></h3>
 
@@ -2285,8 +2295,8 @@ Hawaii/Temperate Pacific/North Atlantic datasets. This has been corrected.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 320. Pamguard stopped reading Click Detector Event data from
+</span>Bug 320. Pamguard stopped reading Click Detector Event data from database
-database when target motion analysis information was encountered. Corrected.</p>
+when target motion analysis information was encountered. Corrected.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2357,9 +2367,10 @@ happens when the user selects save as new configuration. This has been fixed.</p
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 315. code searched for file in working folder, which is the installation
+</span>Bug 315. code searched for file in working folder, which is the
-folder when starting PAMGuard using a shortcut link. But when double-clicking
+installation folder when starting PAMGuard using a shortcut link. But when
-on a psf, the working folder is the location of the psf. This has been fixed.</p>
+double-clicking on a psf, the working folder is the location of the psf. This
+has been fixed.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>7.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -2419,9 +2430,9 @@ dependencies)</span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Other Changes</span></b></p>
 
-<p class=MsoNormal><span lang=EN-US>The installer has been updated to handle both
+<p class=MsoNormal><span lang=EN-US>The installer has been updated to handle
-64 bit and 32 bit installations. PAMGuard psf files are now registered in the
+both 64 bit and 32 bit installations. PAMGuard psf files are now registered in
-Windows Registry, so double-clicking on a psf file should run PAMGuard in
+the Windows Registry, so double-clicking on a psf file should run PAMGuard in
 normal mode (as opposed to Viewer or Mixed modes). Note that the Windows
 Registry can only hold a single executable reference for psf files; therefore,
 for users with multiple installations of PAMGuard, double-clicking on a psf
@@ -2449,12 +2460,12 @@ November 2016</span></h1>
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 Bug 303. Some ASIO sound cards not working with either ASIO system in PAMGuard.
 For the PAMGuard ASIO system, this was due to a data format used by some sound
-cards never being properly implemented. For the “New ASIO system” which
+cards never being properly implemented. For the “New ASIO system” which is
-is based on jAsioHost, the unpacking of that format contained a bug which
+based on jAsioHost, the unpacking of that format contained a bug which returned
-returned incorrect numbers, so data were swamped with noise. Both systems are
+incorrect numbers, so data were swamped with noise. Both systems are now fixed.
-now fixed. By preference, users should use the PAMGuard ASIO system since the
+By preference, users should use the PAMGuard ASIO system since the JAsioHost
-JAsioHost based system seems to drop samples when many channels are running at
+based system seems to drop samples when many channels are running at high
-high sample rate. </span></p>
+sample rate. </span></p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'>2.<span style='font-size-adjust: none;
 font-stretch: normal'><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2741,8 +2752,8 @@ 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. </span></p>
 
-<h1><a name="_Latest_Version_1.15.02"></a><span lang=EN-US>Version 1.15.02
+<h1><a name="_Latest_Version_1.15.02"></a><span lang=EN-US>Version 1.15.02 March
-March 2016</span></h1>
+2016</span></h1>
 
 <p class=MsoNormal>A number of small bug fixes following release of 1.15.00.</p>
 
@@ -2894,13 +2905,13 @@ for details. </span></p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span><span lang=EN-US>GPS Loading into PAMGuard Viewer. This has been
+</span><span lang=EN-US>GPS Loading into PAMGuard Viewer. This has been modified
-modified so that the rules governing GPS data collection and storage also apply
+so that the rules governing GPS data collection and storage also apply when
-when loading data from the database. For instance, if you've stored all GPS
+loading data from the database. For instance, if you've stored all GPS data,
-data, you've probably got a record every second in the database which can
+you've probably got a record every second in the database which can create
-create memory overflows if you try to load a lot of data in the viewer. You can
+memory overflows if you try to load a lot of data in the viewer. You can now
-now tell PAMGuard to only load a data point every n seconds which will reduce
+tell PAMGuard to only load a data point every n seconds which will reduce the
-the number of points loaded. Useful when making large scale overview maps of a
+number of points loaded. Useful when making large scale overview maps of a
 survey. </span></p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>4.</span><span
@@ -3199,9 +3210,8 @@ to read on a time. Fixed</p>
 
 <p class=MsoNormal><i>Menu Layout</i></p>
 
-<p class=MsoNormal>The PAMGuard menus have been rearranged into a more
+<p class=MsoNormal>The PAMGuard menus have been rearranged into a more intuitive
-intuitive grouping which we believe will help users find functionality more
+grouping which we believe will help users find functionality more easily. </p>
-easily. </p>
 
 <p class=MsoNormal>'Detection' menu has been renamed to 'Settings' since many
 menu items within this menu were not directly to do with 'Detection'.</p>
@@ -3292,9 +3302,9 @@ of third octave noise bands. See online help for details. </p>
 
 <p class=MsoNormal><i>Filtered Noise Measurement</i> (Sound Processing Group)</p>
 
-<p class=MsoNormal>This module, developed by Douglas Gillespie, measures noise
+<p class=MsoNormal>This module, developed by Douglas Gillespie, measures noise levels
-levels in a single frequency band using a variety of filter functions. See
+in a single frequency band using a variety of filter functions. See online help
-online help for details. </p>
+for details. </p>
 
 <p class=MsoNormal><i>Envelope Tracing</i> (Beta Only, Sound Processing Group)</p>
 
@@ -3330,11 +3340,10 @@ different. Details are available in the online help. </p>
 <p class=MsoNormal><i>FLAC File Support</i></p>
 
 <p class=MsoNormal>Can now read raw audio data direct from FLAC files. <a
-href="http://en.wikipedia.org/wiki/FLAC">FLAC</a> is a lossless compression
+href="http://en.wikipedia.org/wiki/FLAC">FLAC</a> is a lossless compression algorithm
-algorithm for audio data. Files, or folders of files are accessed in the same
+for audio data. Files, or folders of files are accessed in the same way as WAV
-way as WAV and AIFF files in the Sound Acquisition module. In a future release
+and AIFF files in the Sound Acquisition module. In a future release we also
-we also hope to provide support for writing FLAC files from the sound recorder
+hope to provide support for writing FLAC files from the sound recorder module. </p>
-module. </p>
 
 <p class=MsoNormal><i>Sound Recorder Module</i></p>
 
@@ -3402,8 +3411,8 @@ whistle.</p>
  <li class=MsoNormal style='margin-bottom:0cm'>Airgun display. If this was
      included in the PAMGuard model before the GPS module it would hang
      PAMGuard. This has been rectified. </li>
- <li class=MsoNormal style='margin-bottom:0cm'>Fixed occasional exceptions in the
+ <li class=MsoNormal style='margin-bottom:0cm'>Fixed occasional exceptions in
-     sound output modules when playing back from files. </li>
+     the sound output modules when playing back from files. </li>
  <li class=MsoNormal style='margin-bottom:0cm'>Fixed exceptions in spectrogram
      user interface. </li>
  <li class=MsoNormal style='margin-bottom:0cm'>Fixed National Instruments sound
@@ -3485,8 +3494,8 @@ other data sources for the PAMGuard viewer. </p>
 storage to the database offline for any module having both binary and database
 storage. </p>
 
-<p class=MsoNormal style='margin-left:36.0pt'>Can create a blank MS Access database
+<p class=MsoNormal style='margin-left:36.0pt'>Can create a blank MS Access
-(2007 and later *.accdb formats only).</p>
+database (2007 and later *.accdb formats only).</p>
 
 <p class=MsoNormal style='margin-left:36.0pt'>Can open MS Access from within
 PAMGuard to make it easier to view database content. </p>
@@ -3805,10 +3814,10 @@ source, even if that data source is loaded after the FFT module is created.</p>
 
 <p class=MsoNormal>1. Binary storage module. </p>
 
-<p class=MsoNormal>Performs a parallel role to the PAMGAURD database but uses binary
+<p class=MsoNormal>Performs a parallel role to the PAMGAURD database but uses
-files in a proprietary format which is considerably more efficient for data of
+binary files in a proprietary format which is considerably more efficient for
-unknown length such as whistle contours or small clips of click waveform. This
+data of unknown length such as whistle contours or small clips of click
-feature is currently implemented in the following modules:</p>
+waveform. This feature is currently implemented in the following modules:</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -4017,8 +4026,8 @@ column was setting to zero. This is now fixed</p>
 
 <p class=MsoNormal>Ishmael Detectors</p>
 
-<p class=MsoNormal>Better rendering of detection boxes on spectrogram display and
+<p class=MsoNormal>Better rendering of detection boxes on spectrogram display
-more meaningful names in spectrogram display menu.</p>
+and more meaningful names in spectrogram display menu.</p>
 
 <p class=MsoNormal>Sound acquisition</p>
 
@@ -4107,8 +4116,8 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>This results in a major speed up of data exchange between modules and
+</span>This results in a major speed up of data exchange between modules and can
-can lead to a x4 improvement in overall performance. </p>
+lead to a x4 improvement in overall performance. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -4221,9 +4230,9 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Channel lists in output data streams of Decimator and other modules
+</span>Channel lists in output data streams of Decimator and other modules fixed,
-fixed, so that when channel numbers change, downstream modules configurations
+so that when channel numbers change, downstream modules configurations get the
-get the correct list of available channels. </p>
+correct list of available channels. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -4846,8 +4855,8 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 <p class=MsoNormal>&nbsp;</p>
 
 <p class=MsoNormal><a name="_Toc312065304"></a><a name="_Toc312063949"></a><span
-class=Heading2Char><span style='font-size:13.0pt'>1.0Beta 22 Jan 2008 -
+class=Heading2Char><span style='font-size:13.0pt'>1.0Beta 22 Jan 2008 - Pamguard
-Pamguard starts two releases, core and beta release</span></span>, </p>
+starts two releases, core and beta release</span></span>, </p>
 
 <p class=MsoNormal>this is the beta release</p>
 

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.09aa</version>
+  <version>2.02.10</version>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
   <url>www.pamguard.org</url>
   <organization>
@@ -100,16 +100,6 @@
                 </transformer>
                 <transformer />
               </transformers>
-              <filters>
-                <filter>
-                  <artifact>*:*</artifact>
-                  <excludes>
-                    <exclude>META-INF/*.SF</exclude>
-                    <exclude>META-INF/*.DSA</exclude>
-                    <exclude>META-INF/*.RSA</exclude>
-                  </excludes>
-                </filter>
-              </filters>
             </configuration>
           </execution>
         </executions>
@@ -117,6 +107,16 @@
           <transformers>
             <transformer />
           </transformers>
+          <filters>
+            <filter>
+              <artifact>*:*</artifact>
+              <excludes>
+                <exclude>META-INF/*.SF</exclude>
+                <exclude>META-INF/*.DSA</exclude>
+                <exclude>META-INF/*.RSA</exclude>
+              </excludes>
+            </filter>
+          </filters>
         </configuration>
       </plugin>
       <plugin>

pom.xml

@@ -5,7 +5,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.09ab</version>
+  <version>2.02.10</version>
   <name>Pamguard Java12+</name>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
 	<url>www.pamguard.org</url>

src/Acquisition/pamAudio/WavAudioFile.java

@@ -14,6 +14,7 @@ import javax.sound.sampled.UnsupportedAudioFileException;
 import org.codehaus.plexus.util.FileUtils;
 import Acquisition.offlineFuncs.AquisitionLoadPoint;
 import PamDetection.RawDataUnit;
+import PamguardMVC.PamConstants;
 //import PamUtils.CPUMonitor;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.dataOffline.OfflineDataLoadInfo;
@@ -47,6 +48,8 @@ public class WavAudioFile implements PamAudioFileLoader {
 	 * Get the file extensions associated with loading these data. 
 	 */
 	protected ArrayList<String> fileExtensions; 
+	
+	private double[] channelBackground = new double[PamConstants.MAX_CHANNELS];
 
 	public WavAudioFile() {
 		fileExtensions = new ArrayList<String>(Arrays.asList(new String[]{".wav", ".aif", ".aiff"})); 
@@ -190,6 +193,9 @@ public class WavAudioFile implements PamAudioFileLoader {
 
 				newDataUnit = new RawDataUnit(ms, 1 << ichan, totalSamples, newSamples);
 				newDataUnit.setFileSamples(totalSamples + skipped / frameSize); //set the number samples into the wav file. 
+				
+				removeDCComponent(doubleData[ichan], ichan, audioFormat);
+				
 				newDataUnit.setRawData(doubleData[ichan], true);
 
 				//System.out.println("New wav data: " + PamCalendar.formatDateTime(newDataUnit.getTimeMilliseconds()));
@@ -211,6 +217,26 @@ public class WavAudioFile implements PamAudioFileLoader {
 	}
 
 
+	private void removeDCComponent(double[] ds, int channel, AudioFormat audioFormat) {
+		/*
+		 *  do a simple background subtraction with about a 1s time constant. 
+		 *  If the background is currently zero initialise it to the mean data value.  
+		 */
+		double alpha = 1./audioFormat.getSampleRate();
+		double alpha_1 = 1.-alpha;
+		double bg = channelBackground[channel];
+		if (bg == 0.) {
+			for (int i = 0; i < ds.length; i++) {
+				bg += ds[i];
+			}
+			bg /= ds.length;
+		}
+		for (int i = 0; i < ds.length; i++) {
+			ds[i] -= bg;
+			bg = bg*alpha_1 + ds[i]*alpha;
+		}
+	}
+
 	/**
 	 * Open a sound file. 
 	 * @param soundFile

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 = "2.02.09ab";
+	static public final String version = "2.02.10";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "18 January 2024";
+	static public final String date = "30 January 2024";
 	
 //	/**
 //	 * Release type - Beta or Core

src/PamUtils/worker/filelist/FileListWorker.java

@@ -228,6 +228,7 @@ public abstract class FileListWorker<T extends File> implements PamWorkWrapper<F
 	@Override
 	public final void taskFinished(FileListData<T> result) {
 		oldFileList = result;
+		sortFiles(result);
 		fileListUser.newFileList(result);
 	}