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Merge branch 'main' of https://github.com/macster110/PAMGuard

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7
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176
README.html
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@ -388,7 +388,7 @@ PamguardBeta_ViewerMode.exe):</p>
<h1><a name="_LATEST_VERSION_2.02.03"></a><a name="_VERSION_2.02.07_January"></a><a
name="_Latest_Version_2.02.10"></a><em><span style='font-size:12.0pt;
font-family:"Cambria",serif;font-style:normal'><a href="#_Version_2.02.11_April">Latest
Version 2.02.11 April 2024</a></span></em></h1>
Version 2.02.12 June 2024</a></span></em></h1>
<h1><em><span style='font-size:12.0pt;font-family:"Cambria",serif;font-style:
normal'><a href="#_Version_2.02.10_January">Version 2.02.10 January 2024</a></span></em></h1>
@ -465,22 +465,36 @@ Version 2.00.10 June 2017</a></span></h1>
name="_Latest_Version_2.02.06"></a><a name="_Latest_Version_2.02.07"></a><a
name="_Latest_Version_2.02.08"></a><a name="_Version_2.02.09_June"></a><a
name="_Version_2.02.10_January"></a><a name="_Version_2.02.11_April"></a>Version
2.02.11 April 2024</h1>
2.02.12 June 2024</h1>
<p class=MsoNormal>&nbsp;</p>
<h2>New Features</h2>
<p class=MsoNormal>Deep Learning Classifier. Major upgrade to support for Deep
Learning models in PAMGuard. See online help for details.</p>
<p class=MsoNormal>Click detector: Remembers locations of displays and doesn’t
continually reset them. </p>
<p class=MsoNormal>Help for Matched Click Classifier</p>
<p class=MsoNormal>Help for Matched Click Classifier.</p>
<p class=MsoNormal>Project information dialog. This allows capture of essential
project information to store with your data. See menu item Settings/Project
information.</p>
<h2>Tethys Database</h2>
<p class=MsoNormal>Many users will be aware that we’re integrating an interface
to the <a href="https://tethys.sdsu.edu/">Tethys Database</a> into PAMGuard.
Some basic features are available for testing. If interested, please contact
the PAMGuard support team. </p>
<h2>Bug Fixes</h2>
<p class=MsoNormal>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. </p>
that had become corrupted so added code to relink offline clicks to their
corresponding clicks from binary data. </p>
<p class=MsoNormal>Drawing non-acoustic data: Data that were not associated
with any hydrophones, e.g. visual sightings in Logger forms were not drawing on
@ -497,14 +511,35 @@ as PAMGuard stops / restarts. </p>
function fixed and now inserts correct times of start and ends of events into
database. </p>
<p class=MsoNormal>Clip generator. Changes to ensure PAMGuard keeps audio data
long enough to make clips. In some circumstances data were being discarded too
early so clips could not be created. </p>
<p class=MsoNormal>Acquisition “Skip initial seconds” feature, designed to
remove high sample levels e.g. from calibration tones at start of a soundtrap
recording was not working with the click detector. This is fixed but replacing
all data with 0’s and still sending data. Note that this may lead to
artificially low noise measures at the start of a file. </p>
<p class=MsoNormal>Data reprocessing options. Updated to ensure that the option
&quot;Start normally. Note risk of overwriting!&quot; is always available. Also
improved code naming binary files to attempt to push them to exact times,
rather than a couple of seconds after the hour. </p>
<p class=MsoNormal>improved code naming binary files to attempt to push them to
exact times, rather than a couple of seconds after the hour. </p>
<p class=MsoNormal>Updated icons to improve display on high definition screens.
</p>
<h1>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
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. </span></p>
@ -532,9 +567,9 @@ correctly saving updated bearings to the database. Now fixed. </span></p>
<p class=MsoNormal><b><span lang=EN-US>ROCCA Classifier fixes</span></b></p>
<p class=MsoNormal><span lang=EN-US>Allow Rocca to run without classifiers: Fixed
bug that threw an error if no classifier files were &nbsp;specified in Rocca
Params dialog</span></p>
<p class=MsoNormal><span lang=EN-US>Allow Rocca to run without classifiers:
Fixed bug that threw an error if no classifier files were &nbsp;specified in
Rocca Params dialog</span></p>
<p class=MsoNormal><span lang=EN-US>Fix memory issue with
RoccaContourDataBlocks not being released for garbage collection</span></p>
@ -1128,8 +1163,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>4. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>Bug
&nbsp; 456. Under certain conditions, the Ishmael detection plugin that is
shown at the bottom of the spectrogram can disappear about 500 msec behind the
&nbsp; 456. Under certain conditions, the Ishmael detection plugin that is shown
at the bottom of the spectrogram can disappear about 500 msec behind the
current time. </p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5. </span><span
@ -1218,10 +1253,10 @@ lang=EN-US> </span>Add functionality for bluetooth headsets. </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>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). </p>
lang=EN-US> </span>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). </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
@ -1232,8 +1267,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
Add 15 minute data load option to viewer mode. </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>
Add 3D map for target motion module. </p>
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>Add 3D map for target motion 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><span
@ -1259,12 +1294,12 @@ lang=EN-US> </span>Added channel display to noise one band measurement display.
</p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
Added Azigram module, to work in conjunction with Difar. </p>
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 Azigram module, to work in conjunction with Difar. </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>
Added beaked whale to sim sounds </p>
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 beaked whale to sim sounds </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
@ -1301,8 +1336,9 @@ PSFX files when PAMGuard exits.</p>
<p class=MsoNormal><b><span lang=EN-US>Bug Fixes</span></b></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 433. Custom storage options were being lost when Pamguard restarted.</p>
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>Bug 433. Custom storage options were being lost when
Pamguard restarted.</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
@ -1310,8 +1346,8 @@ lang=EN-US> </span>Bug 434. Pamguard Viewer mode was having problems importing
settings from psfx file.</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>
Bug 435. Logger forms subtabs not working.</p>
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>Bug 435. Logger forms subtabs not working.</p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>4. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@ -1392,8 +1428,8 @@ classify clicks. </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 option in Sound Acquisition settings dialog to
override filename time stamp and use PC local time instead. </p>
lang=EN-US> </span>Added option in Sound Acquisition settings dialog to override
filename time stamp and use PC local time instead. </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
@ -1415,9 +1451,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
Implemented a simple UDP output for PAMGuard alarms. </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>
Changes to Spectrogram Mark Observers, to allow individual channels to be
selected instead of the spectrogram panel as a whole. </p>
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>Changes to Spectrogram Mark Observers, to allow individual
channels to be selected instead of the spectrogram panel as a whole. </p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>8. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@ -1452,9 +1488,9 @@ be compatible with this version, and vice-versa.</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>
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.</p>
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.</p>
<!-- ************************************************************************************************************************** --><!-- ************************************************************************************************************************** -->
@ -1688,8 +1724,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
<p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></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>
Improvement to Range Rings in Map display.</p>
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>Improvement to Range Rings in Map display.</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>
@ -2158,7 +2194,7 @@ showing. </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>Bug 323. Difar module.</span> Fixed a couple of small
</span><span lang=EN-US>Bug 323. Difar module. </span>Fixed a couple of small
bugs in the DIFAR system which caused it to not work if old configuratins were
used. </p>
@ -2304,8 +2340,8 @@ the new version. However please note the following:</span></p>
<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><span lang=EN-US>New classes will be added to the configuration files,
so they will no longer work with older PAMGuard versions.</span></p>
</span><span lang=EN-US>New classes will be added to the configuration files, so
they will no longer work with older PAMGuard versions.</span></p>
<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -2428,8 +2464,8 @@ milliseconds. However, getDuration actually returns the number of samples.
<p class=MsoNormal><b><span lang=EN-US>Plug-Ins</span></b></p>
<p class=MsoNormal><span lang=EN-US>A major change in this version of PAMGuard
is how plug-ins are managed. PAMGuard now has the ability to dynamically load
<p class=MsoNormal><span lang=EN-US>A major change in this version of PAMGuard is
how plug-ins are managed. PAMGuard now has the ability to dynamically load
plug-in modules (saved as jar files) at runtime. This will greatly simplify the
process of testing and distributing newly developed modules, since only a small
jar file will be required rather than a new bespoke PAMGuard installation.</span></p>
@ -2438,9 +2474,9 @@ jar file will be required rather than a new bespoke PAMGuard installation.</span
unchanged, in most cases simply requiring the addition of an interface class.
&nbsp;Instructions for the development of new modules utilizing the plug-in
scheme can be found <a href="http://www.pamguard.org/16_HowtomakePlug-Ins.html"
target="_blank">here</a>. &nbsp;Plug-in modules can be downloaded from the
PAMGuard website here, but developers are encouraged to host and maintain their
own modules.</span></p>
target="_blank">here</a>. &nbsp;Plug-in modules can be downloaded from the PAMGuard
website here, but developers are encouraged to host and maintain their own
modules.</span></p>
<p class=MsoNormal><span lang=EN-US>Modules of interest to the general PAM
community will remain as part of the core PAMGuard installation. However,
@ -2615,9 +2651,9 @@ main click detector display. </span></p>
<p class=MsoNormal><b><span lang=EN-US>Target Motion Analysis</span></b></p>
<p class=MsoNormal><span lang=EN-US>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:</span></p>
<p class=MsoNormal><span lang=EN-US>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:</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;
@ -3055,8 +3091,8 @@ allocation to allow more memory for the database interface. Hopefully Fixed. </p
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'><span
lang=EN-AU>9.</span><span lang=EN-AU style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>Bug 239. <span lang=EN-AU>Fixed bug in the DIFAR module that was incorrectly
preventing cross-fixes for some calls.</span></p>
</span>Bug 239. <span lang=EN-AU>Fixed bug in the DIFAR module that was
incorrectly preventing cross-fixes for some calls.</span></p>
<p class=MsoNormal>Details of these bugs can be found at <a
href="https://sourceforge.net/p/pamguard/bugs">https://sourceforge.net/p/pamguard/bugs</a></p>
@ -3515,9 +3551,9 @@ to these menus to provide additional information to users. &nbsp;</p>
<p class=MsoNormal style='margin-left:36.0pt'><i>Radar Display</i></p>
<p class=MsoNormal style='margin-left:36.0pt'>Functionality has been added to the
radar display so that bearings can be shown relative to either the vessel or to
true North. </p>
<p class=MsoNormal style='margin-left:36.0pt'>Functionality has been added to
the radar display so that bearings can be shown relative to either the vessel
or to true North. </p>
<p class=MsoNormal style='margin-left:36.0pt'>Better control of data in viewer
mode, making is easy to scroll through and view data for short time periods. </p>
@ -3872,11 +3908,11 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
<p class=MsoNormal>2. Improved offline viewer functionality. </p>
<p class=MsoNormal>The offline viewer is much improved with better data
scrolling and the ability to view data either stored in the database or the
binary storage system. Work has stated on functions which read and use data
stored in audio files. This is currently limited to re-calculating and
displaying displaying spectrogram data during viewer mode operation.&nbsp; </p>
<p class=MsoNormal>The offline viewer is much improved with better data scrolling
and the ability to view data either stored in the database or the binary
storage system. Work has stated on functions which read and use data stored in
audio files. This is currently limited to re-calculating and displaying
displaying spectrogram data during viewer mode operation.&nbsp; </p>
<p class=MsoNormal>3. Heading sensor readout</p>
@ -3977,8 +4013,8 @@ channels 0 and 1. Similarly if you switched sound cards, you may have to
reconfigure every detector and several of the displays to handle the changes in
channel numbering. </p>
<p class=MsoNormal>I have spent a considerable amount of time trying to work
out a better system for handling channel numbering in PAMGUARD and have decided
<p class=MsoNormal>I have spent a considerable amount of time trying to work out
a better system for handling channel numbering in PAMGUARD and have decided
that the only practical thing to do is to force all software channel numbering
back to a zero indexed system. i.e. even if you read out hardware channels
3,4,5 and 6, within PAMGUARD, everywhere apart from the Sound acquisition
@ -4302,11 +4338,11 @@ 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>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.&nbsp; </p>
</span>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.&nbsp; </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;
@ -4374,8 +4410,8 @@ online help. </p>
<p class=MsoNormal><b>PAMGUARD Mixed Mode operation</b></p>
<p class=MsoNormal>Analyses data from wav or AIF file and synchronises it with GPS
data reloaded from a database so that detected sounds may be correctly
<p class=MsoNormal>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,
@ -4566,9 +4602,9 @@ a serial port </p>
<p class=MsoNormal>New Likelihood detector. </p>
<p class=MsoNormal>The likelihood detector module is an implementation of a
likelihood ratio test with flexible algorithms and configuration to estimate
likelihood. It is </p>
<p class=MsoNormal>The likelihood detector module is an implementation of a likelihood
ratio test with flexible algorithms and configuration to estimate likelihood.
It is </p>
<p class=MsoNormal>suitable for detecting both short duration Odontocete clicks
(Sperm, Beaked, etc.) as well as moderate duration Mysticete calls (Humpback,

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dependency-reduced-pom.xml
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@ -4,7 +4,7 @@
<groupId>org.pamguard</groupId>
<artifactId>Pamguard</artifactId>
<name>Pamguard</name>
<version>2.02.11d</version>
<version>2.02.12</version>
<description>Pamguard using Maven to control dependencies</description>
<url>www.pamguard.org</url>
<organization>

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readme.md
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@ -6,19 +6,21 @@ PAMGuard is a bioacoustics analysis program designed for use in real time resear
## Why do we need PAMGuard?
PAMGuard fufills two main requirements within marine bioacoustics
1) **Real time operation**: Almost all PAMGuard features and modules work in real time - this allows scientists and industry to detect, classify and loclaise animals in real time on a standard consumer laptop, enabling mitigations and research survey without expensive bespoke software solutions and the transparncy of open source software.
1) **Real time operation**: Almost all PAMGuard features and modules work in real time - this allows scientists and industry to detect, classify and localise the position of animals in real time on a standard consumer laptop, enabling mitigation and research surveys without expensive bespoke software solutions and the transparncy of open source software.
2) **Processing and visuslisation of large datasets**: Off-the-shelf autonomous PAM devices, large scale surveys involving drifters, towed arrays and bottom mounted devices and real time continuous monitoring system all generate huge volumes of data whcih requires automated analysis approaches. PAMGuard allows the processing of very large passive acoustic datasets using automated algorothms and provides visualisation tools for a manual analyst to check the results.
2) **Processing and visuslisation of large datasets**: Off-the-shelf autonomous PAM devices, large scale surveys involving drifters, towed arrays, glidders, bottom mounted devices and real time continuous monitoring system all generate huge volumes of data whcih requires automated analysis approaches. PAMGuard allows the processing of very large passive acoustic datasets using automated algorothms and crucially provides comprehensive visualisation tools for a manual analyst to check the results.
## Installation
PAMGuard is available on Windows and can be downloaded from the [PAMGuard website](www.pamguard.org). Note that we are considering MacOS installers but they are not available at this time.
PAMGuard is available on Windows and can be downloaded from the [PAMGuard website](www.pamguard.org). Note that we are considering MacOS and Linux installers but they are not available at this time.
## Tutorial
## Quick start tutorial
PAMGuard is a modular program with two modes; real-time and viewer. Typically a user will start with real-time model, either in the field collecting data or post processing sound files from a recorder. Once data are processed, users move on to viewer mode where data can be explored and further processed.
Upon opening PAMGuard for the first time you are greeted with a blank screen. You must add a series of modules to create the desired acosutic workflow. For example if processing sound files then first add the Sound Acquisition module **_File->Add Modules->Sound Processing->Sound Acquisition_**. Then add the desired detection algorothms e.g. **_File->Add Modules->Detector->Click Detectors_**. Some modules (such as the click detector) have their own displays, others are added to more generalised displays. For example, the whislte and moan detector module shows detections on a spectrgram display. First add a new tab using **_File->Add Modules->Displays->User Display**. Click on the user display tab and then from the top menu select **_User display-> New Spectrgram_**. Right click on the added spectrgram and select whistle and moan contours to show whistle detections overlaid on the raw spectrgram.
Upon opening PAMGuard for the first time you are greeted with a blank screen. You must add a series of modules to create the desired acosutic workflow - this is referred to as PAMGuard *data model*. For example if processing sound files then first add the Sound Acquisition module **_File->Add Modules->Sound Processing->Sound Acquisition_**. Then add the desired detection algorothms e.g. **_File->Add Modules->Detector->Click Detectors_**. Some modules (such as the click detector) have their own bespoke displays, others are added to more generalised displays. For example, the whistle and moan detector module shows detections on a spectrgram display, time base display, map etc.. First add a new tab using **_File->Add Modules->Displays->User Display**. Click on the user display tab and then from the top menu select **_User display-> New Spectrogram_**. Right click on the added spectrgram and select whistle and moan contours to show whistle detections overlaid on the raw spectrgram.
Make sure to add the database and binary file storage modules **_File->Add Modules->Utilities->..._**) to save data then press the run button (red button) and data will process. PAMGuard can handle huge datasets so runing might take hours or even days. Progress is shown on the bottom of the screen.
Make sure to add the database and binary file storage modules **_File->Add Modules->Utilities->..._**) to save data then press the run button (red button) and data will process. PAMGuard can handle huge datasets so running might take hours or even days. Progress is shown on the bottom of the screen.
Once the data has run, open PAMGuard viewer mode. Select the database you used to process the data along and thebianry file storage path and PAMGuard will open, showing an overview of the dataset in a new _Data map_ tab. Right click anywhere on the data map and select "Center data here" - PAMGuard will load the data for the selected period which can be explored using whichever displays have been added to the data model.
## Features
### Hardware integration
@ -49,20 +51,22 @@ Almsot all detection data can be visualised on a map. PAMGaurd also supports plo
An important aspect of PAMGuard is the ability for users to explore porcessed data. PAMGuard allows users to visualise data at multiple different times scales, from inspecting individual waveforms microseconds long to datagrams showing detector output or soundscape metrics over days, weeks or even years.
### Advanced manual annotation
The displays within PAMGuard support a variety of manual annottion tools.
The displays within PAMGuard support a variety of manual annotation tools. Users can add data to annotations in multiple ways, from simple text annotations to complex forms created by users.
### Deep learning integration
PAMGuard allows users to run their own deep learning models using the deep learning module. AI can therfore be integrated into PAMGuard workflows, allowing for much more efficient analysis of data.
PAMGuard allows users to run their own deep learning models using the deep learning module. AI can therfore be integrated into PAMGuard workflows, allowing for more efficient analysis of data.
### Metadata standard and Tethys compatibility
PAMGuard Integrates with Tethys
PAMGuard Integrates with Tethys database. Users can export processed PAMGuard data to a Tethys database seamlessly; this ifeature is great for large scale projects or organisatiosn with long term datasets.
## Feature roadmap
There's lots of features we would like to add to PAMGuard. If you want to add a feature you can either code it up yourself in Java and submit a pull request or get in touch with us to discuss how to it might be integrated. Some smaller features might be in our roadmap anyway but larger features usually require funding. Some features we are thinking about (but do not necassarily have time for yet) are;
* Support for decidecade noise bands (base 10 filter bank) in noise band monitor to meet Euopean standards
* Capabaility to export data directly from PAMGaurd e.g. as MAT files.
* Automated test suite to make releases more stable. Note that unit and integration tests are also being slowly incorporated.
* Capabaility to export data directly from PAMGaurd e.g. as MAT files (in progress).
* Automated test suite to make releases more stable. Note that unit and integration tests are also being slowly incorporated.
* Support for ARM based computers (in progress).
* A graphical user interface and Python library for training PAMGuard compatible deep learning models.
## Development
This is the main code repository for the PAMGuard software and was created on 7 January 2022 from a [sourceforge SVN repository](https://sourceforge.net/p/pamguard/svn/HEAD/tree/) revision r6278.

9
src/Acquisition/FileInputSystem.java
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@ -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;
@ -602,7 +603,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
audioStream.close();
}
System.out.println("FileInputSystem - prepareInputFile");
// System.out.println("FileInputSystem - prepareInputFile");
audioStream = PamAudioFileManager.getInstance().getAudioInputStream(currentFile);
@ -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);
}

1706
src/PamController/PamController.java
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File diff suppressed because it is too large Load Diff

4
src/PamController/PamguardVersionInfo.java
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@ -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 = "2.02.12";
/**
* Release date
*/
static public final String date = "30 May 2024";
static public final String date = "24 June 2024";
// /**
// * Release type - Beta or Core

15
src/PamController/fileprocessing/ReprocessChoiceDialog.java
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@ -4,6 +4,8 @@ import java.awt.BorderLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.List;
import javax.swing.ButtonGroup;
@ -64,15 +66,28 @@ public class ReprocessChoiceDialog extends PamDialog {
List<ReprocessStoreChoice> userChoices = choiceSummary.getChoices();
choiceButtons = new JRadioButton[userChoices.size()];
ButtonGroup bg = new ButtonGroup();
SelAction selAction = new SelAction();
for (int i = 0; i < userChoices.size(); i++) {
ReprocessStoreChoice aChoice = userChoices.get(i);
choiceButtons[i] = new JRadioButton(aChoice.toString());
choiceButtons[i].setToolTipText(aChoice.getToolTip());
bg.add(choiceButtons[i]);
choiceButtons[i].addActionListener(selAction);
choicePanel.add(choiceButtons[i], c);
c.gridy++;
}
setDialogComponent(mainPanel);
getCancelButton().setVisible(false);
getOkButton().setEnabled(false);
}
private class SelAction implements ActionListener {
@Override
public void actionPerformed(ActionEvent e) {
getOkButton().setEnabled(true);
}
}
public static ReprocessStoreChoice showDialog(Window parentFrame, StoreChoiceSummary choices) {

4
src/PamController/fileprocessing/ReprocessManager.java
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@ -62,7 +62,7 @@ public class ReprocessManager {
*/
boolean setupOK = setupInputStream(choiceSummary, choice);
if (choice == ReprocessStoreChoice.DONTSSTART) {
if (choice == null || choice == ReprocessStoreChoice.DONTSSTART) {
return false;
}
@ -172,6 +172,8 @@ public class ReprocessManager {
choiceSummary.addChoice(ReprocessStoreChoice.STARTNORMAL);
return choiceSummary;
}
choiceSummary.addChoice(ReprocessStoreChoice.STARTNORMAL);
ArrayList<PamControlledUnit> outputStores = PamController.getInstance().findControlledUnits(DataOutputStore.class, true);
boolean partStores = false;

3
src/PamController/fileprocessing/StoreChoiceSummary.java
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@ -65,6 +65,9 @@ public class StoreChoiceSummary {
* @param choice
*/
public void addChoice(ReprocessStoreChoice choice) {
if (choices.contains(choice)) {
return;
}
choices.add(choice);
}

2
src/PamModel/PamModel.java
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@ -472,7 +472,7 @@ final public class PamModel implements PamSettings {
mi.setModulesMenuGroup(utilitiesGroup);
mi.setMaxNumber(1);
//mi.addGUICompatabilityFlag(PamGUIManager.FX); //has FX enabled GUI.
// mi.setHidden(SMRUEnable.isEnable() == false);
mi.setHidden(SMRUEnable.isEnable() == false);
}
/*

10
src/PamUtils/PamCalendar.java
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@ -25,6 +25,7 @@ import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.time.LocalDateTime;
import java.time.ZoneOffset;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.Locale;
@ -32,6 +33,7 @@ import java.util.TimeZone;
import PamController.PamController;
import PamUtils.time.CalendarControl;
import binaryFileStorage.BinaryStore;
/**
@ -85,7 +87,7 @@ public class PamCalendar {
* viewPositions which is the number of milliseconds from the sessionsStartTime.
*/
private static long viewPosition;
/**
* If files are being analysed, return the time based on the file
@ -880,14 +882,18 @@ public class PamCalendar {
*/
public static void setSessionStartTime(long sessionStartTime) {
PamCalendar.sessionStartTime = sessionStartTime;
PamController.getInstance().updateMasterClock(getTimeInMillis());
}
/**
*
* @param soundFileTimeMillis The start time of a sound file
* Relative time within a sound file. This is always just added to sessionStartTime
* to give an absolute time.
* @param soundFileTimeMillis The relative time of a sound file.
*/
public static void setSoundFileTimeInMillis(long soundFileTimeMillis) {
PamCalendar.soundFileTimeInMillis = soundFileTimeMillis;
PamController.getInstance().updateMasterClock(getTimeInMillis());
}
/**

25
src/PamView/PamAWTUtils.java
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@ -159,4 +159,29 @@ public class PamAWTUtils {
return bestPoint;
}
/**
* Convert a colour to an int.
* @param c - the colour to change.
* @return the int representation of the colour
*/
public static int colorToInt(java.awt.Color c) {
int r = (int) Math.round(c.getRed());
int g = (int) Math.round(c.getGreen());
int b = (int) Math.round(c.getBlue());
return (r << 16) | (g << 8) | b;
}
/**
* Convert an int encoded with a colour to a Color object.
* @param value - the int to convert to colour
* @return the Color object for the int
*/
public static java.awt.Color intToColor(int value) {
int r = (value >>> 16) & 0xFF;
int g = (value >>> 8) & 0xFF;
int b = value & 0xFF;
return new java.awt.Color(r,g,b);
}
}

5
src/PamView/dialog/GenericSwingDialog.java
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@ -10,6 +10,8 @@ import javax.swing.JComponent;
import javax.swing.JPanel;
import javax.swing.border.EmptyBorder;
import PamController.PamController;
public class GenericSwingDialog extends PamDialog {
private boolean allOk;
@ -45,6 +47,9 @@ public class GenericSwingDialog extends PamDialog {
* @return
*/
public static boolean showDialog(Window parentFrame, String title, Point screenPoint, PamDialogPanel ...dialogPanels) {
if (parentFrame == null) {
parentFrame = PamController.getMainFrame();
}
GenericSwingDialog swingDialog = new GenericSwingDialog(parentFrame, title, dialogPanels);
swingDialog.setParams();
swingDialog.pack();

1
src/PamView/dialog/PamDialogPanel.java
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@ -5,6 +5,7 @@ import javax.swing.JComponent;
/**
* General class for dialog panels which will be incorporated into one or
* more actual dialogs.
* Can be quickly opened with GenericSwingDialog
* @author Doug Gillespie
*
*/

28
src/PamView/symbol/modifier/PeakFreqModifier.java
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@ -5,6 +5,7 @@ import java.awt.Color;
import PamUtils.PamUtils;
import PamView.GeneralProjector;
import PamView.PamSymbolType;
import PamView.dialog.PamDialogPanel;
import PamView.symbol.PamSymbolChooser;
import PamView.symbol.SymbolData;
import PamguardMVC.PamDataUnit;
@ -45,7 +46,15 @@ public class PeakFreqModifier extends SymbolModifier {
*/
private ColourArrayType colourArrayType;
private PeakFreqOptionsPane peakFreqOptions;
/**
* JavaFX pane for frequency symbol options.
*/
private PeakFreqOptionsPane peakFreqOptionsPaneFX;
/**
* Swing panel for frequency symbol options
*/
private PamDialogPanel peakFreqOptionsPanel;
public PeakFreqModifier(PamSymbolChooser symbolChooser) {
super(PEAK_FREQ_MODIFIER_NAME, symbolChooser, SymbolModType.FILLCOLOUR | SymbolModType.LINECOLOUR );
@ -130,11 +139,20 @@ public class PeakFreqModifier extends SymbolModifier {
@Override
public SymbolModifierPane getOptionsPane() {
//System.out.println("PEAK FREQ COLOUR ARRAY2: " + peakFreqSymbolOptions.freqColourArray);
if (this.peakFreqOptions==null) {
peakFreqOptions = new PeakFreqOptionsPane(this);
peakFreqOptions.setParams();
if (this.peakFreqOptionsPaneFX==null) {
peakFreqOptionsPaneFX = new PeakFreqOptionsPane(this);
peakFreqOptionsPaneFX.setParams();
}
return peakFreqOptions;
return peakFreqOptionsPaneFX;
}
public PamDialogPanel getDialogPanel() {
//System.out.println("PEAK FREQ COLOUR ARRAY2: " + peakFreqSymbolOptions.freqColourArray);
if (this.peakFreqOptionsPanel==null) {
peakFreqOptionsPanel = new PeakFreqOptionsPanel(this);
peakFreqOptionsPanel.setParams();
}
return peakFreqOptionsPanel;
}
@Override

203
src/PamView/symbol/modifier/PeakFreqOptionsPanel.java Normal file
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@ -0,0 +1,203 @@
package PamView.symbol.modifier;
import java.awt.Dimension;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JSpinner;
import javax.swing.SpinnerNumberModel;
import javax.swing.border.TitledBorder;
import PamView.ColourComboBox;
import PamView.dialog.PamDialogPanel;
import PamView.panel.PamPanel;
import pamViewFX.fxNodes.utilsFX.PamUtilsFX;
/**
* Swing panel for changing parameters for the peak frequency symbol chooser.
*
* @author Jamie Macaulay
*/
public class PeakFreqOptionsPanel implements PamDialogPanel {
private PeakFreqModifier freqSymbolModifer;
private PamPanel mainPanel;
private JSpinner minFreq;
private JSpinner maxFreq;
private ColourComboBox colourBox;
public PeakFreqOptionsPanel(PeakFreqModifier symbolModifer) {
this.freqSymbolModifer=symbolModifer;
mainPanel = createFreqPaneL();
}
/**
* Pane which changes the frequency limits.
* @return pane with controls to change freq. limits.
*/
private PamPanel createFreqPaneL(){
PamPanel holder = new PamPanel();
holder.setLayout(new GridBagLayout());
holder.setBorder(new TitledBorder("Peak frequency colour map"));
GridBagConstraints c = new GridBagConstraints();
c.gridy=0;
c.gridx=0;
//doesn't seem to work so added spaces in labels instead
c.ipadx = 5;
c.anchor =GridBagConstraints.EAST;
holder.add(new JLabel("Min. freq"), c);
c.gridx++;
c.anchor =GridBagConstraints.WEST;
minFreq = new JSpinner(new SpinnerNumberModel(0., 0., 10000000., 1000.));
//make the lock button the same height as the spinner
Dimension prefSize = minFreq.getPreferredSize();
minFreq.setPreferredSize(new Dimension(90, prefSize.height));
holder.add(minFreq, c);
c.gridx++;
c.ipadx = 5;
c.anchor =GridBagConstraints.EAST;
holder.add(new JLabel(" Max. freq"), c);
c.gridx++;
c.ipadx = 5;
c.anchor =GridBagConstraints.WEST;
maxFreq =new JSpinner(new SpinnerNumberModel(1000., 1., Math.max(1000.,freqSymbolModifer.getSymbolChooser().getPamDataBlock().getSampleRate()/2.), 1000.));
maxFreq.setPreferredSize(new Dimension(90, prefSize.height));
holder.add(maxFreq, c);
c.gridx++;
c.ipadx = 5;
c.anchor =GridBagConstraints.WEST;
holder.add(new JLabel(" Hz"), c);
c.gridy++;
c.ipadx = 5;
c.gridwidth=2;
c.gridx=0;
c.anchor =GridBagConstraints.EAST;
holder.add(new JLabel("Freq. colour map"), c);
c.gridx=2;
c.gridwidth=3;
colourBox = new ColourComboBox();
c.anchor =GridBagConstraints.WEST;
prefSize = colourBox.getPreferredSize();
colourBox.setPreferredSize(new Dimension(200, prefSize.height));
holder.add(colourBox, c);
return holder;
}
@Override
public JComponent getDialogComponent() {
return mainPanel;
}
@Override
public boolean getParams(){
//bit messy but works /
// PeakFreqSymbolOptions symbolOptions = (PeakFreqSymbolOptions) standardSymbolOptions.getModifierParams(this.getSymbolModifier().getName());
PeakFreqSymbolOptions symbolOptions = (PeakFreqSymbolOptions)freqSymbolModifer.getSymbolModifierParams().clone();
//must make sure we do not call get parameters during a set parameters - the listeners on the controls call getParams so all goes
//haywire if the setParams is not set properly.
//System.out.println("GETPARAMS: " + ColourArray.getColorArrayType(this.colourBox.getSelectionModel().getSelectedItem()) + " " + setParams);
symbolOptions.freqLimts=new double[] {(double) minFreq.getValue(), (double) maxFreq.getValue()};
symbolOptions.freqColourArray = PamUtilsFX.swingColArray2FX(this.colourBox.getSelectedColourMap());
//System.out.println("StandardSymbolModifierPane : getParams(): new mod: " +mod);
freqSymbolModifer.setSymbolModifierParams(symbolOptions);
System.out.println("Get freq limits: 1: " + symbolOptions.freqLimts[0] + " " + symbolOptions.freqLimts[1] + " " + (double) maxFreq.getValue());
return true;
}
@Override
public void setParams() {
// StandardSymbolOptions standardSymbolOptions = (StandardSymbolOptions) getSymbolModifier().getSymbolChooser().getSymbolOptions();
// PeakFreqSymbolOptions symbolOptions = (PeakFreqSymbolOptions) standardSymbolOptions.getModifierParams(this.getSymbolModifier().getName());
PeakFreqSymbolOptions symbolOptions = (PeakFreqSymbolOptions)freqSymbolModifer.getSymbolModifierParams();
//now set frequency parameters;
checkFreqLimits( symbolOptions ) ;
minFreq.setValue(symbolOptions.freqLimts[0]);
maxFreq.setValue(symbolOptions.freqLimts[1]);
colourBox.setSelectedColourMap((PamUtilsFX.fxColArray2Swing(symbolOptions.freqColourArray)));
}
/**
* Check the frequency limits make sense for the given datablock
* @param symbolOptions - the peak frequency options.
*/
private void checkFreqLimits(PeakFreqSymbolOptions symbolOptions ) {
System.out.println("Check freq limits: 1: " + symbolOptions.freqLimts[0] + " " + symbolOptions.freqLimts[1]);
SpinnerNumberModel spinnerValFact = (SpinnerNumberModel) maxFreq.getModel();
spinnerValFact.setMaximum(getSampleRate() /2.);
//for some reason also need to set this
spinnerValFact.setMinimum(1.);
//set reasonable step sizes
if (getSampleRate()>=10000) {
spinnerValFact.setStepSize(1000.);
}
else if (getSampleRate()>=2000){
spinnerValFact.setStepSize(200.);
}
else {
spinnerValFact.setStepSize(50.);
}
if (symbolOptions.freqLimts==null) {
symbolOptions.freqLimts= new double[] {0, getSampleRate() /2};
}
System.out.println("Check freq limits: 2: " + symbolOptions.freqLimts[0] + " " + symbolOptions.freqLimts[1]);
//check nyquist for upper limit
if (symbolOptions.freqLimts[1]>getSampleRate() /2) {
symbolOptions.freqLimts[1]=getSampleRate() /2;
}
//check nyquist for lower limit
if (symbolOptions.freqLimts[0]>getSampleRate() /2) {
symbolOptions.freqLimts[0]=0;
}
}
private float getSampleRate() {
return freqSymbolModifer.getSymbolChooser().getPamDataBlock().getSampleRate();
}
}

3
src/PamView/symbol/modifier/SymbolModifier.java
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@ -150,7 +150,8 @@ abstract public class SymbolModifier {
if (dialogPanel == null) {
return null;
}
JMenuItem menuItem = new JMenuItem("Options ...");
JMenuItem menuItem = new JMenuItem("More options ...");
menuItem.setToolTipText("More symbol options");
menuItem.addActionListener(new ActionListener() {
@Override

37
src/PamView/symbol/modifier/swing/ModifierTreeNode.java
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@ -8,12 +8,13 @@ import java.util.Enumeration;
import javax.swing.tree.TreeNode;
import PamUtils.PamUtils;
import PamView.dialog.PamDialogPanel;
import PamView.symbol.modifier.SymbolModifier;
public class ModifierTreeNode implements TreeNode {
private SymbolModifier modifier;
private SymbolTreeRoot rootNode;
private ArrayList<ChoiceTreeNode> choiceNodes;
private ArrayList<TreeNode> choiceNodes;
public ModifierTreeNode(SymbolTreeRoot rootNode, SymbolModifier modifier) {
super();
@ -22,17 +23,25 @@ public class ModifierTreeNode implements TreeNode {
int modBits = modifier.getModifyableBits();
int nMod = Integer.bitCount(modBits);
choiceNodes = new ArrayList<>();
int leafIndex = 0;
for (int i = 0; i < nMod; i++) {
choiceNodes.add(new ChoiceTreeNode(this, 1<<PamUtils.getNthChannel(i, modBits), i));
choiceNodes.add(new ChoiceTreeNode(this, 1<<PamUtils.getNthChannel(i, modBits), leafIndex++));
}
PamDialogPanel optionsPanel = modifier.getDialogPanel();
if (optionsPanel != null) {
choiceNodes.add(new OptionsTreeNode(this, modifier, optionsPanel, leafIndex++));
}
}
@Override
public TreeNode getChildAt(int childIndex) {
return choiceNodes.get(childIndex);
// return
// return
}
@Override
@ -73,16 +82,22 @@ public class ModifierTreeNode implements TreeNode {
}
public void setModBitmap(int modBitMap) {
for (ChoiceTreeNode cN : choiceNodes) {
cN.checkBox.setSelected((cN.selectionBit & modBitMap) != 0);
for (TreeNode tN : choiceNodes) {
if (tN instanceof ChoiceTreeNode) {
ChoiceTreeNode cN = (ChoiceTreeNode) tN;
cN.checkBox.setSelected((cN.selectionBit & modBitMap) != 0);
}
}
}
public int getModBitmap() {
int mp = 0;
for (ChoiceTreeNode cN : choiceNodes) {
if (cN.checkBox.isSelected()) {
mp |= cN.selectionBit;
for (TreeNode tN : choiceNodes) {
if (tN instanceof ChoiceTreeNode) {
ChoiceTreeNode cN = (ChoiceTreeNode) tN;
if (cN.checkBox.isSelected()) {
mp |= cN.selectionBit;
}
}
}
return mp;

81
src/PamView/symbol/modifier/swing/OptionsTreeNode.java Normal file
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@ -0,0 +1,81 @@
package PamView.symbol.modifier.swing;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Enumeration;
import javax.swing.JButton;
import javax.swing.tree.TreeNode;
import PamView.dialog.GenericSwingDialog;
import PamView.dialog.PamDialogPanel;
import PamView.symbol.modifier.SymbolModifier;
public class OptionsTreeNode implements TreeNode {
private ModifierTreeNode parent;
private SymbolModifier modifier;
private PamDialogPanel optionsPanel;
protected JButton optionsButton;
private int leafIndex;
public OptionsTreeNode(ModifierTreeNode parent, SymbolModifier modifier, PamDialogPanel optionsPanel, int leafIndex) {
this.parent = parent;
this.modifier = modifier;
this.optionsPanel = optionsPanel;
this.leafIndex = leafIndex;
optionsButton = new JButton("more ...");
optionsButton.setToolTipText("More symbol options");
optionsButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
showOptions();
}
});
}
private void showOptions() {
optionsPanel.setParams();
boolean ok = GenericSwingDialog.showDialog(null, "Options", optionsPanel);
if (ok) {
optionsPanel.getParams();
}
}
@Override
public TreeNode getChildAt(int childIndex) {
return null;
}
@Override
public int getChildCount() {
return 0;
}
@Override
public TreeNode getParent() {
return parent;
}
@Override
public int getIndex(TreeNode node) {
return leafIndex;
}
@Override
public boolean getAllowsChildren() {
return false;
}
@Override
public boolean isLeaf() {
return true;
}
@Override
public Enumeration<? extends TreeNode> children() {
return null;
}
}

3
src/PamView/symbol/modifier/swing/SymbolModifierPanel.java
View File

@ -18,12 +18,10 @@ import javax.swing.tree.TreePath;
import PamView.dialog.DialogScrollPane;
import PamView.dialog.PamDialogPanel;
import PamView.symbol.PamSymbolChooser;
import PamView.symbol.StandardSymbolChooser;
import PamView.symbol.StandardSymbolOptions;
import PamView.symbol.modifier.SymbolModifier;
import PamView.symbol.modifier.SymbolModifierParams;
import PamguardMVC.debug.Debug;
/**
* Panel to include in a dialog with options to select and activate a variety of symbol modifiers.
@ -137,6 +135,7 @@ public class SymbolModifierPanel implements PamDialogPanel {
JMenuItem optsItem = modifier.getModifierOptionsMenu();
if (optsItem != null) {
popMenu.add(optsItem);
popMenu.addSeparator();
}
}
if (nodeInd > 0) {

4
src/PamView/symbol/modifier/swing/SymbolTreeRenderer.java
View File

@ -43,6 +43,10 @@ public class SymbolTreeRenderer extends DefaultTreeCellRenderer {
if (value instanceof ChoiceTreeNode) {
return checkboxChoice(tree, (ChoiceTreeNode) value, sel, expanded, leaf, row, hasFocus);
}
if (value instanceof OptionsTreeNode) {
return ((OptionsTreeNode) value).optionsButton;
}
Component component = super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
if (value instanceof ModifierTreeNode) {

23
src/PamguardMVC/PamRawDataBlock.java
View File

@ -257,12 +257,13 @@ public class PamRawDataBlock extends AcousticDataBlock<RawDataUnit> {
synchronized public RawDataUnit[] getAvailableSamples(long startMillis, long durationMillis, int channelMap) throws RawDataUnavailableException {
RawDataUnit firstUnit = getFirstUnit();
if (firstUnit == null) {
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_NOT_ARRIVED, startMillis, (int) durationMillis);
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_NOT_ARRIVED, 0,0, startMillis, (int) durationMillis);
}
long firstMillis = firstUnit.getTimeMilliseconds();
long firstSamples = firstUnit.getStartSample();
RawDataUnit lastUnit = getLastUnit();
long lastMillis = lastUnit.getEndTimeInMilliseconds();
long lastSample = lastUnit.getStartSample()+lastUnit.getSampleDuration();
long firstAvailableMillis = Math.max(firstMillis, startMillis);
@ -272,7 +273,8 @@ public class PamRawDataBlock extends AcousticDataBlock<RawDataUnit> {
double[][] data = getSamplesForMillis(firstAvailableMillis, lastAvailableMillis-firstAvailableMillis, channelMap);
if (data == null) {
// this shouldn't happen. If an exception wasn't thrown from getSamples... then data should no tb enull
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_NOT_ARRIVED, startMillis, (int) durationMillis);
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_NOT_ARRIVED,
firstSamples, lastSample, startMillis, (int) durationMillis);
}
RawDataUnit[] dataUnits = new RawDataUnit[data.length];
for (int i = 0; i < data.length; i++) {
@ -298,7 +300,7 @@ public class PamRawDataBlock extends AcousticDataBlock<RawDataUnit> {
synchronized public double[][] getSamplesForMillis(long startMillis, long durationMillis, int channelMap) throws RawDataUnavailableException {
RawDataUnit firstUnit = getFirstUnit();
if (firstUnit == null) {
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_NOT_ARRIVED, startMillis, (int) durationMillis);
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_NOT_ARRIVED, 0, 0, startMillis, (int) durationMillis);
}
long firstMillis = firstUnit.getTimeMilliseconds();
long firstSamples = firstUnit.getStartSample();
@ -317,23 +319,28 @@ public class PamRawDataBlock extends AcousticDataBlock<RawDataUnit> {
// run a few tests ...
int chanOverlap = channelMap & getChannelMap();
if (chanOverlap != channelMap) {
throw new RawDataUnavailableException(this, RawDataUnavailableException.INVALID_CHANNEL_LIST, startSample, duration);
throw new RawDataUnavailableException(this, RawDataUnavailableException.INVALID_CHANNEL_LIST, 0,0,startSample, duration);
}
if (duration < 0) {
throw new RawDataUnavailableException(this, RawDataUnavailableException.NEGATIVE_DURATION, startSample, duration);
throw new RawDataUnavailableException(this, RawDataUnavailableException.NEGATIVE_DURATION,0,0, startSample, duration);
}
RawDataUnit dataUnit = getFirstUnit();
if (dataUnit == null) {
return null;
}
if (dataUnit.getStartSample() > startSample) {
RawDataUnit lastUnit = getLastUnit();
long firstSample = dataUnit.getStartSample();
long lastSample = lastUnit.getStartSample()+lastUnit.getSampleDuration();
if (firstSample > startSample) {
// System.out.println("Earliest start sample : " + dataUnit.getStartSample());
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_ALREADY_DISCARDED, startSample, duration);
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_ALREADY_DISCARDED,
firstSample, lastSample, startSample, duration);
}
dataUnit = getLastUnit();
if (hasLastSample(dataUnit, startSample+duration, channelMap) == false) {
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_NOT_ARRIVED, startSample, duration);
throw new RawDataUnavailableException(this, RawDataUnavailableException.DATA_NOT_ARRIVED,
firstSample, lastSample, startSample, duration);
}
int nChan = PamUtils.getNumChannels(channelMap);

26
src/PamguardMVC/RawDataUnavailableException.java
View File

@ -21,6 +21,10 @@ public class RawDataUnavailableException extends Exception {
private long startSample;
private int duration;
private long availableStart;
private long availableEnd;
/**
* @return the dataCause
*/
@ -34,10 +38,12 @@ public class RawDataUnavailableException extends Exception {
* @param startSample
* @param cause
*/
public RawDataUnavailableException(PamRawDataBlock rawDataBlock, int dataCause, long startSample, int duration) {
public RawDataUnavailableException(PamRawDataBlock rawDataBlock, int dataCause, long availStart, long availEnd, long startSample, int duration) {
super();
this.rawDataBlock = rawDataBlock;
this.dataCause = dataCause;
this.availableStart = availStart;
this.availableEnd = availEnd;
this.startSample = startSample;
this.duration = duration;
}
@ -55,8 +61,8 @@ public class RawDataUnavailableException extends Exception {
public String getMessage() {
switch (dataCause) {
case DATA_ALREADY_DISCARDED:
return String.format("Samples %d length %d requested from %s have already been discarded", startSample, duration,
rawDataBlock.getDataName());
return String.format("Samples %d length %d requested from %s have already been discarded. %d to %d available", startSample, duration,
rawDataBlock.getDataName(), availableStart, availableEnd);
case DATA_NOT_ARRIVED:
return String.format("Samples %d length %d requested from %s have not yet arrived",
startSample, duration, rawDataBlock.getDataName());
@ -70,6 +76,20 @@ public class RawDataUnavailableException extends Exception {
}
return super.getMessage();
}
/**
* @return the availableStart
*/
public long getAvailableStart() {
return availableStart;
}
/**
* @return the availableEnd
*/
public long getAvailableEnd() {
return availableEnd;
}
}

2
src/PamguardMVC/ThreadedObserver.java
View File

@ -8,6 +8,7 @@ import Acquisition.AcquisitionControl;
import Acquisition.AcquisitionProcess;
import Acquisition.DaqSystem;
import PamController.PamController;
import PamModel.PamModel;
import PamUtils.PamCalendar;
import PamguardMVC.debug.Debug;
@ -130,6 +131,7 @@ public class ThreadedObserver implements PamObserver {
}
}
}
h += PamModel.getPamModel().getPamModelSettings().getThreadingJitterMillis()*2;
return h;
}

3
src/PamguardMVC/dataSelector/CompoundDataSelector.java
View File

@ -95,6 +95,9 @@ public class CompoundDataSelector extends DataSelector {
score = Math.max(score, score2); // take the largest
}
}
// System.out.println("Hello Compound Data selector: " + score);
return score;
}

16
src/PamguardMVC/dataSelector/DataSelectDialog.java
View File

@ -76,6 +76,22 @@ public class DataSelectDialog extends PamDialog {
// }
}
public boolean setTab(int tabIndex) {
if (tabPane == null) {
return false;
}
if (tabIndex < 0 || tabIndex >= tabPane.getTabCount()) {
return false;
}
try {
tabPane.setSelectedIndex(tabIndex);
}
catch (Exception e) {
return false;
}
return true;
}
public boolean showDialog() {
if (dataPanel != null) {
dataPanel.setParams();

17
src/PamguardMVC/dataSelector/DataSelectorDialogPaneFX.java
View File

@ -91,10 +91,19 @@ public class DataSelectorDialogPaneFX extends DynamicSettingsPane<Boolean> {
}
andButton.setOnAction(event -> enableComponent());
orButton.setOnAction(event -> enableComponent());
disableButton.setOnAction(event -> enableComponent());
andButton.setOnAction(event -> {
enableComponent();
notifySettingsListeners();
});
orButton.setOnAction(event ->{
enableComponent();
notifySettingsListeners();
});
disableButton.setOnAction(event ->{
enableComponent();
notifySettingsListeners();
});
buttonPane = new HBox(); // Use HBox for horizontal button layout
buttonPane.setSpacing(5);
buttonPane.setAlignment(Pos.CENTER);

23
src/Spectrogram/ColourRangeSlider.java
View File

@ -6,6 +6,11 @@ import PamView.ColourArray;
import PamView.ColourArray.ColourArrayType;
import PamView.sliders.PamRangeSlider;
/**
* A range slider which shows a colour gradient between two thumbs.
*
* @author Jamie Macaulay
*/
public class ColourRangeSlider extends PamRangeSlider {
/**
@ -18,13 +23,29 @@ public class ColourRangeSlider extends PamRangeSlider {
}
public ColourRangeSlider(int min, int max){
super(min,max, JSlider.VERTICAL);
super(min, max,JSlider.VERTICAL);
}
public ColourRangeSlider(int min, int max, int orientation){
super(min, max,orientation);
}
public ColourRangeSlider(int orientation){
super(orientation);
}
/**
* Set the colour map type to show between the two thumbs.
* @param colourMap - the colour map to show.
*/
public void setColourMap(ColourArrayType colourMap){
((ColourRangeSliderUI) getUI()).setColourMap(colourMap);
}
/**
* Set a custom colour map type to show between the two thumbs.
* @param colourMap - the colour map to show.
*/
public void setColourMap(ColourArray colourMap){
((ColourRangeSliderUI) getUI()).setColourMap(colourMap);
}

108
src/Spectrogram/ColourRangeSliderUI.java
View File

@ -8,8 +8,7 @@ import java.awt.geom.AffineTransform;
import java.awt.image.BufferedImage;
import java.awt.image.WritableRaster;
import javax.swing.JSlider;
import PamView.ColourArray;
import PamView.ColourArray.ColourArrayType;
@ -78,6 +77,8 @@ public class ColourRangeSliderUI extends PamRangeSliderUI {
private void createColourMapImage(){
if (b.getOrientation() == JSlider.VERTICAL) {
// now make a standard amplitude image
if (colourArray != null && colourArray.length > 0) {
amplitudeImage = new BufferedImage(1, colourArray.length,
@ -87,6 +88,15 @@ public class ColourRangeSliderUI extends PamRangeSliderUI {
raster.setPixel(0, colourArray.length - i - 1, colourArray[i]);
}
}
}
else {
amplitudeImage = new BufferedImage(colourArray.length, 1,
BufferedImage.TYPE_INT_RGB);
WritableRaster raster = amplitudeImage.getRaster();
for (int i = 0; i < colourArray.length; i++) {
raster.setPixel(i, 0,colourArray[i]);
}
}
}
@ -119,26 +129,98 @@ public class ColourRangeSliderUI extends PamRangeSliderUI {
Rectangle trackBounds = trackRect;
// Determine position of selected range by moving from the middle
// of one thumb to the other.
int lowerY = thumbRect.y + (thumbRect.width / 2);
int upperY = getUpperThumbRect().y + (getUpperThumbRect().width / 2);
// Determine track position.
int cx = (trackBounds.width / 2) - 2;
// Save colour and shift position.
Color oldColor = g.getColor();
g.translate(trackBounds.x + cx, trackBounds.y);
drawColourMapVert( g, lowerY - trackBounds.y, upperY - trackBounds.y, -(getUpperThumbRect().width /4)-trackBounds.x,(getUpperThumbRect().width / 2)-trackBounds.x+(trackBounds.width / 4)+2);
int cx;
if (b.getOrientation() == JSlider.VERTICAL) {
// Determine position of selected range by moving from the middle
// of one thumb to the other.
int lowerY = thumbRect.y + (thumbRect.width / 2);
int upperY = getUpperThumbRect().y + (getUpperThumbRect().width / 2);
// Determine track position.
cx = (trackBounds.width / 2) - 2;
g.translate(trackBounds.x + cx, trackBounds.y);
drawColourMapVert( g, lowerY - trackBounds.y, upperY - trackBounds.y, -(getUpperThumbRect().width /4)-trackBounds.x,(getUpperThumbRect().width / 2)-trackBounds.x+(trackBounds.width / 4)+2);
cx = (trackBounds.width / 2) - 2;
g.translate(-(trackBounds.x + cx), -trackBounds.y);
}
else {
// Determine position of selected range by moving from the middle
// of one thumb to the other.
int lowerX = thumbRect.x;
int upperX = getUpperThumbRect().x;
// Determine track position.
cx = (trackBounds.width / 2) - 2;
// -(getUpperThumbRect().height /4)-trackBounds.y, (getUpperThumbRect().height / 2)-trackBounds.y+(trackBounds.height / 4)+2
drawColourMapHorz(g, trackBounds.height/2-getUpperThumbRect().height/2, trackBounds.height/2+getUpperThumbRect().height/2, lowerX + getUpperThumbRect().width/2, upperX+ getUpperThumbRect().width/2);
}
// Restore position and colour.
g.translate(-(trackBounds.x + cx), -trackBounds.y);
g.setColor(oldColor);
}
/**
* Draw the colour map between the two thumbs in the slider bar. Colour the section above the top most thumb
* and the section below the lower most thumb with the color map extremes.
* @param g- graphics
* @param y1
* @param y2
* @param x1
* @param x2
*/
private void drawColourMapHorz(Graphics g, int y1, int y2, int x1, int x2){
if (amplitudeImage == null) return;
Graphics2D g2d = (Graphics2D) g;
int width=Math.abs(x2-x1);
int height=Math.abs(y2-y1);
// System.out.println("Width: " + width + " " + height + " x1 " + x1);
//calculate the distance between thumbs
double ascaleX = width
/ (double) amplitudeImage.getWidth(null);
double ascaleY = height
/ (double) amplitudeImage.getHeight(null);
AffineTransform xform = new AffineTransform();
// xform.translate(1, amplitudeImage.getWidth(null));
xform.scale(ascaleX, ascaleY);
//translate to the correct location;
g2d.translate(x1, y1);
//now translate back for the rest of the operations;
g2d.drawImage(amplitudeImage, xform, b);
//translate back to our original position.
g2d.translate(-x1, -y1);
//go to the left of the lower thumb;
// g2d.translate(0, height);
g2d.setColor(new Color((int) colourArray[0][0],(int)colourArray[0][1],(int) colourArray[0][2]));
for (int i=y1; i<y2; i++){
g2d.drawLine(0,i,x1, i);
}
//color left of the thumb
g2d.setColor(new Color((int) colourArray[colourArray.length-1][0],(int)colourArray[colourArray.length-1][1],(int) colourArray[colourArray.length-1][2]));
for (int i=y1; i<y2; i++){
g2d.drawLine(x2,i, trackRect.width + thumbRect.width/2, i);
}
}
/**
* Draw the colour map between the two thumbs in the slider bar. Colour the section above the top most thumb
* and the section below the lower most thumb with the color map extremes.

13
src/binaryFileStorage/BinaryStore.java
View File

@ -228,6 +228,7 @@ PamSettingsSource, DataOutputStore {
super.pamToStart();
prepareStores();
openStores();
binaryStoreProcess.checkFileTimer();
}
@Override
@ -245,9 +246,9 @@ PamSettingsSource, DataOutputStore {
* Called from the process to close and reopen each datastream in
* a new file. Probably gets called about once an hour on the hour.
*/
protected void reOpenStores(int endReason) {
protected synchronized void reOpenStores(int endReason, long newFileTime) {
long dataTime = PamCalendar.getTimeInMillis();
long dataTime = newFileTime;//PamCalendar.getTimeInMillis();
long analTime = System.currentTimeMillis();
BinaryOutputStream dataStream;
for (int i = 0; i < storageStreams.size(); i++) {
@ -536,7 +537,7 @@ PamSettingsSource, DataOutputStore {
*/
if (immediateChanges) {
if (storesOpen) {
reOpenStores(BinaryFooter.END_UNKNOWN);
reOpenStores(BinaryFooter.END_UNKNOWN, PamCalendar.getTimeInMillis());
}
}
@ -2601,5 +2602,11 @@ PamSettingsSource, DataOutputStore {
public DataIntegrityChecker getInegrityChecker() {
return new BinaryIntegrityChecker(this);
}
/**
* @return the binaryStoreProcess
*/
public BinaryStoreProcess getBinaryStoreProcess() {
return binaryStoreProcess;
}
}

77
src/binaryFileStorage/BinaryStoreProcess.java
View File

@ -7,37 +7,43 @@ import PamUtils.PamCalendar;
import PamguardMVC.PamProcess;
public class BinaryStoreProcess extends PamProcess {
private BinaryStore binaryStore;
private long startTime;
private long nextFileTime;
private Timer timer;
private Object timerSynch = new Object();
public BinaryStoreProcess(BinaryStore binaryStore) {
super(binaryStore, null);
this.binaryStore = binaryStore;
}
@Override
public String getProcessName() {
return "Binary store file control";
}
public synchronized void checkFileTime() {
public synchronized void checkFileTime(long masterClockTime) {
// if (binaryStore.binaryStoreSettings.autoNewFiles &&
// PamCalendar.getTimeInMillis() >= nextFileTime) {
// startNewFiles();
// }
if (binaryStore.binaryStoreSettings.autoNewFiles &&
PamCalendar.getTimeInMillis() >= nextFileTime) {
startNewFiles();
masterClockTime >= nextFileTime) {
startNewFiles(masterClockTime);
}
}
private synchronized void startNewFiles() {
private synchronized void startNewFiles(long masterClockTime) {
nextFileTime += binaryStore.binaryStoreSettings.fileSeconds * 1000;
binaryStore.reOpenStores(BinaryFooter.END_FILETOOLONG);
binaryStore.reOpenStores(BinaryFooter.END_FILETOOLONG, masterClockTime);
}
@ -46,24 +52,55 @@ public class BinaryStoreProcess extends PamProcess {
startTime = PamCalendar.getTimeInMillis();
long round = binaryStore.binaryStoreSettings.fileSeconds * 1000;
nextFileTime = (startTime/round) * round + round;
// System.out.println("Next file start at " + PamCalendar.formatDateTime(nextFileTime));
timer = new Timer();
timer.schedule(new FileTimerTask(), 1000, 1000);
// System.out.println("Next file start at " + PamCalendar.formatDateTime(nextFileTime));
}
public void checkFileTimer() {
boolean needTimer = PamCalendar.isSoundFile() == false;
if (needTimer) {
startTimer();
}
else {
stopTimer();
}
}
private void startTimer() {
synchronized (timerSynch) {
if (timer == null) {
timer = new Timer();
timer.schedule(new FileTimerTask(), 1000, 1000);
}
}
}
private void stopTimer() {
synchronized (timerSynch) {
if (timer != null) {
timer.cancel();
timer = null;
}
}
}
// @Override
// public void masterClockUpdate(long timeMilliseconds, long sampleNumber) {
// super.masterClockUpdate(timeMilliseconds, sampleNumber);
// checkFileTime(timeMilliseconds);
// }
class FileTimerTask extends TimerTask {
@Override
public void run() {
checkFileTime();
checkFileTime(PamCalendar.getTimeInMillis());
}
}
@Override
public void pamStop() {
if (timer != null) {
timer.cancel();
}
stopTimer();
}
}

14
src/clickDetector/BTAmplitudeSelector.java
View File

@ -29,6 +29,7 @@ import PamView.PamSymbolType;
import PamView.dialog.PamDialog;
import PamView.dialog.PamDialogPanel;
import PamView.dialog.PamGridBagContraints;
import clickDetector.dataSelector.ClickDataSelector;
import pamMaths.HistogramDisplay;
import pamMaths.HistogramGraphicsLayer;
import pamMaths.PamHistogram;
@ -59,6 +60,7 @@ public class BTAmplitudeSelector implements PamDialogPanel {
private JCheckBox amplitudeSelect;
private JTextField minAmplitude;
private JFrame ownerFrame;
private ClickDataSelector dataSelector;
/**
* @param btDisplay
*/
@ -66,6 +68,7 @@ public class BTAmplitudeSelector implements PamDialogPanel {
super();
this.clickControl = clickControl;
this.btDisplay = btDisplay;
dataSelector = btDisplay.getDataSelector();
clickDataBlock = clickControl.getClickDataBlock();
histoPlot = new HistogramDisplay();
histoPlot.setGraphicsOverLayer(histoOverLayer = new HistoOverLayer());
@ -125,7 +128,8 @@ public class BTAmplitudeSelector implements PamDialogPanel {
axMin = allHistogram.getScaleMinVal();
axMax = allHistogram.getScaleMaxVal();
plotRectangle = g.getClipBounds();
double dx = (btDisplayParameters.minAmplitude - axMin) / (axMax-axMin) * plotRectangle.width;
// double dx = (btDisplayParameters.minAmplitude - axMin) / (axMax-axMin) * plotRectangle.width;
double dx = (dataSelector.getParams().minimumAmplitude - axMin) / (axMax-axMin) * plotRectangle.width;
int x = (int) Math.round(dx);
g.setColor(Color.RED);
g.drawLine(x, 0, x, plotRectangle.height);
@ -151,7 +155,7 @@ public class BTAmplitudeSelector implements PamDialogPanel {
double newAmp = (double) mouseEvent.getX() / histoOverLayer.plotRectangle.width *
(histoOverLayer.axMax-histoOverLayer.axMin) + histoOverLayer.axMin;
BTDisplayParameters btDisplayParameters = btDisplay.getBtDisplayParameters();
btDisplayParameters.minAmplitude = newAmp;
dataSelector.getParams().minimumAmplitude = newAmp;
ampCtrlPanel.setParams(btDisplayParameters);
redrawHisto();
//
@ -173,7 +177,7 @@ public class BTAmplitudeSelector implements PamDialogPanel {
if (btDisplayParameters.amplitudeSelect == false) {
return false;
}
double dx = (btDisplayParameters.minAmplitude - histoOverLayer.axMin) /
double dx = (dataSelector.getParams().minimumAmplitude - histoOverLayer.axMin) /
(histoOverLayer.axMax-histoOverLayer.axMin) * histoOverLayer.plotRectangle.width;
int x = (int) Math.round(dx);
if (Math.abs(e.getX()-x) > 10) {
@ -213,14 +217,14 @@ public class BTAmplitudeSelector implements PamDialogPanel {
}
private void setParams(BTDisplayParameters btParams) {
amplitudeSelect.setSelected(btParams.amplitudeSelect);
minAmplitude.setText(String.format("%3.1f", btParams.minAmplitude));
minAmplitude.setText(String.format("%3.1f", dataSelector.getParams().minimumAmplitude));
enableControls();
}
private boolean getParams(BTDisplayParameters btParams) {
btParams.amplitudeSelect = amplitudeSelect.isSelected();
try {
btParams.minAmplitude = Double.valueOf(minAmplitude.getText());
dataSelector.getParams().minimumAmplitude = Double.valueOf(minAmplitude.getText());
}
catch (NumberFormatException e) {
return false;

82
src/clickDetector/BTDisplayParameters.java
View File

@ -44,17 +44,17 @@ public class BTDisplayParameters implements Serializable, Cloneable, ManagedPara
public int nBearingGridLines = 1;
public int nAmplitudeGridLines = 0;
public int nICIGridLines = 0;
public boolean showEchoes = true;
// public boolean showEchoes = true;
public int minClickLength = 2, maxClickLength = 12;
public int minClickHeight = 2, maxClickHeight = 12;
private double timeRange = 10;
public int displayChannels = 0;
public boolean view360;
public boolean amplitudeSelect = false;
public double minAmplitude = 0;
// public double minAmplitude = 0;
public boolean showUnassignedICI = false;
public boolean showEventsOnly = false;
public boolean showANDEvents = true;
// public boolean showEventsOnly = false;
// public boolean showANDEvents = true;
public boolean logICIScale;
public int angleRotation = ROTATE_TOARRAY;
@ -65,7 +65,7 @@ public class BTDisplayParameters implements Serializable, Cloneable, ManagedPara
/*
* Show identified species
*/
private boolean[] showSpeciesList;
// private boolean[] showSpeciesList;
public int colourScheme = COLOUR_BY_TRAIN;
@ -83,7 +83,7 @@ public class BTDisplayParameters implements Serializable, Cloneable, ManagedPara
} catch (CloneNotSupportedException Ex) {
Ex.printStackTrace();
}
showSpeciesList = null;
// showSpeciesList = null;
return null;
}
@ -107,49 +107,49 @@ public class BTDisplayParameters implements Serializable, Cloneable, ManagedPara
/**
* @return the showSpeciesList
*/
public boolean getShowSpecies(int speciesIndex) {
if (showSpeciesList != null && showSpeciesList.length > speciesIndex) {
return showSpeciesList[speciesIndex];
}
makeShowSpeciesList(speciesIndex);
return true;
}
private void makeShowSpeciesList(int maxIndex) {
if (showSpeciesList == null) {
showSpeciesList = new boolean[0];
}
else if (showSpeciesList.length > maxIndex) {
return;
}
int oldLength = showSpeciesList.length;
showSpeciesList = Arrays.copyOf(showSpeciesList, maxIndex + 1);
for (int i = oldLength; i <= maxIndex; i++) {
showSpeciesList[i] = true;
}
}
// public boolean getShowSpecies(int speciesIndex) {
// if (showSpeciesList != null && showSpeciesList.length > speciesIndex) {
// return showSpeciesList[speciesIndex];
// }
// makeShowSpeciesList(speciesIndex);
// return true;
// }
// private void makeShowSpeciesList(int maxIndex) {
// if (showSpeciesList == null) {
// showSpeciesList = new boolean[0];
// }
// else if (showSpeciesList.length > maxIndex) {
// return;
// }
// int oldLength = showSpeciesList.length;
// showSpeciesList = Arrays.copyOf(showSpeciesList, maxIndex + 1);
// for (int i = oldLength; i <= maxIndex; i++) {
// showSpeciesList[i] = true;
// }
// }
/**
* @param showSpeciesList the showSpeciesList to set
*/
public void setShowSpecies(int speciesIndex, boolean showSpecies) {
makeShowSpeciesList(speciesIndex);
showSpeciesList[speciesIndex] = showSpecies;
}
// public void setShowSpecies(int speciesIndex, boolean showSpecies) {
// makeShowSpeciesList(speciesIndex);
// showSpeciesList[speciesIndex] = showSpecies;
// }
@Override
public PamParameterSet getParameterSet() {
PamParameterSet ps = PamParameterSet.autoGenerate(this, ParameterSetType.DETECTOR);
try {
Field field = this.getClass().getDeclaredField("showSpeciesList");
ps.put(new PrivatePamParameterData(this, field) {
@Override
public Object getData() throws IllegalArgumentException, IllegalAccessException {
return showSpeciesList;
}
});
} catch (NoSuchFieldException | SecurityException e) {
e.printStackTrace();
}
// try {
// Field field = this.getClass().getDeclaredField("showSpeciesList");
// ps.put(new PrivatePamParameterData(this, field) {
// @Override
// public Object getData() throws IllegalArgumentException, IllegalAccessException {
// return showSpeciesList;
// }
// });
// } catch (NoSuchFieldException | SecurityException e) {
// e.printStackTrace();
// }
return ps;
}

142
src/clickDetector/ClickBTDisplay.java
View File

@ -34,6 +34,7 @@ import java.awt.Insets;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.RenderingHints;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.AdjustmentEvent;
@ -115,9 +116,12 @@ import PamguardMVC.PamDataBlock;
import PamguardMVC.PamDataUnit;
import PamguardMVC.PamObservable;
import PamguardMVC.PamObserver;
import PamguardMVC.dataSelector.DataSelectDialog;
import PamguardMVC.superdet.SuperDetection;
import clickDetector.ClickClassifiers.ClickIdInformation;
import clickDetector.ClickClassifiers.ClickIdentifier;
import clickDetector.alarm.ClickAlarmParameters;
import clickDetector.dataSelector.ClickDataSelector;
import clickDetector.dialogs.ClickDisplayDialog;
import clickDetector.offlineFuncs.OfflineEventDataBlock;
import clickDetector.offlineFuncs.OfflineEventDataUnit;
@ -2244,7 +2248,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
PamDataBlock<ClickDetection> clickData = clickControl.getClickDataBlock();
int nAll = clickData.getUnitsCount();
String txt = String.format("%d of %d loaded clicks will not be displayed because their amplitude is < %3.1fdB",
n, nAll, btDisplayParameters.minAmplitude);
n, nAll, getDataSelector().getParams().minimumAmplitude);
Insets insets = getInsets();
int x = insets.left;
int y = getHeight()-5;
@ -2383,19 +2387,33 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
}
menuItem = new JMenuItem("Settings ...");
menuItem.setToolTipText("Display options");
menuItem.addActionListener(new SettingsMenuAction());
menu.add(menuItem);
menuItem = new JMenuItem("Click data selector ...");
menuItem.setToolTipText("Detailed data selection options");
menuItem.addActionListener(new DataSelectorAction());
menu.add(menuItem);
menuItem = new JMenuItem("Show amplitude selector ...");
menuItem.setToolTipText("Graphical amplitude selector display");
menuItem.addActionListener(new AmplitudeSelector());
menu.add(menuItem);
menu.addSeparator();
ArrayList<JMenuItem> colOptList = getSymbolChooser().getQuickMenuItems(clickControl.getGuiFrame(), this, "Colour by ", SymbolModType.EVERYTHING, true);
ArrayList<JMenuItem> colOptList = getSymbolChooser().getQuickMenuItems(clickControl.getGuiFrame(), this, "Colour by ", SymbolModType.EVERYTHING, false);
if (colOptList != null) {
for (JMenuItem menuIt : colOptList) {
menu.add(menuIt);
}
menu.addSeparator();
}
menuItem = new JMenuItem("More symbol options ...");
menuItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
showDataSymbolOptions(1);
}
});
menu.add(menuItem);
menu.addSeparator();
// menuItem = new JCheckBoxMenuItem("Colour by species id",
// btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_SPECIES);
@ -2470,7 +2488,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
return menu;
}
/**
* Looks through the current modules and finds if there is a target motion or static localiser
*/
@ -2771,7 +2789,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
BTDisplayParameters newParameters =
ClickDisplayDialog.showDialog(clickControl,
clickControl.getGuiFrame(), btDisplayParameters);
clickControl.getGuiFrame(), btDisplayParameters, getDataSelector().getClickAlarmParameters());
if (newParameters != null){
btDisplayParameters = newParameters.clone();
if (getVScaleManager() != null) {
@ -2788,6 +2806,15 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
}
}
/**
* Get a data selector specific to this display.
* @return click data selector specific to this display.
*/
public ClickDataSelector getDataSelector() {
return (ClickDataSelector) clickControl.getClickDataBlock().getDataSelector(getUnitName(), false);
}
class AmplitudeSelector implements ActionListener {
@Override
@ -2795,6 +2822,13 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
showAmplitudeSelector();
}
}
class DataSelectorAction implements ActionListener {
@Override
public void actionPerformed(ActionEvent e) {
showDataSelector();
}
}
private void showAmplitudeSelector() {
@ -2814,6 +2848,38 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
// }
}
/**
* Show a dialog with both data and symbol options, but go to the correct tab.
* @param selectedTab
* @return
*/
private boolean showDataSymbolOptions(int selectedTab) {
Window javaFrame = clickControl.getGuiFrame();
DataSelectDialog dataSelectDialog = new DataSelectDialog(javaFrame, clickControl.getClickDataBlock(), getDataSelector(), symbolChooser);
if (javaFrame == null) {
dataSelectDialog.moveToMouseLocation();
}
dataSelectDialog.setTab(selectedTab);
boolean ok = dataSelectDialog.showDialog();
if (ok) {
repaintBoth();
if (clickControl.getOfflineToolbar() != null) {
clickControl.getOfflineToolbar().displayActivated(clickBTDisplay);
}
}
return ok;
}
public void showDataSelector() {
// if (getDataSelector().showSelectDialog(clickControl.getGuiFrame())) {
// repaintBoth();
// if (clickControl.getOfflineToolbar() != null) {
// clickControl.getOfflineToolbar().displayActivated(clickBTDisplay);
// }
// };
showDataSymbolOptions(0);
}
private void checkBTAmplitudeSelectHisto() {
if (btAmplitudeSelector == null) {
return;
@ -3036,15 +3102,15 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
zoomer.paintShape(g, this, true);
}
// long t1 = System.nanoTime();
synchronized (clickData.getSynchLock()) {
// long t2 = System.nanoTime();
// double ms = ((double) (t2-t1)) / 1000000.;
// if (btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI) {
// sortTempICIs();
// }
ArrayList<ClickDetection> clickCopy = clickData.getDataCopy(displayStartMillis, displayStartMillis+displayLengthMillis, true, getDataSelector());
if (clickCopy.size() == 0) {
return;
}
ListIterator<ClickDetection> clickIterator = clickCopy.listIterator(clickCopy.size()-1);
ListIterator<ClickDetection> clickIterator = clickData.getListIterator(PamDataBlock.ITERATOR_END);
// synchronized (clickData.getSynchLock()) {
//
// ListIterator<ClickDetection> clickIterator = clickData.getListIterator(PamDataBlock.ITERATOR_END);
while (clickIterator.hasPrevious()) {
click = clickIterator.previous();
if (shouldPlot(prevPlottedClick)){
@ -3060,11 +3126,6 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
if (shouldPlot(prevPlottedClick)){ // and draw the last one !
drawClick(g, prevPlottedClick, clipRectangle);
}
// g.drawString(String.format("Wait synch %3.3fms", ms), 0, 20);
}
// long t3 = System.nanoTime();
// g.drawString(String.format("Last draw %3.3fms", lastPaintTime), 0, 20);
// lastPaintTime = ((double) (t3-t0)) / 1000000.;
}
@Override
@ -3342,7 +3403,9 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
else if (btDisplayParameters.colourScheme == BTDisplayParameters.COLOUR_BY_HYDROPHONE) {
keyPanel.add(new TextKeyItem("Colour by hydrophone"));
}
if (btDisplayParameters.getShowSpecies(0)) {
ClickAlarmParameters selectParams = getDataSelector().getParams();
// if (btDisplayParameters.getShowSpecies(0)) {
if (selectParams.onlineAutoEvents | selectParams.onlineManualEvents) {
keyPanel.add(symbolChooser.getDefaultSymbol(true).makeKeyItem("Unidentified species"));
}
@ -3354,7 +3417,8 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
PamSymbol[] symbols = clickControl.getClickIdentifier().getSymbols();
if (speciesList != null) {
for (int i = 0; i < speciesList.length; i++) {
if (btDisplayParameters.getShowSpecies(i+1)) {
if (selectParams.getUseSpecies(i+1)) {
// if (btDisplayParameters.getShowSpecies(i+1)) {
if (btDisplayParameters.colourScheme != BTDisplayParameters.COLOUR_BY_TRAIN) {
keyPanel.add(symbols[i].makeKeyItem(speciesList[i]));
}
@ -3423,11 +3487,12 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
PamDataBlock<ClickDetection> clickData = clickControl.getClickDataBlock();
ClickDetection click;
int n = 0;
double minAmpli = getDataSelector().getParams().minimumAmplitude;
synchronized (clickData.getSynchLock()) {
ListIterator<ClickDetection> clickIterator = clickData.getListIterator(0);
while (clickIterator.hasNext()) {
click = clickIterator.next();
if (click.getAmplitudeDB() < btDisplayParameters.minAmplitude) {
if (click.getAmplitudeDB() < minAmpli) {
n++;
}
}
@ -3448,29 +3513,30 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
*/
synchronized boolean shouldPlot(ClickDetection click) {
if (click == null) return false;
if (!clickInTimeWindow(click)) return false;
if (btDisplayParameters.showEchoes == false && click.isEcho()) {
return false;
}
// if (!clickInTimeWindow(click)) return false;
// if (btDisplayParameters.showEchoes == false && click.isEcho()) {
// return false;
// }
if (btDisplayParameters.VScale == BTDisplayParameters.DISPLAY_ICI) {
// if (btDisplayParameters.showUnassignedICI == false && click.getICI() < 0) return false;
if (btDisplayParameters.showUnassignedICI == false && click.getSuperDetectionsCount() <= 0) return false;
// otherwise may be ok, since will estimate all ici's on teh fly.
}
if (btDisplayParameters.amplitudeSelect && click.getAmplitudeDB() < btDisplayParameters.minAmplitude) {
return false;
}
// if (btDisplayParameters.amplitudeSelect && click.getAmplitudeDB() < btDisplayParameters.minAmplitude) {
// return false;
// }
if (btDisplayParameters.displayChannels > 0 && (btDisplayParameters.displayChannels & click.getChannelBitmap()) == 0) return false;
int speciesIndex = clickControl.getClickIdentifier().codeToListIndex(click.getClickType());
boolean showSpecies = btDisplayParameters.getShowSpecies(speciesIndex+1);
boolean showEvents = (btDisplayParameters.showEventsOnly == false || click.getSuperDetectionsCount() > 0);
if (btDisplayParameters.showANDEvents) {
return showSpecies & showEvents;
}
else {
return showSpecies | showEvents;
}
// int speciesIndex = clickControl.getClickIdentifier().codeToListIndex(click.getClickType());
// boolean showSpecies = btDisplayParameters.getShowSpecies(speciesIndex+1);
// boolean showEvents = (btDisplayParameters.showEventsOnly == false || click.getSuperDetectionsCount() > 0);
// if (btDisplayParameters.showANDEvents) {
// return showSpecies & showEvents;
// }
// else {
// return showSpecies | showEvents;
// }
return true;
}
/**
@ -4085,7 +4151,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
amplitudeSelectorLabel.setText("");
}
else {
String txt = String.format(" Amplitude Selector showing clicks > %3.1fdB", btDisplayParameters.minAmplitude);
String txt = String.format(" Amplitude Selector showing clicks > %3.1fdB", getDataSelector().getParams().minimumAmplitude);
amplitudeSelectorLabel.setText(txt);
}
}

4
src/clickDetector/ClickDetector.java
View File

@ -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;

33
src/clickDetector/alarm/ClickAlarmParameters.java
View File

@ -17,10 +17,12 @@ public class ClickAlarmParameters extends DataSelectParams implements Cloneable,
public static final long serialVersionUID = 1L;
private boolean[] useSpeciesList;
private double[] speciesWeightings;
public boolean useEchoes;
public boolean scoreByAmplitude;
public boolean onlineAutoEvents, onlineManualEvents;
public boolean useEchoes = true;
public boolean scoreByAmplitude; // alarm options, probably not used any more.
public double minimumAmplitude;
public boolean onlineAutoEvents = true, onlineManualEvents = true;
public int minICIMillis;
private boolean clicksOREvents = false;
/*
* Which events to use ...
*/
@ -165,5 +167,30 @@ public class ClickAlarmParameters extends DataSelectParams implements Cloneable,
return ps;
}
/**
* @return the clicksOREvents
*/
public boolean isClicksOREvents() {
return clicksOREvents;
}
/**
* @param clicksOREvents the clicksOREvents to set
*/
public void setClicksOREvents(boolean clicksOREvents) {
this.clicksOREvents = clicksOREvents;
}
/**
* @return the clicksANDEvents
*/
public boolean isClicksANDEvents() {
return !clicksOREvents;
}
public void setClicksANDEvents(boolean clicksANDEvents) {
this.clicksOREvents = !clicksANDEvents;
}
}

44
src/clickDetector/dataSelector/ClickDataSelector.java
View File

@ -38,9 +38,9 @@ public class ClickDataSelector extends DataSelector {
@Override
public PamDialogPanel getDialogPanel() {
if (clickSelectPanel == null) {
// if (clickSelectPanel == null) {
clickSelectPanel = new ClickSelectPanel(this, allowScores, useEventTypes);
}
// }
return clickSelectPanel;
}
@Override
@ -60,19 +60,25 @@ public class ClickDataSelector extends DataSelector {
if (clickAlarmParameters.useEchoes == false && click.isEcho()) {
return 0;
}
/**
* First score based on whether the event panel is in use and
* criteria satisfied.
*/
double score = scoreClick(click);
if (useEventTypes) {
if (wantEventType(click) == false) {
return 0;
double eventScore = scoreEventType(click);
if (clickAlarmParameters.isClicksANDEvents()) {
score = Math.min(score, eventScore);
}
else {
score = Math.max(score, eventScore);
}
}
return score;
/*
* Now score based on whether or not it's individual click type is wanted.
*/
}
private double scoreClick(ClickDetection click) {
if (click.getAmplitudeDB() < clickAlarmParameters.minimumAmplitude) {
return 0;
}
ClickIdentifier clickIdentifier = clickControl.getClickIdentifier();
int code = click.getClickType();
if (code > 0 && clickIdentifier != null) {
@ -81,13 +87,13 @@ public class ClickDataSelector extends DataSelector {
boolean enabled = clickAlarmParameters.getUseSpecies(code);
if (enabled == false) {
return 0;
}
if (isAllowScores()) {
}if (isAllowScores()) {
return clickAlarmParameters.getSpeciesWeight(code);
}
else {
return 1;
}
}
/**
@ -95,7 +101,7 @@ public class ClickDataSelector extends DataSelector {
* @param click
* @return
*/
private boolean wantEventType(ClickDetection click) {
private double scoreEventType(ClickDetection click) {
OfflineEventDataUnit oev = null;
try {
@ -107,7 +113,7 @@ public class ClickDataSelector extends DataSelector {
int eventId = click.getOfflineEventID();
if (oev == null) {
return clickAlarmParameters.unassignedEvents;
return clickAlarmParameters.unassignedEvents ? 1 : 0;
}
// see if there is a super detection and see if it's got a comment.
@ -118,10 +124,10 @@ public class ClickDataSelector extends DataSelector {
isAutomatic = comment.startsWith("Automatic");
}
if (isAutomatic && clickAlarmParameters.onlineAutoEvents) {
return true;
return 1;
}
else if (clickAlarmParameters.onlineManualEvents) {
return true;
return 1;
}
// if (clickAlarmParameters.onlineAutoEvents && comment.startsWith("Automatic")) {
// return true;
@ -134,7 +140,7 @@ public class ClickDataSelector extends DataSelector {
* list of event types and see if it's wanted.
*/
String evType = oev.getEventType();
return clickAlarmParameters.isUseEventType(evType);
return clickAlarmParameters.isUseEventType(evType) ? 1 : 0;
}
@ -188,7 +194,7 @@ public class ClickDataSelector extends DataSelector {
* @see PamguardMVC.dataSelector.DataSelector#getParams()
*/
@Override
public DataSelectParams getParams() {
public ClickAlarmParameters getParams() {
return clickAlarmParameters;
}

69
src/clickDetector/dataSelector/ClickSelectPanel.java
View File

@ -4,6 +4,7 @@ import generalDatabase.lookupTables.LookUpTables;
import generalDatabase.lookupTables.LookupList;
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
@ -13,11 +14,13 @@ import java.awt.event.ActionListener;
import javax.swing.BoxLayout;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextField;
import javax.swing.border.EmptyBorder;
import javax.swing.border.TitledBorder;
import PamController.PamController;
@ -42,6 +45,7 @@ public class ClickSelectPanel implements PamDialogPanel {
private ClickDataSelector clickDataSelector;
private JPanel mainPanel;
private boolean isViewer;
private JComboBox<String> andOrBox;
public static final String mainTip = "You should select options in both the Click Type and the Event Type panels";
@ -70,10 +74,12 @@ public class ClickSelectPanel implements PamDialogPanel {
public void setParams() {
eventTypePanel.setParams();
speciesPanel.setParams();
andOrBox.setSelectedIndex(clickDataSelector.getParams().isClicksANDEvents() ? 0 : 1);
}
@Override
public boolean getParams() {
clickDataSelector.getParams().setClicksANDEvents(andOrBox.getSelectedIndex() == 0);
return (speciesPanel.getParams() & eventTypePanel.getParams());
}
@ -163,17 +169,26 @@ public class ClickSelectPanel implements PamDialogPanel {
// JRadioButton andEvents, orEvents;
// JRadioButton anyEvents, onlyEvents;
private JCheckBox useEchoes;
private JTextField minAmplitude;
private JCheckBox scoreByAmplitude;
private JTextField minICI;
SpeciesPanel () {
super();
setLayout(new BorderLayout());
// setLayout(new BorderLayout());
setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
northPanel = new JPanel();
northPanel.setLayout(new GridBagLayout());
GridBagConstraints c = new PamGridBagContraints();
c.gridwidth = 3;
c.gridwidth = 1;
c.anchor = GridBagConstraints.WEST;
northPanel.add(new JLabel("Minimum amplitude ", JLabel.RIGHT), c);
c.gridx++;
northPanel.add(minAmplitude = new JTextField(4), c);
c.gridx++;
northPanel.add(new JLabel(" dB"));
c.gridx = 0;
c.gridy++;
northPanel.add(new PamAlignmentPanel(useEchoes = new JCheckBox("Use Echoes"), BorderLayout.WEST), c);
c.gridwidth = 1;
c.gridy++;
@ -185,35 +200,50 @@ public class ClickSelectPanel implements PamDialogPanel {
// minICI.setToolTipText("Minimum ICI in milliseconds");
// c.gridx++;
// northPanel.add(new JLabel(" ms", JLabel.LEFT), c);
c.gridwidth = 3;
c.gridy++;
c.gridx = 0;
northPanel.add(scoreByAmplitude = new JCheckBox("Score by amplitude"), c);
scoreByAmplitude.setVisible(allowScores);
scoreByAmplitude.addActionListener(new AllSpeciesListener());
scoreByAmplitude = new JCheckBox("Score by amplitude");
if (allowScores) {
c.gridwidth = 3;
c.gridy++;
c.gridx = 0;
northPanel.add(scoreByAmplitude, c);
scoreByAmplitude.setVisible(allowScores);
scoreByAmplitude.addActionListener(new AllSpeciesListener());
}
WestAlignedPanel walpn;
add(BorderLayout.NORTH, walpn = new WestAlignedPanel(northPanel));
walpn.setBorder(new SeparatorBorder("Echoes"));
this.add(walpn = new WestAlignedPanel(northPanel));
walpn.setBorder(new SeparatorBorder("Click Selection"));
JPanel centralOuterPanel = new JPanel(new BorderLayout());
centralPanel.setLayout(new GridBagLayout());
centralOuterPanel.setBorder(new SeparatorBorder("Click Type Selection"));
centralOuterPanel.setBorder(new SeparatorBorder("Click Types"));
add(BorderLayout.CENTER, centralOuterPanel);
this.add(centralOuterPanel);
JScrollPane scrollPane = new DialogScrollPane(new PamAlignmentPanel(centralPanel, BorderLayout.WEST), 10);
centralOuterPanel.add(BorderLayout.CENTER, scrollPane);
centralEastPanel.setLayout(new GridBagLayout());
c = new PamGridBagContraints();
centralEastPanel.add(selectAll = new JButton("Select All"), c);
c.gridx++;
centralEastPanel.add(clearAll = new JButton("Clear All"), c);
c.ipady = 0;
c.insets.bottom = c.insets.top = c.insets.left = c.insets.right = 0;
centralEastPanel.add(selectAll = new JButton("All"), c);
c.gridy++;
centralEastPanel.add(clearAll = new JButton("None"), c);
selectAll.setBorder(new EmptyBorder(3,3,2,3));
clearAll.setBorder(new EmptyBorder(3,3,2,3));
selectAll.addActionListener(new AutoSelect(true));
clearAll.addActionListener(new AutoSelect(false));
centralOuterPanel.add(BorderLayout.SOUTH, new PamAlignmentPanel(centralEastPanel, BorderLayout.WEST));
centralOuterPanel.add(BorderLayout.EAST, new PamAlignmentPanel(centralEastPanel, BorderLayout.NORTH));
centralOuterPanel.setToolTipText(mainTip);
this.add(andOrBox = new JComboBox<>());
andOrBox.setToolTipText("Select how to logically combine the click and event selections");
andOrBox.addItem("AND");
andOrBox.addItem("OR");
JPanel emptyPanel = new JPanel();
emptyPanel.setPreferredSize(new Dimension(10, 5));
this.add(emptyPanel);
setToolTipText(mainTip);
}
@ -254,6 +284,7 @@ public class ClickSelectPanel implements PamDialogPanel {
}
}
useEchoes.setSelected(clickAlarmParameters.useEchoes);
minAmplitude.setText(String.format("%3.1f", clickAlarmParameters.minimumAmplitude));
minICI.setText(String.format("%d", clickAlarmParameters.minICIMillis));
scoreByAmplitude.setSelected(clickAlarmParameters.scoreByAmplitude);
allWeight.setText(String.format("%3.1f", clickAlarmParameters.getSpeciesWeight(0)));
@ -279,6 +310,12 @@ public class ClickSelectPanel implements PamDialogPanel {
ClickAlarmParameters clickAlarmParameters = clickDataSelector.getClickAlarmParameters().clone();
clickAlarmParameters.useEchoes = useEchoes.isSelected();
try {
clickAlarmParameters.minimumAmplitude = Double.valueOf(minAmplitude.getText());
}
catch (NumberFormatException e) {
return PamDialog.showWarning(null, "Minimum amplitude", "Invalid minimum amplitude value");
}
try {
clickAlarmParameters.minICIMillis = Integer.valueOf(minICI.getText());
}

45
src/clickDetector/dialogs/ClickDisplayDialog.java
View File

@ -31,6 +31,7 @@ import PamView.dialog.warn.WarnOnce;
import clickDetector.BTDisplayParameters;
import clickDetector.ClickControl;
import clickDetector.ClickClassifiers.ClickIdentifier;
import clickDetector.alarm.ClickAlarmParameters;
/**
* Dialog for basic click display parameters
@ -57,6 +58,8 @@ public class ClickDisplayDialog extends PamDialog implements ActionListener {
private SizePanel sizePanel;
private SpeciesPanel speciesPanel;
private JComboBox<String> angleTypes;
private ClickAlarmParameters clickSelectParams;
private ClickDisplayDialog(Window owner) {
@ -86,12 +89,13 @@ public class ClickDisplayDialog extends PamDialog implements ActionListener {
}
public static BTDisplayParameters showDialog(ClickControl clickControl, Window parentFrame, BTDisplayParameters btDisplayParameters) {
public static BTDisplayParameters showDialog(ClickControl clickControl, Window parentFrame, BTDisplayParameters btDisplayParameters, ClickAlarmParameters clickSelectParams) {
if (singleInstance == null || singleInstance.getOwner() != parentFrame) {
singleInstance = new ClickDisplayDialog(parentFrame);
}
singleInstance.clickControl = clickControl;
singleInstance.btDisplayParameters = btDisplayParameters.clone();
singleInstance.clickSelectParams = clickSelectParams;
singleInstance.setParams(btDisplayParameters);
singleInstance.setVisible(true);
return singleInstance.btDisplayParameters;
@ -514,14 +518,16 @@ public class ClickDisplayDialog extends PamDialog implements ActionListener {
}
}
}
showEchoes.setSelected(btDisplayParameters.showEchoes);
showEchoes.setSelected(clickSelectParams.useEchoes);
if (species == null) {
showAll.setSelected(true);
}
else {
showAll.setSelected(btDisplayParameters.getShowSpecies(0));
// showAll.setSelected(btDisplayParameters.getShowSpecies(0));
showAll.setSelected(clickSelectParams.getUseSpecies(0));
for (int i = 0; i < species.length; i++) {
species[i].setSelected(btDisplayParameters.getShowSpecies(i+1));
species[i].setSelected(clickSelectParams.getUseSpecies(i+1));
// species[i].setSelected(btDisplayParameters.getShowSpecies(i+1));
}
// if (btDisplayParameters.showSpeciesList != null) {
// for (int i = 0; i < Math.min(species.length, btDisplayParameters.showSpeciesList.length);i++) {
@ -529,9 +535,10 @@ public class ClickDisplayDialog extends PamDialog implements ActionListener {
// }
// }
}
clicksInAnEvent.setSelected(btDisplayParameters.showEventsOnly);
andOrSelection.setSelectedIndex(btDisplayParameters.showANDEvents ? 0: 1);
clicksInAnEvent.setSelected(clickSelectParams.onlineAutoEvents | clickSelectParams.onlineAutoEvents);
// clicksInAnEvent.setSelected(btDisplayParameters.showEventsOnly);
// andOrSelection.setSelectedIndex(btDisplayParameters.showANDEvents ? 0: 1);
// orEvents.setSelected(!btDisplayParameters.showANDEvents);
// andEvents.setSelected(btDisplayParameters.showANDEvents);
// anyEvents.setSelected(!btDisplayParameters.showEventsOnly);
@ -540,19 +547,17 @@ public class ClickDisplayDialog extends PamDialog implements ActionListener {
enableButtons();
}
boolean getParams() {
btDisplayParameters.showEchoes = showEchoes.isSelected();
btDisplayParameters.setShowSpecies(0, showAll.isSelected());
if (species != null) {
for (int i = 0; i < species.length; i++) {
btDisplayParameters.setShowSpecies(i+1, species[i].isSelected());
}
}
btDisplayParameters.showEventsOnly = clicksInAnEvent.isSelected();
btDisplayParameters.showANDEvents = (andOrSelection.getSelectedIndex() == 0);
// btDisplayParameters.showANDEvents = andEvents.isSelected();
// btDisplayParameters.showEventsOnly = onlyEvents.isSelected();
// clickSelectParams.useEchoes = showEchoes.isSelected();
// btDisplayParameters.setShowSpecies(0, showAll.isSelected());
// if (species != null) {
// for (int i = 0; i < species.length; i++) {
// btDisplayParameters.setShowSpecies(i+1, species[i].isSelected());
// }
//
// }
//
// btDisplayParameters.showEventsOnly = clicksInAnEvent.isSelected();
// btDisplayParameters.showANDEvents = (andOrSelection.getSelectedIndex() == 0);
return true;
}
class AllSpeciesListener implements ActionListener {

45
src/clickDetector/offlineFuncs/OfflineToolbar.java
View File

@ -31,12 +31,15 @@ import clickDetector.ClickBTDisplay;
import clickDetector.ClickControl;
import clickDetector.ClickDisplay;
import clickDetector.ClickClassifiers.ClickIdentifier;
import clickDetector.alarm.ClickAlarmParameters;
import clickDetector.dataSelector.ClickDataSelector;
import PamView.PamToolBar;
import PamView.component.PamSettingsIconButton;
import PamView.dialog.PamCheckBox;
import PamView.dialog.PamLabel;
import PamView.dialog.PamRadioButton;
import PamView.panel.PamPanel;
import PamguardMVC.dataSelector.DataSelectParams;
public class OfflineToolbar {
@ -252,19 +255,29 @@ public class OfflineToolbar {
return;
}
try {
ClickDataSelector clickDataSelector = currentBTDisplay.getDataSelector();
ClickAlarmParameters selectParams = clickDataSelector.getParams();
BTDisplayParameters btDisplayParameters = currentBTDisplay.getBtDisplayParameters();
btDisplayParameters.setShowSpecies(0, showNonSpecies.isSelected());
btDisplayParameters.showEchoes = showEchoes.isSelected();
selectParams.setUseSpecies(0, showNonSpecies.isSelected());
// btDisplayParameters.setShowSpecies(0, showNonSpecies.isSelected());
// btDisplayParameters.showEchoes = showEchoes.isSelected();
selectParams.useEchoes = showEchoes.isSelected();
if (clicksInAnEvent != null) {
btDisplayParameters.showEventsOnly = clicksInAnEvent.isSelected();
// btDisplayParameters.showEventsOnly = clicksInAnEvent.isSelected();
// selectParams.onlineAutoEvents = selectParams.onlineManualEvents = true;
selectParams.unassignedEvents =clicksInAnEvent.isSelected() == false;
}
if (andOrSelection != null) {
btDisplayParameters.showANDEvents = (andOrSelection.getSelectedIndex() == 0);
selectParams.setClicksANDEvents(andOrSelection.getSelectedIndex() == 0);
// btDisplayParameters.showANDEvents = (andOrSelection.getSelectedIndex() == 0);
}
if (speciesButtons != null) {
int n = speciesButtons.length;
for (int i = 0; i < n; i++) {
btDisplayParameters.setShowSpecies(i+1, speciesButtons[i].isSelected());
selectParams.setUseSpecies(i+1, speciesButtons[i].isSelected());
// btDisplayParameters.setShowSpecies(i+1, speciesButtons[i].isSelected());
}
}
currentBTDisplay.repaintTotal();
@ -275,23 +288,35 @@ public class OfflineToolbar {
}
private void checkButtons(BTDisplayParameters btDisplayParameters) {
showEchoes.setSelected(btDisplayParameters.showEchoes);
showNonSpecies.setSelected(btDisplayParameters.getShowSpecies(0));
ClickDataSelector clickDataSelector = currentBTDisplay.getDataSelector();
ClickAlarmParameters selectParams = clickDataSelector.getParams();
showEchoes.setSelected(selectParams.useEchoes);
showNonSpecies.setSelected(selectParams.getUseSpecies(0));
// showNonSpecies.setSelected(btDisplayParameters.getShowSpecies(0));
boolean anySel = false;;
if (clicksInAnEvent != null) {
clicksInAnEvent.setSelected(btDisplayParameters.showEventsOnly);
clicksInAnEvent.setSelected(selectParams.unassignedEvents == false);
anySel |= clicksInAnEvent.isSelected();
// clicksInAnEvent.setSelected(btDisplayParameters.showEventsOnly);
}
if (speciesButtons != null) {
int n = speciesButtons.length;
for (int i = 0; i < n; i++) {
speciesButtons[i].setSelected(btDisplayParameters.getShowSpecies(i+1));
speciesButtons[i].setSelected(selectParams.getUseSpecies(i+1));
anySel |= speciesButtons[i].isSelected();
// speciesButtons[i].setSelected(btDisplayParameters.getShowSpecies(i+1));
}
}
// setting combo box fires actionlistener, so we have to make sure that all checkboxes have been properly set first
// or else they will get cleared later
if (andOrSelection != null) {
andOrSelection.setSelectedIndex(btDisplayParameters.showANDEvents ? 0: 1);
andOrSelection.setSelectedIndex(selectParams.isClicksANDEvents() ? 0 : 1);
// andOrSelection.setSelectedIndex(btDisplayParameters.showANDEvents ? 0: 1);
}
firstSetup = true;
if (anySel) {
selectParams.setCombinationFlag(DataSelectParams.DATA_SELECT_AND);
}
}
}

43
src/clickDetector/tdPlots/ClickClassSymbolModifier.java
View File

@ -1,7 +1,13 @@
package clickDetector.tdPlots;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
import javax.swing.JPanel;
import javax.swing.border.TitledBorder;
import PamView.GeneralProjector;
import PamView.PamSymbol;
import PamView.dialog.PamDialogPanel;
import PamView.symbol.PamSymbolChooser;
import PamView.symbol.SymbolData;
import PamView.symbol.modifier.SymbolModType;
@ -32,4 +38,41 @@ public class ClickClassSymbolModifier extends SymbolModifier {
}
}
@Override
public PamDialogPanel getDialogPanel() {
// Just a play to check buttons and menus work. Not actually used at all so revert to super: returns null.
return super.getDialogPanel();
// return new DumyPanel();
}
private class DumyPanel implements PamDialogPanel {
private JPanel mainPanel;
public DumyPanel() {
super();
mainPanel = new JPanel();
mainPanel.setBorder(new TitledBorder("More options"));
mainPanel.add(new JCheckBox("Dummy option"));
}
@Override
public JComponent getDialogComponent() {
// TODO Auto-generated method stub
return mainPanel;
}
@Override
public void setParams() {
// TODO Auto-generated method stub
}
@Override
public boolean getParams() {
// TODO Auto-generated method stub
return false;
}
}
}

11
src/clickDetector/tdPlots/ClickPlotInfo.java
View File

@ -9,6 +9,8 @@ import clickDetector.BTDisplayParameters;
import clickDetector.ClickControl;
import clickDetector.ClickDetection;
import clickDetector.ClickDisplayManagerParameters;
import clickDetector.alarm.ClickAlarmParameters;
import clickDetector.dataSelector.ClickDataSelector;
import clickDetector.dialogs.ClickDisplayDialog;
import PamView.GeneralProjector.ParameterType;
import PamView.GeneralProjector.ParameterUnits;
@ -52,6 +54,10 @@ public class ClickPlotInfo extends TDDataInfo {
allScaleInfo[3] = slantScaleInfo;
clickHidingDialog = new ClickHidingDialog(this);
}
ClickDataSelector getDataSelector() {
return (ClickDataSelector) clickControl.getClickDataBlock().getDataSelector("ClickTDPlots", false);
}
@Override
public Double getDataValue(PamDataUnit pamDataUnit) {
@ -110,7 +116,8 @@ public class ClickPlotInfo extends TDDataInfo {
private synchronized boolean shouldPlot(ClickDetection click) {
if (click == null) return false;
if (btDisplayParams.showEchoes == false && click.isEcho()) {
boolean showEchoes = getDataSelector().getClickAlarmParameters().useEchoes;
if (showEchoes == false && click.isEcho()) {
return false;
}
@ -170,7 +177,7 @@ public class ClickPlotInfo extends TDDataInfo {
*/
@Override
public boolean editOptions(Window frame) {
BTDisplayParameters newParams = ClickDisplayDialog.showDialog(clickControl, frame, btDisplayParams);
BTDisplayParameters newParams = ClickDisplayDialog.showDialog(clickControl, frame, btDisplayParams, getDataSelector().getClickAlarmParameters());
if (newParams != null) {
btDisplayParams = newParams.clone();
updateSettings();

28
src/clipgenerator/ClipProcess.java
View File

@ -140,10 +140,13 @@ public class ClipProcess extends SpectrogramMarkProcess {
clipErr = clipRequest.clipBlockProcess.processClipRequest(clipRequest);
switch (clipErr) {
case 0: // no error - clip should have been created.
li.remove();
break;
case RawDataUnavailableException.DATA_ALREADY_DISCARDED:
case RawDataUnavailableException.INVALID_CHANNEL_LIST:
// System.out.println("Clip error : " + clipErr);
// System.out.println("Clip error : " + clipErr);
li.remove();
break;
case RawDataUnavailableException.DATA_NOT_ARRIVED:
continue; // hopefully, will get this next time !
}
@ -230,6 +233,17 @@ public class ClipProcess extends SpectrogramMarkProcess {
}
minH = Math.max(minH, clipBlockProcesses[i].getRequiredDataHistory(o, arg));
}
ClipRequest firstClip = null;
synchronized(clipRequestSynch) {
if (clipRequestQueue.size() > 0) {
firstClip = clipRequestQueue.get(0);
}
}
if (firstClip != null) {
minH += firstClip.dataUnit.getDurationInMilliseconds();
}
minH += Math.max(3000, 192000/(long)getSampleRate());
if (specMouseDown) {
minH = Math.max(minH, masterClockTime-specMouseDowntime);
@ -453,8 +467,7 @@ public class ClipProcess extends SpectrogramMarkProcess {
this.dataBlock = dataBlock;
this.clipGenSetting = clipGenSetting;
clipBudgetMaker = new StandardClipBudgetMaker(this);
dataBlock.addObserver(this, true);
dataBlock.addObserver(this, false);
if (rawDataBlock != null) {
int chanMap = decideChannelMap(rawDataBlock.getChannelMap());
@ -499,6 +512,7 @@ public class ClipProcess extends SpectrogramMarkProcess {
rawData = rawDataBlock.getSamples(rawStart, (int) (rawEnd-rawStart), channelMap);
}
catch (RawDataUnavailableException e) {
System.out.println(e.getMessage());
return e.getDataCause();
}
if (rawData==null) {
@ -583,9 +597,15 @@ public class ClipProcess extends SpectrogramMarkProcess {
public PamObserver getObserverObject() {
return clipProcess.getObserverObject();
}
@Override
public long getRequiredDataHistory(PamObservable o, Object arg) {
return (long) ((clipGenSetting.preSeconds+clipGenSetting.postSeconds) * 1000.);
long h = (long) ((clipGenSetting.preSeconds+clipGenSetting.postSeconds) * 1000.);
// if (dataBlock != null) {
// can't do this since dataBlock is observing this, so will wrap.
// h += dataBlock.getRequiredHistory();
// }
return h;
}

21
src/dataPlotsFX/clickPlotFX/ClickControlPane2.java
View File

@ -230,7 +230,16 @@ public class ClickControlPane2 extends PamBorderPane implements TDSettingsPane {
dataSelectPane.addSettingsListener(()->{
//dynamic settings pane so have to repaint whenever a control is selected.
getParams();
clickPlotInfo.getTDGraph().repaint(0);
/**
* If there are raw amplitude or frequency panes that have a buffer of painted units then
* these have to be cleared for the data selector
*/
clickPlotInfo.getClickRawPlotManager().clear();
clickPlotInfo.getClickFFTPlotManager().clear();
clickPlotInfo.getTDGraph().repaint(50);
});
this.setCenter(tabPane);
@ -244,7 +253,7 @@ public class ClickControlPane2 extends PamBorderPane implements TDSettingsPane {
* @return the data select pane.
*/
private DynamicSettingsPane<Boolean> createDataSelectPane(){
System.out.println("DATA SELECTOR: " + clickPlotInfo.getClickDataSelector());
// System.out.println("DATA SELECTOR: " + clickPlotInfo.getClickDataSelector());
return clickPlotInfo.getClickDataSelector().getDialogPaneFX();
}
@ -449,7 +458,7 @@ public class ClickControlPane2 extends PamBorderPane implements TDSettingsPane {
PamVBox vBox = new PamVBox();
vBox.setSpacing(5);
minMaxWidthPane = new DualControlField<Double>("Min", "Max" , "", 2, 100, 1);
minMaxWidthPane = new DualControlField<Double>("", "" , "", 2, 100, 1);
minMaxWidthPane.addChangeListener((obsval, oldval, newval)->{
newSettings();
//do not allow the min ti be larger than the max.
@ -472,7 +481,7 @@ public class ClickControlPane2 extends PamBorderPane implements TDSettingsPane {
//height pane
minMaxHeightPane = new DualControlField<Double>("Min", "Max" , "", 2, 100, 1);
minMaxHeightPane = new DualControlField<Double>("", "" , "", 2, 100, 1);
minMaxHeightPane.addChangeListener((obsval, oldval, newval)->{
newSettings();
//do not allow the min ti be larger than the max.
@ -519,7 +528,7 @@ public class ClickControlPane2 extends PamBorderPane implements TDSettingsPane {
getParams();
//on a parameter change must clear the FFT plot.
clickPlotInfo.getClickFFTplotManager().clear();
clickPlotInfo.getClickFFTPlotManager().clear();
clickPlotInfo.getClickRawPlotManager().clear();
clickPlotInfo.getTDGraph().repaint(milliswait);
@ -773,7 +782,7 @@ public class ClickControlPane2 extends PamBorderPane implements TDSettingsPane {
clickPlotInfo.getClickDisplayParams().fftHop = this.fftSpinnerHop.getValue().intValue();
clickPlotInfo.getClickDisplayParams().fftLength = this.fftSpinnerLength.getValue().intValue();
clickPlotInfo.getClickDisplayParams().colourMap = this.spectroControlPane.getColourArrayType();
clickPlotInfo.getClickFFTplotManager().update();
clickPlotInfo.getClickFFTPlotManager().update();
/*** Data select pane****/
//dynamic settings pane so have to repaint whenever a control is selected.

34
src/dataPlotsFX/clickPlotFX/ClickPlotInfoFX.java
View File

@ -238,7 +238,7 @@ public class ClickPlotInfoFX extends TDDataInfoFX {
ClickDetection click = (ClickDetection) pamDataUnit;
//first check we can generally plot the click
if (!shouldPlot(click)) return null;
// if (!shouldPlot(click)) return null;
//click has passed the first test! Now get the correct data value;
Double val = null;
switch (getCurrentScaleInfo().getDataType()) {
@ -599,21 +599,21 @@ public class ClickPlotInfoFX extends TDDataInfoFX {
// }
/***
* Used to determine which clicks should be plotted on the display by using the click data selector.
* @param click - the click to check.
* @return true to plot the click.
*/
private synchronized boolean shouldPlot(ClickDetection click) {
if (click == null) return false;
dataSelector.scoreData(click);
if (clickDisplayParams.displayChannels > 0 && (clickDisplayParams.displayChannels & click.getChannelBitmap()) == 0) return false;
return true;
}
// /***
// * Used to determine which clicks should be plotted on the display by using the click data selector.
// * @param click - the click to check.
// * @return true to plot the click.
// */
// private synchronized boolean shouldPlot(ClickDetection click) {
//
// if (click == null) return false;
//
// if (dataSelector.scoreData(click)<=0) return false;
//
// if (clickDisplayParams.displayChannels > 0 && (clickDisplayParams.displayChannels & click.getChannelBitmap()) == 0) return false;
//
// return true;
// }
@Override
public TDSymbolChooserFX getSymbolChooser() {
@ -931,7 +931,7 @@ public class ClickPlotInfoFX extends TDDataInfoFX {
* time/frequency displays...
* @return The FFT plot manager.
*/
public ClickFFTPlotManager2 getClickFFTplotManager() {
public ClickFFTPlotManager2 getClickFFTPlotManager() {
return clickFFTplotManager;
}

1
src/dataPlotsFX/data/RawWavePlotManager.java
View File

@ -318,7 +318,6 @@ public abstract class RawWavePlotManager {
//check if we can plot click on this plot pane.
if (!rawClipInfo.shouldDraw(plotNumber, pamDataUnit)) {
//System.out.println("Shoudl not draw!");
return null;
}

5
src/dataPlotsFX/layout/TDGraphFX.java
View File

@ -901,13 +901,14 @@ public class TDGraphFX extends PamBorderPane {
}
/**
* A tgool tip for detections.
* A Tooltip for showing information about detections.
*
* @author Jamie Macaulay
*
*/
private class TDTooltip extends Tooltip {
private static final double TOOL_TIP_DELAY = 60; //seconds
private TDPlotPane plotPanel;
/**
@ -917,6 +918,8 @@ public class TDGraphFX extends PamBorderPane {
public TDTooltip(TDPlotPane aPlot) {
super("Test tooltip");
this.plotPanel = aPlot;
//make the Tooltip last a little longer
this.setShowDelay(Duration.seconds(TOOL_TIP_DELAY));
/*
* See https://bugs.openjdk.java.net/browse/JDK-8090477 fr info about tool tip
* timing on these displys.

2
src/dataPlotsFX/rawDataPlotFX/RawSoundPlotDataFX.java
View File

@ -382,7 +382,7 @@ public class RawSoundPlotDataFX {
if (soundStore.currentRawDataMillis==0){
if (++timeErrors < 10) {
System.err.println("RawSoundPlotData: Raw sound data has no associated millisecond time: "+ soundStore.currentRawDataMillis);
// System.err.println("RawSoundPlotData: Raw sound data has no associated millisecond time: "+ soundStore.currentRawDataMillis);
}
return;
}

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10
src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_Bugs.html
View File

@ -9,8 +9,14 @@
<body>
<h1 id="pamguard-s-deep-learning-module">PAMGuard&#39;s Deep
Learning Module</h1>
<h2 id="common-bugs-and-mistakes">Common Bugs and Mistakes</h2>
<br>
<h2 id="common-bugs-and-mistakes">Common bugs and mistakes</h2>
<p>The first time you use the module and/or load a different type
of model e.g. a tensorflow or pytorch model, you must be connected to
the internet.</p>
<p>You must install the correct version of CUDA for hardware
acceleration using an Nvidea GPU. See the currently supported CUDA
versions on the Pytorch and Tensorflow websites.</p>
<p>You should always have deep learning models in their own folder.
Do not have any additional jar files or other programming related
things (like .dll files) in the same or sub folders. This has been

89
src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_CreateAndConfig.html
View File

@ -7,20 +7,18 @@
</head>
<body>
<h1 id="pamguard-s-deep-learning-module">PAMGuard Deep
Learning Module</h1>
<h2 id="creation-and-config">Creation and Configuration</h2>
<br>
<h3 id="creating-an-instance-of-the-module">Creating an instance
of the module</h3>
<h1 id="pamguard-s-deep-learning-module">PAMGuard Deep Learning
Module</h1>
<h2 id="creating-an-instance-of-the-module">Creating an instance
of the module</h2>
<p>
The module can be added from the <em>File&gt; Add modules &gt;
Classifier &gt; Raw deep learning classifier</em> menu or by right
clicking in the data model. More than one instance of the module can
be added if multiple deep learning models are required.
</p>
<br>
<h3 id="module-settings">Module settings</h3>
<h2 id="module-settings">Module settings</h2>
<p>
The module settings are opened by selecting the <em>Settings &gt;
Raw deep learning classifier</em> menu. The main settings pane is shown
@ -28,18 +26,18 @@
and <em>Deep Learning Model</em>
</p>
<p align="center">
<img width="700" height="630"
src="images/deep_leanring_module_help.png">
<img src="images/deep_leanring_module_help.png">
</p>
<p>
<em>The main settings pane for the deep learning module with
descriptions</em>
</p>
<br>
<h3 id="raw-sound-data">Raw Sound Data</h3>
<p>The deep learning module accepts any raw data source i.e., any
data source that contains raw waveform data.</p>
data source that contains raw waveform data e.g. clicks, clips and
Ishmael detections. Note that the module accepts whislte and moan
detections but only if a delphinID classifier has been loaded.</p>
<p>If the data is continuous, e.g. from the Sound Acquisition
module then deep learning detections are saved to PAMGuard&#39;s data
management system if they pass a user defined prediction threshold.
@ -57,7 +55,6 @@
processes. So, for example if channels 0 and 2 are in a group, then
the raw waveform data from both channel 0 and 2 will be saved and can
be used in downstream processes, e.g., for localisation.</p>
<br>
<h3 id="segmentation">Segmentation</h3>
<p>
The segmentation section defines how the raw data is segmented. Some
@ -72,7 +69,6 @@
re-merge</em> is the maximum number of segments that can form a single
data unit before a new data unit is automatically created.
</p>
<br>
<h3 id="deep-learning-model">Deep Learning Model</h3>
<p>The deep learning model section is used to select the deep
learning model. The drop down menu is used to select the framework the
@ -92,14 +88,12 @@
</p>
<p>Once the model has loaded there some unique options depending on
the currently selected framework.</p>
<br>
<h4 id="generic-model">Generic Model</h4>
<p>
A generic model must be set up via the <em>Advanced</em> menu button.
</p>
<p align="center">
<img width="700" height="700"
src="images/advanced_settings_generic_1.png">
<img src="images/advanced_settings_generic_1.png">
</p>
<p>
@ -124,8 +118,7 @@
including the shape of the input data e.g. a 100x50 image.
</p>
<p align="center">
<img width="700" height="700"
src="images/advanced_settings_generic_2.png">
<img src="images/advanced_settings_generic_2.png">
</p>
<p>
@ -146,16 +139,15 @@
transforms and input and output data whenever settings up a new
PAMGuard data model and allow easier sharing of classifiers amongst
researchers.</p>
<br>
<h4 id="animalspot-and-ketos-models">AnimalSpot and Ketos models</h4>
<h4 id="koogu-ketos-animalspot-pamguard-zip-and-delphinid-models">Koogu,
Ketos, AnimalSpot, PAMGuard zip and delphinID models</h4>
<p>
If using an AnimalSpot or Ketos model then all transforms are
automatically set up. The transforms can be viewed and altered via the
Advanced menu button but in the majority of cases these settings
should not be used. It is advisable to select &quot;Use default
segment length&quot; to change the <em>Window length</em> to the
default for the selected model. Note that this is often necessary for
Ketos models but usually not a requirement for AnimalSpot models.
If using a deep learning model from a supported framework then all
transforms are automatically set up. The transforms can be viewed and
altered via the Advanced menu button but in the majority of cases
these settings should not be used. For some models, it is advisable to
select &quot;Use default segment length&quot; to change the <em>Window
length</em> to the default for the selected model.
</p>
<p align="center">
<img width="700" height="700"
@ -163,18 +155,43 @@
</p>
<p>
<em>An AnimalSpot or Ketos model will automatically create a list
of transforms with the appropriate settings. These is no need to use
the advanced pane but it is there in case users wish to change
transform settings for some reason</em>
<em>An AnimalSpot, Ketos or other supported deep learning model
will automatically create a list of transforms with the appropriate
settings. These is no need to use the advanced pane but it is there
in case users wish to change transform settings for some reason</em>
</p>
<h3 id="default-models">Default Models</h3>
<p>Default models are selectable from the menu button in the Deep
Learning Pane. Default models are deep learning classifiers which are
open source, known to be effective and have have been published in
open access academic litrature; they are downloaded directly from a
GitHub repository and then all associated settings are automtically
applied. The default model selection pane also contains hyperlinks to
the papers descirbing each model which will take users directly to the
relvent website.</p>
<p align="center">
<img src="images/default_settings_humpback_1.png">
</p>
<p>
<em>Default models can be downloaded. Default models are models
which are published, open and have been known to work well amongst
the bioacoustics community. More will be added to PAMGaurd over time.
If you you would like your model to become a defualt model then drop
PAMGuard support an email.</em>
</p>
<br>
<br>
<br>
<p class="prevLink"><a href="rawDeepLearning_overview.html">Previous:
Overview</a></p>
<p class="nextLink"><a href="rawDeepLearning_Running.html">Next:
Running the Deep Learning module</a></p>
<p class="prevLink">
<a href="rawDeepLearning_overview.html">Previous: Overview</a>
</p>
<p class="nextLink">
<a href="rawDeepLearning_Running.html">Next: Running the Deep
Learning module</a>
</p>
<br>
<br>
<br>

22
src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_Results.html
View File

@ -9,12 +9,12 @@
<body>
<h1 id="pamguard-s-deep-learning-module">PAMGuard&#39;s Deep
Learning Module</h1>
<h2 id="viewing-and-exporting-results">Viewing and exporting
results</h2>
<br>
<p>Output from the deep learning module can be viewed in PAMGuard
viewer mode, or extracted from binary files using MATLAB or R.</p>
<br>
<h3 id="pamguard-viewer-mode">PAMGuard viewer mode</h3>
<p>Detections form continuous raw data are shown in the datagram in
the same way as all data streams in PAMGuard.</p>
@ -32,7 +32,7 @@
manual analyst can quickly navigate to detections with high prediction
values for a certain class. Hovering over or right clicking on a data
unit in the time display and selecting the information button, will
show the data unit&#39;s metadata, including the prediction values for all
show the data unit’s metadata, including the prediction values for all
output classes from the deep learning model.</p>
<p align="center">
<img src="images/bat_time_base_display.png">
@ -50,7 +50,6 @@
deep learning prediction values. The spectrogram will also show deep
learning detections as translucent blue boxes (these must be selected
in the right click menu).</p>
<br>
<h3 id="matlab">MATLAB</h3>
<p>The easiest way to export to MATLAB is to select the desired
units in the time base display, right click and select the MATLAB
@ -96,7 +95,7 @@ predicitons = dldetections(<span class="hljs-number">1</span>).annotations.dlcla
waveform data in each structure;</p>
<pre>
<code class="lang-matlab">
<span class="hljs-comment">% plot all the spectrograms.</span>
<span class="hljs-comment">% plot all the spectrograms.</span>
clf
tiledlayout(<span class="hljs-number">5</span>,<span class="hljs-number">5</span>)
<span class="hljs-keyword">for</span> <span class="hljs-built_in">i</span>=<span
@ -155,7 +154,6 @@ tiledlayout(<span class="hljs-number">5</span>,<span class="hljs-number">5</span
<em>Right whale detections from a deep learning model imported
and then plotted in MATLAB</em>
</p>
<br>
<h3 id="r">R</h3>
<p>In the same way as MATLAB export, the PAMGuard time base display
and export selected data units directly to an R struct which can be
@ -165,13 +163,17 @@ tiledlayout(<span class="hljs-number">5</span>,<span class="hljs-number">5</span
functions compared to the MATLAB library. The PAMBinaries R library
can be found <a href="https://github.com/TaikiSan21/PamBinaries">here</a>.
</p>
<br>
<br>
<br>
<p class="prevLink"><a href="rawDeepLearning_Running.html">Previous:
Running the Deep Learning module</a></p>
<p class="nextLink"><a href="rawDeepLearning_Bugs.html">Next:
Common Bugs and Mistakes</a></p>
<p class="prevLink">
<a href="rawDeepLearning_Running.html">Previous: Running the Deep
Learning module</a>
</p>
<p class="nextLink">
<a href="rawDeepLearning_Bugs.html">Next: Common Bugs and Mistakes</a>
</p>
<br>
<br>
<br>

15
src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_Running.html
View File

@ -10,12 +10,10 @@
<h1 id="pamguard-s-deep-learning-module">PAMGuard&#39;s Deep
Learning Module</h1>
<h2 id="running">Running</h2>
<br>
<h3 id="real-time">Real time</h3>
<p>In real time, the deep learning model runs automatically when
processing starts. A warning will appear if there are issues with the
model and/or it cannot cope with real time speeds.</p>
<br>
<h3 id="viewer-mode">Viewer Mode</h3>
<p>
The deep learning module can be re-run on <em>detector</em> data (e.g.
@ -26,13 +24,18 @@
Detections without a deep learning annotation will have one added and
detections with an existing annotation will have it overwritten.
</p>
<br>
<br>
<br>
<p class="prevLink"><a href="rawDeepLearning_CreateAndConfig.html">Previous:
Creating and Configuring the Deep Learning module</a></p>
<p class="nextLink"><a href="rawDeepLearning_Results.html">Next:
Viewing and Exporting Results</a></p>
<p class="prevLink">
<a href="rawDeepLearning_CreateAndConfig.html">Previous: Creating
and Configuring the Deep Learning module</a>
</p>
<p class="nextLink">
<a href="rawDeepLearning_Results.html">Next: Viewing and Exporting
Results</a>
</p>
<br>
<br>
<br>

48
src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_overview.html
View File

@ -7,10 +7,11 @@
</head>
<body>
<h1 id="pamguard-s-deep-learning-module">PAMGuard Deep
Learning Module</h1>
<h1 id="pamguard-s-deep-learning-module">PAMGuard&#39;s deep
learning module</h1>
<p>Note: this module requires an internet connection upon first use
to download correct libraries.</p>
<h2 id="overview">Overview</h2>
<p>PAMGuard&#39;s deep learning module allows users to deploy a
large variety of deep learning models natively in PAMGuard. It is core
module, fully integrated into PAMGuard&#39;s display and data
@ -19,9 +20,7 @@
signal and can integrate into multiple types of acoustic analysis
workflows, for example post analysis of recorder data or used as part
of real time localisation workflow.</p>
<br>
<h3 id="how-it-works">How it works</h3>
<h2 id="how-it-works">How it works</h2>
<p>The deep learning module accepts raw data from different types
of data sources, e.g. from the Sound Acquisition module, clicks and
clips. It segments data into equal sized chunks with a specified
@ -32,8 +31,7 @@
learning model, then can be automatically set up by PAMGuard.
Currently there are three implemented frameworks</p>
<p align="center">
<img width="900" height="370"
src="images/deep_learning_module_process.png">
<img src="images/deep_learning_module_process.png">
</p>
<p>
@ -44,7 +42,6 @@
the model are saved and can be viewed in real time (e.g. mitigation)
or in post processing (e.g. data from SoundTraps).</em>
</p>
<br>
<h3 id="generic-model">Generic Model</h3>
<p>
A generic model allows a user to load any model compatible with the <a
@ -54,12 +51,11 @@
existing framework instead of a generic model as these models will
automatically generate the required transforms.
</p>
<br>
<h3 id="animalspot">AnimalSpot</h3>
<p>
<a href="https://github.com/ChristianBergler/ANIMAL-SPOT">ANIMAL-SPOT</a>
is a deep learning based framework which was initially designed for <a
href="https://github.com/ChristianBergler/ORCA-SPOT">killer
href="(https://github.com/ChristianBergler/ORCA-SPOT">killer
whale sound detection</a>) in noise heavy underwater recordings (see <a
href="https://www.nature.com/articles/s41598-019-47335-w">Bergler
et al. (2019)</a>). It has now been expanded to a be species independent
@ -68,21 +64,43 @@
AnimalSpot models will automatically set up their own data transforms
and output classes.
</p>
<br>
<h3 id="ketos">Ketos</h3>
<p>
<a href="https://meridian.cs.dal.ca/2015/04/12/ketos/">Ketos</a> is an
acoustic deep learning framework based on Tensorflow and developed by
<a href="https://meridian.cs.dal.ca/">MERIDIAN</a>. It has excellent
resources and tutorials and Python libraries can be installed easily
via pip. Imported Ketos model will automatically set up their own data
via pip. Imported Ketos (.ktpb) models will automatically set up their
own data transforms and output classes.
</p>
<h3 id="koogu">Koogu</h3>
<p>
<a href="https://shyamblast.github.io/Koogu/en/stable/">Koogu </a> is
a Python package which allows users to train a deep learning model.
Koogu helps users by integrating with some frequency used annotation
programs and provides tools to train and test classifiers. Imported
Koogu models (.kgu) will automatically set up their own data
transforms and output classes.
</p>
<h3 id="pamguardzip">PAMGuardZip</h3>
<p>
PAMGuard zip models consist of a deep learning model (either a
Tensorflow saved_model.pb or PyTorch <em>*.py model) alongside a
PAMGuard metdata file (</em>.pdtf*) within a zip archive. The metadata
file contains all the information needed for PAMGaurd to set up the
model. PAMGuard will import the zip file, decompress it and search for
the relevent deep learning model and metadata file then set up all
settings accordingly. This framework allows users to easily share
pre-tested PAMGuard compatible models.
</p>
<br>
<br>
<br>
<p class="nextLink"><a href="rawDeepLearning_CreateAndConfig.html">Next:
Creating and Configuring the Deep Learning module</a></p>
<p class="nextLink">
<a href="rawDeepLearning_CreateAndConfig.html">Next: Creating and
Configuring the Deep Learning module</a>
</p>
<br>
<br>
<br>

39
src/loggerForms/controls/CounterControl.java
View File

@ -21,6 +21,7 @@ public class CounterControl extends SimpleControl {
Character suffix;
public enum CounterSuffix {NOSUFFIX, CHARSUFFIX};
public CounterControl(ControlDescription controlDescription,
LoggerForm loggerForm) {
@ -36,25 +37,19 @@ public class CounterControl extends SimpleControl {
}
private String calculateCounter() {
int num = FormCounterManagement.getInstance().getCounterNumber(this,controlDescription.getFormDescription().getDBTABLENAME());
String numSt = Integer.toString(num);
int nZeros = 3-numSt.length();
String tSt = "";
for (int i=0;i<nZeros;i++){
tSt+="0";
// System.out.println(tSt);
}
numSt = tSt+numSt;
String numSt = String.format("%03d", num);
// int nZeros = 3-numSt.length();
//
// String tSt = "";
// for (int i=0;i<nZeros;i++){
// tSt+="0";
//// System.out.println(tSt);
// }
//
// numSt = tSt+numSt;
// System.out.println(tSt);
// System.out.println(numSt);
@ -109,31 +104,19 @@ public class CounterControl extends SimpleControl {
}
@Override
AbstractFormatter getAbstractformatter() {
DefaultFormatter formatter = new DefaultFormatter();
return formatter;
}
public void updateCounter() {
if (loggerForm.getNewOrEdit()==LoggerForm.EditDataForm) return;
// System.out.println("updateCounter");
setData(calculateCounter());
}
}

7
src/loggerForms/formdesign/controlpropsets/CounterPropertySet.java
View File

@ -2,7 +2,9 @@ package loggerForms.formdesign.controlpropsets;
import loggerForms.FormDescription;
import loggerForms.UDColName;
import loggerForms.controlDescriptions.ControlTypes;
import loggerForms.formdesign.ControlTitle;
import loggerForms.formdesign.itempanels.BooleanCtrlColPanel;
import loggerForms.formdesign.itempanels.CtrlColPanel;
public class CounterPropertySet extends BasePropertySet {
@ -15,12 +17,17 @@ public class CounterPropertySet extends BasePropertySet {
@Override
public CtrlColPanel getItemPropertyPanel(ControlTitle selTitle,
UDColName propertyName) {
// if (selTitle.getType() == ControlTypes.COUNTER) {
// System.out.println("counter");
// }
switch (propertyName) {
case Plot:
case Autoclear:
case ReadOnly:
case AutoUpdate:
return null;
// case Topic:
// return new BooleanCtrlColPanel(selTitle, new );
}
return super.getItemPropertyPanel(selTitle, propertyName);
}

2
src/pamMaths/PamVector.java
View File

@ -905,7 +905,7 @@ public class PamVector implements Serializable, Cloneable, PamCoordinate, Manage
}
double[] angs = new double[3];
angs[0] = vectors[0].getHeading();
angs[1] = vectors[1].getPitch();
angs[1] = vectors[0].getPitch();
if (vectors.length >= 2) {
angs[2] = vectors[1].getPitch();
}

8
src/pamViewFX/PamGuiFX.java
View File

@ -35,6 +35,7 @@ import dataModelFX.DataModelPaneFX;
import org.controlsfx.control.ToggleSwitch;
/**
* A pane which holds a set of tabs.
*
@ -125,7 +126,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
this.pamGuiManagerFX=pamGuiManagerFX;
this.mainTabPane = mainTabPane;
Pane layout=createMainPane(mainTabPane, stage);
Node layout=createMainPane(mainTabPane, stage);
//add main pane to PamGui
this.getChildren().add(layout);
@ -140,7 +141,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
//create the main tab pane.
this.mainTabPane = new PamTabPane();
Pane layout=createMainPane(mainTabPane, stage);
Node layout=createMainPane(mainTabPane, stage);
//add main pane to PamGui
this.getChildren().add(layout);
@ -154,7 +155,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
* @param stage - the stage holding this GUI.
* @return a pane which sits in the stage.
*/
private Pane createMainPane(PamTabPane mainTabPane, Stage stage){
private Node createMainPane(PamTabPane mainTabPane, Stage stage){
//create the pane which holds tab pane
final PamBorderPane layout = new PamBorderPane();
@ -261,7 +262,6 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
PamBorderPane layoutHolder=new PamBorderPane(layout);
layoutHolder.setTop(hidingLoadPane);
return layoutHolder;

18
src/pamViewFX/PamGuiTabFX.java
View File

@ -253,6 +253,10 @@ public class PamGuiTabFX extends PamTabFX {
double r1 = 1 - r;
int smallWindows = 0;
//the padding between windows
double padding = 10;
ArrayList<PamGuiInternalPane> dw = internalPanes;
@ -268,7 +272,9 @@ public class PamGuiTabFX extends PamTabFX {
//now place windows in correct position
//large windows
double x, y, w, h = 0;
double x, y, w, h = 0.;
double pad =0.;
if (largeWindows > 0) {
x = 0;
y = 0;
@ -284,7 +290,10 @@ public class PamGuiTabFX extends PamTabFX {
if (dw.get(i).getUserDisplayNode().isMinorDisplay()== true) continue;
dw.get(i).setPaneLayout(x, y);
dw.get(i).setPaneSize(w, h);
//set the padding if the pane is not the last pane.
pad = (i== dw.size()-1) ? 0 : padding;
dw.get(i).setPaneSize(w - (horz? pad:0), h - (horz? 0:pad));
if (horz) x += w;
else y += h;
}
@ -307,7 +316,10 @@ public class PamGuiTabFX extends PamTabFX {
for (int i = 0; i < dw.size(); i++) {
if (dw.get(i).getUserDisplayNode().isMinorDisplay() == false) continue;
dw.get(i).setPaneLayout(x, y);
dw.get(i).setPaneSize(w, h);
//set the padding if the pane is not the last pane.
pad = (i== dw.size()-1) ? 0 : padding;
dw.get(i).setPaneSize(w- (horz? pad:0), h - (horz? 0:pad));
if (horz) x += w;
else y +=h;
}

110
src/pamViewFX/fxNodes/hidingPane/HidingPane.java
View File

@ -20,7 +20,6 @@ import javafx.beans.property.DoubleProperty;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.geometry.Insets;
/**
* Hiding pane which can be added to any node.
@ -156,7 +155,7 @@ public class HidingPane extends StackPane {
//create a button which hides the side panel
hideButton=createShowButton(false);
styleHideButton(hideButton);
hideButton.setOnAction(new HideButtonPressed());
// hideButton.setOnAction(new HideButtonPressed());
hideButton.setVisible(false);
// hideButton.setStyle("close-button-right");
@ -333,8 +332,6 @@ public class HidingPane extends StackPane {
double dragX=0;
double dragY=0;
double distance=0;
private PamButton createShowButton(final boolean show){
final PamButton pamButton=new PamButton();
@ -343,6 +340,7 @@ public class HidingPane extends StackPane {
@Override public void handle(MouseEvent mouseEvent) {
// record a delta distance for the drag and drop operation.
// System.out.println("HidingPane.showButton - setOnMousePressed");
dragX =mouseEvent.getSceneX();
dragY =mouseEvent.getSceneY();
}
@ -350,10 +348,24 @@ public class HidingPane extends StackPane {
pamButton.setOnMouseReleased(new EventHandler<MouseEvent>() {
@Override public void handle(MouseEvent mouseEvent) {
if (distance==0) return;
// System.out.println("HidingPane.showButton - setOnMouseReleased");
//the mouse has been pressed
if (distance==0) {
if (isShowing()) {
showHidePane(false);
}
else {
showHidePane(true);
}
return;
}
//the mouse has been dragged dragged
distance=sideIndex*distance;
// System.out.println("Mouse released: HidePanel distance: "+distance);
if (!overlay) distance=Math.abs(distance);
//need to see where the drag has ended-if greater than 50% then open but if less then close.
if (!isHorizontal()){
if (distance<expandedSize/2) showHidePane(overlay? true : false);
@ -363,6 +375,7 @@ public class HidingPane extends StackPane {
if (distance<expandedSize/2) showHidePane(overlay? true : false);
if (distance>=expandedSize/2) showHidePane(overlay? false : true);
}
//reset the distance
distance=0;
}
@ -370,12 +383,14 @@ public class HidingPane extends StackPane {
pamButton.setOnMouseDragged(new EventHandler<MouseEvent>() {
@Override public void handle(MouseEvent mouseEvent) {
// System.out.println("HidingPane.showButton - setOnMouseDragged");
if (visibleImmediatly) hidePane.setVisible(true);
else hidePane.setVisible(false);
// hideButton.setVisible(true);
/**
* Work out the distance the panel is to be dragged;
*/
double distance = 0;
if (!isHorizontal()){
if (!show) distance=(mouseEvent.getSceneX()-dragX);
else distance=(mouseEvent.getSceneX()-dragX)+sideIndex*expandedSize;
@ -387,26 +402,28 @@ public class HidingPane extends StackPane {
if (!overlay) distance=expandedSize+sideIndex*distance;
}
// if (show && Math.abs(distance)>expandedSize) return;
translatePanel(distance);
HidingPane.this.distance = distance ;
}
});
pamButton.setOnMouseEntered(new EventHandler<MouseEvent>() {
@Override public void handle(MouseEvent mouseEvent) {
// System.out.println("HidingPane.showButton - mouse entered");
pamButton.setOpacity(1.0);
pamButton.setPadding(new Insets(2.,2.,2.,2.));
}
});
pamButton.setOnMouseExited(new EventHandler<MouseEvent>() {
@Override public void handle(MouseEvent mouseEvent) {
// System.out.println("HidingPane.showButton - mouse exited");
if (show) pamButton.setOpacity(showButtonOpacity);
pamButton.setPadding(new Insets(0.,0.,0.,0.));
}
});
// pamButton.setOnMouseEntered(new EventHandler<MouseEvent>() {
// @Override public void handle(MouseEvent mouseEvent) {
//// System.out.println("HidingPane.showButton - mouse entered");
// pamButton.setOpacity(1.0);
// pamButton.setPadding(new Insets(2.,2.,2.,2.));
// }
// });
//
// pamButton.setOnMouseExited(new EventHandler<MouseEvent>() {
// @Override public void handle(MouseEvent mouseEvent) {
//// System.out.println("HidingPane.showButton - mouse exited");
// if (show) pamButton.setOpacity(showButtonOpacity);
// pamButton.setPadding(new Insets(0.,0.,0.,0.));
// }
// });
// pamButton.setOnMouseClicked(new EventHandler<MouseEvent>() {
// @Override public void handle(MouseEvent mouseEvent) {
@ -415,15 +432,15 @@ public class HidingPane extends StackPane {
// }
// });
pamButton.addEventHandler(ActionEvent.ACTION,new EventHandler<ActionEvent>() {
@Override
public void handle(ActionEvent e) {
System.out.println("HidingPane.showButton - action event clicked");
showHidePane(show);
}
});
// pamButton.addEventHandler(ActionEvent.ACTION,new EventHandler<ActionEvent>() {
// @Override
// public void handle(ActionEvent e) {
// System.out.println("HidingPane.showButton - action event clicked");
// showHidePane(show);
// }
// });
if (show) pamButton.setOpacity(showButtonOpacity);
// if (show) pamButton.setOpacity(showButtonOpacity);
return pamButton;
}
@ -601,7 +618,7 @@ public class HidingPane extends StackPane {
showing.setValue(true);
if (visibleImmediatly) hidePane.setVisible(true);
//hideButton.setVisible(true);
//System.out.println("HidingPane: Open Hide Pane");
// System.out.println("HidingPane: Open Hide Pane");
//open the panel
if (timeLineShow.getStatus()==Status.RUNNING) {
//stops the issue with the hiding pane freezing.
@ -613,7 +630,7 @@ public class HidingPane extends StackPane {
else{
showing.setValue(false);
if (!visibleImmediatly) hidePane.setVisible(false);
//System.out.println("HidingPane: Close Hide Pane");
// System.out.println("HidingPane: Close Hide Pane");
//close the panel
timeLineHide.play();
}
@ -638,17 +655,17 @@ public class HidingPane extends StackPane {
}
}
/**
* Called whenever the pin button is pressed.
* @author Jamie Macaulay
*/
class HideButtonPressed implements EventHandler<ActionEvent>{
@Override
public void handle(ActionEvent arg0) {
showHidePane(false);
}
}
// /**
// * Called whenever the pin button is pressed.
// * @author Jamie Macaulay
// */
// class HideButtonPressed implements EventHandler<ActionEvent>{
//
// @Override
// public void handle(ActionEvent arg0) {
// showHidePane(false);
// }
// }
/**
* Get the button which hides the pane.
@ -732,6 +749,15 @@ public class HidingPane extends StackPane {
return this.showing;
}
/**
* Check whether the hiding pane is showing.
* @return true if showing.
*/
public boolean isShowing(){
return this.showing.get();
}
/**
* Get the opacity of the show button when the mouse is outside the button.
* @return the opacity of the show button.

25
src/pamViewFX/fxNodes/utilsFX/PamUtilsFX.java
View File

@ -16,9 +16,9 @@ import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
import javax.swing.JPopupMenu.Separator;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.JSeparator;
import javax.swing.SwingUtilities;
import PamView.ColourArray.ColourArrayType;
import PamView.PamSymbol;
import javafx.animation.KeyFrame;
import javafx.animation.KeyValue;
@ -54,6 +54,26 @@ import pamViewFX.fxNodes.PamSymbolFX;
*/
public class PamUtilsFX {
/**
* Convert an FX based ColourArrayType to Swing. Note that swing options that do not exist in FX and vice versa will return null.
* @param arrayFX - the FX ColourArrayType.
* @return the Swing ColourArrayType;
*/
public static ColourArrayType fxColArray2Swing(pamViewFX.fxNodes.utilsFX.ColourArray.ColourArrayType arrayFX) {
ColourArrayType type = ColourArrayType.valueOf(arrayFX.toString());
return type;
}
/**
* Convert an Swing based ColourArrayType to FX. Note that swing options that do not exist in FX and vice versa will return null.
* @param arraySwing - the Swing ColourArrayType.
* @return the FX ColourArrayType.
*/
public static pamViewFX.fxNodes.utilsFX.ColourArray.ColourArrayType swingColArray2FX(ColourArrayType arraySwing) {
pamViewFX.fxNodes.utilsFX.ColourArray.ColourArrayType type = pamViewFX.fxNodes.utilsFX.ColourArray.ColourArrayType.valueOf(arraySwing.toString());
return type;
}
/**
*
* @param awtColor
@ -650,7 +670,7 @@ public class PamUtilsFX {
int g = (int) Math.round(c.getGreen() * 255);
int b = (int) Math.round(c.getBlue() * 255);
return (r << 16) | (g << 8) | b;
}
}
/**
* Convert an int encoded with a colour to a Color object.
@ -663,6 +683,5 @@ public class PamUtilsFX {
int b = value & 0xFF;
return Color.rgb(r,g,b);
}
}

47
src/pamViewFX/fxPlotPanes/PlotPane.java
View File

@ -1,6 +1,9 @@
package pamViewFX.fxPlotPanes;
import Layout.PamAxis;
import javafx.beans.binding.Bindings;
import javafx.beans.property.SimpleDoubleProperty;
import javafx.beans.value.ObservableValue;
import javafx.geometry.Side;
import javafx.scene.Node;
import javafx.scene.canvas.Canvas;
@ -256,13 +259,31 @@ public class PlotPane extends PamBorderPane {
PamHBox horzHolder=new PamHBox();
Pane leftPane=new Pane();
//create an observable which is the size of the axis pane if the pane is visible and otherwise
//is zero.
ObservableValue<Number> valLeft = Bindings
.when(yAxisLeftPane.visibleProperty())
.then(yAxisLeftPane.widthProperty())
.otherwise(
new SimpleDoubleProperty(0.)
);
//need both min and pref to make binding work properly;
leftPane.prefWidthProperty().bind(yAxisLeftPane.widthProperty());
leftPane.minWidthProperty().bind(yAxisLeftPane.widthProperty());
leftPane.prefWidthProperty().bind(valLeft);
leftPane.minWidthProperty().bind(valLeft);
Pane rightPane=new Pane();
rightPane.prefWidthProperty().bind(yAxisRightPane.widthProperty());
rightPane.minWidthProperty().bind(yAxisRightPane.widthProperty());
ObservableValue<Number> valRight = Bindings
.when(yAxisRightPane.visibleProperty())
.then(yAxisRightPane.widthProperty())
.otherwise(
new SimpleDoubleProperty(0.)
);
rightPane.prefWidthProperty().bind(valRight);
rightPane.minWidthProperty().bind(valRight);
horzHolder.getChildren().addAll(leftPane, axisPane, rightPane);
//axisPane.toFront(); this changes the order of children in a PamHBox.
@ -369,8 +390,8 @@ public class PlotPane extends PamBorderPane {
//holderPane.getChildren().clear();
//HACK- 05/08/2016 have to do this because there is a bug in switching children postions in a border pane.
//casues a duplicate childrne error.
//HACK- 05/08/2016 have to do this because there is a bug in switching children positions in a border pane.
//causes duplicate children error
holderPane.setRight(null);
holderPane.setLeft(null);
holderPane.setTop(null);
@ -385,24 +406,30 @@ public class PlotPane extends PamBorderPane {
else if (topBorder > 0) {
// holderPane.setTopSpace(topBorder);
}
if (bottom) {
holderPane.setBottom(bottomHolder);
}
else if (bottomBorder > 0) {
// holderPane.setBottomSpace(bottomBorder);
}
if (right) {
holderPane.setRight(yAxisRightPane) ;
yAxisRightPane.setVisible(true);
}
else if (rightBorder > 0){
// holderPane.setRightSpace(rightBorder);
else {
yAxisRightPane.setVisible(false);
}
if (left) {
holderPane.setLeft(yAxisLeftPane) ;
yAxisLeftPane.setVisible(true);
}
else if (leftBorder > 0) {
// holderPane.setLeftSpace(leftBorder);
else {
yAxisLeftPane.setVisible(false);
}
holderPane.setCenter(canvasHolder);
//bottomHolder.toBack();

11
src/pamViewFX/symbol/PeakFreqOptionsPane.java
View File

@ -179,6 +179,17 @@ public class PeakFreqOptionsPane extends StandardSymbolModifierPane {
DoubleSpinnerValueFactory spinnerValFact = (DoubleSpinnerValueFactory) maxFreq.getValueFactory();
spinnerValFact.maxProperty().set(getSampleRate() /2);
//set reasonable step sizes
if (getSampleRate()>=10000) {
spinnerValFact.amountToStepByProperty().set(1000.);
}
else if (getSampleRate()>=2000){
spinnerValFact.amountToStepByProperty().set(200.);
}
else {
spinnerValFact.amountToStepByProperty().set(50.);
}
if (symbolOptions.freqLimts==null) {

1
src/rawDeepLearningClassifier/DLControl.java
View File

@ -561,6 +561,7 @@ public class DLControl extends PamControlledUnit implements PamSettings {
* @return the number of classes.
*/
public int getNumClasses() {
if (getDLModel()==null) return 0;
return getDLModel().getNumClasses();
}

4
src/rawDeepLearningClassifier/dataPlotFX/DLPredictionPane.java
View File

@ -19,7 +19,9 @@ import pamViewFX.fxNodes.utilityPanes.PamToggleSwitch;
import rawDeepLearningClassifier.dlClassification.DLClassName;
/*
* Symbol Options for the annotation pane
* Symbol Options for the annotation pane.
*
* @author Jamie Macaulay
*/
public class DLPredictionPane extends PamBorderPane implements TDSettingsPane {

37
src/rawDeepLearningClassifier/dataPlotFX/DLSymbolModifier.java
View File

@ -1,10 +1,14 @@
package rawDeepLearningClassifier.dataPlotFX;
import java.awt.Color;
import java.awt.event.ActionEvent;
import PamController.PamController;
import PamUtils.PamArrayUtils;
import PamView.GeneralProjector;
import PamView.PamSymbolType;
import PamView.dialog.GenericSwingDialog;
import PamView.dialog.PamDialogPanel;
import PamView.symbol.PamSymbolChooser;
import PamView.symbol.SymbolData;
import PamView.symbol.modifier.SymbolModType;
@ -21,10 +25,10 @@ import rawDeepLearningClassifier.logging.DLAnnotationType;
/**
* The DL symbol modifier. Colours symbols by eother the vlaue of the prediction by a user selected class
* or by the class with the highest prediction value.
* The DL symbol modifier. Colours symbols by either the value of the prediction
* by a user selected class or by the class with the highest prediction value.
*
* @author Jamie Macaulay.
* @author Jamie Macaulay.
*
*/
public class DLSymbolModifier extends SymbolModifier {
@ -38,12 +42,12 @@ public class DLSymbolModifier extends SymbolModifier {
/**
* The symbol options pane.
* JavaFX symbol options pane.
*/
private DLSymbolOptionPane optionsPane;
/**
* Rge DL annotation type.
* The DL annotation type.
*/
private DLAnnotationType dlAnnotType;
@ -57,6 +61,11 @@ public class DLSymbolModifier extends SymbolModifier {
private ColourArray colourArray;
/**
* Swing option panel for the symbol chooser.
*/
private DLSymbolOptionPanel optionsPanel;
public DLSymbolModifier(PamSymbolChooser symbolChooser, DLAnnotationType dlAnnotType) {
@ -226,6 +235,7 @@ public class DLSymbolModifier extends SymbolModifier {
* Get the JavaFX symbol options pane that has options for the symbol pane.
* @return the symbol options pane.
*/
@Override
public SymbolModifierPane getOptionsPane() {
if (optionsPane == null) {
optionsPane = new DLSymbolOptionPane(this);
@ -233,6 +243,23 @@ public class DLSymbolModifier extends SymbolModifier {
return optionsPane;
}
@Override
public PamDialogPanel getDialogPanel() {
if (optionsPanel == null) {
optionsPanel = new DLSymbolOptionPanel(this);
}
return optionsPanel;
}
/**
* Default behaviour to show the dialog panel.
* @param e
* @param dialogPanel
*/
protected void showOptionsDialog(ActionEvent e, PamDialogPanel dialogPanel) {
GenericSwingDialog.showDialog(PamController.getMainFrame(), getName() + " options", dialogPanel);
}
public DLAnnotationType getDLAnnotType() {
return dlAnnotType;

8
src/rawDeepLearningClassifier/dataPlotFX/DLSymbolOptionPane.java
View File

@ -29,7 +29,9 @@ import rawDeepLearningClassifier.dlClassification.DLClassName;
/*
* Symbol Options for the annotation pane
* Symbol Options for the annotation pane.
*
* @author Jamie Macaulay
*/
public class DLSymbolOptionPane extends StandardSymbolModifierPane {
@ -390,11 +392,11 @@ public class DLSymbolOptionPane extends StandardSymbolModifierPane {
// b1.setSelected(false);
// b2.setSelected(false);
if (symbolOptions.colTypeSelection == DLSymbolModifierParams.PREDICITON_COL) b1.setSelected(true);
if (symbolOptions.colTypeSelection == DLSymbolModifierParams.PREDICITON_COL) b2.setSelected(true);
if (symbolOptions.colTypeSelection == DLSymbolModifierParams.CLASS_COL) b2.setSelected(true);
setSettingsPane();
symbolOptions.colTypeSelection = b1.isSelected() ? DLSymbolModifierParams.PREDICITON_COL : DLSymbolModifierParams.CLASS_COL;
// symbolOptions.colTypeSelection = b1.isSelected() ? DLSymbolModifierParams.PREDICITON_COL : DLSymbolModifierParams.CLASS_COL;
//set the parameters for colouring by prediction
setPredictionColParams(symbolOptions);

424
src/rawDeepLearningClassifier/dataPlotFX/DLSymbolOptionPanel.java Normal file
View File

@ -0,0 +1,424 @@
package rawDeepLearningClassifier.dataPlotFX;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.AbstractButton;
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
import javax.swing.JColorChooser;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JSlider;
import javax.swing.JToggleButton;
import javax.swing.border.TitledBorder;
import PamView.ColourComboBox;
import PamView.PamAWTUtils;
import PamView.dialog.GenericSwingDialog;
import PamView.dialog.PamButton;
import PamView.dialog.PamDialogPanel;
import PamView.panel.PamPanel;
import PamView.symbol.StandardSymbolOptions;
import PamView.symbol.modifier.SymbolModifier;
import Spectrogram.ColourRangeSlider;
import pamViewFX.fxNodes.utilsFX.ColourArray;
import pamViewFX.fxNodes.utilsFX.PamUtilsFX;
import rawDeepLearningClassifier.dlClassification.DLClassName;
/**
*
* Swing symbol options for the annotation pane.
*
* @author Jamie Macaulay
*/
public class DLSymbolOptionPanel implements PamDialogPanel, ActionListener {
private static final long serialVersionUID = 1L;
private static final double CLASS_NAME_BOX_WIDTH = 130;
private DLSymbolModifier dlSymbolModifier;
/**
* The color range slider for coloring probabilities.
*/
private ColourRangeSlider colorRangeSlider;
/**
* The combo box allowing users to select which class to show.
*/
private JComboBox<String> classNameBox;
private JComboBox<String> classNameBox2;
/**
* Check box allowing users only to show only those detections which have passed binary classification.
*/
private JCheckBox showOnlyBinary;
/**
* Color picker which allows a user to select the gradient for coloring predictions
*/
private ColourComboBox colorComboBox;
/**
* Color picker which allows a user to select color for each class.
*/
private JColorChooser colorPicker;
private boolean initialized = true;
/**
* Pane which holds controls for changing the colour based on prediciton value
*/
private JPanel probPane;
/**
* Pane which holds controls for changing the colour based on the highest prediction value
*/
private JPanel classPane;
private PamPanel holder;
/**
* Button to select how to colour.
*/
private JToggleButton b1, b2;
private PamPanel mainPanel;
private int[] classColours;
private AbstractButton colourButton;
public DLSymbolOptionPanel(SymbolModifier symbolModifer) {
this.dlSymbolModifier = (DLSymbolModifier) symbolModifer;
probPane = createProbPane();
probPane.setBorder(new TitledBorder("Colour by prediction value"));
classPane = createClassPane();
classPane.setBorder(new TitledBorder("Colour by class"));
b1 = new JToggleButton("Prediction");
b1.setPreferredSize(new Dimension(100, 25)); // Set preferred size
b2 = new JToggleButton("Class");
b2.setPreferredSize(new Dimension(100, 25));
ButtonGroup buttonGroup = new ButtonGroup(); // Group toggle buttons
buttonGroup.add(b1);
buttonGroup.add(b2);
b1.addActionListener(this);
b2.addActionListener(this);
JPanel segmentedButtonPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
segmentedButtonPanel.add(b1);
segmentedButtonPanel.add(b2);
holder = new PamPanel();
holder.setLayout(new BorderLayout());
holder.add(new JLabel("Hello"), BorderLayout.NORTH);
mainPanel = new PamPanel();
mainPanel.setLayout(new BorderLayout());
mainPanel.add(segmentedButtonPanel, BorderLayout.NORTH);
mainPanel.add(holder, BorderLayout.CENTER);
mainPanel.add(showOnlyBinary = new JCheckBox("Show only binary classification"), BorderLayout.SOUTH);
setSettingsPane();
initialized = true;
}
@Override
public JComponent getDialogComponent() {
return mainPanel;
}
@Override
public void setParams() {
//get the symbool options
DLSymbolModifierParams symbolOptions = dlSymbolModifier.getSymbolModifierParams();
// b1.setSelected(false);
// b2.setSelected(false);
if (symbolOptions.colTypeSelection == DLSymbolModifierParams.PREDICITON_COL) b1.setSelected(true);
if (symbolOptions.colTypeSelection == DLSymbolModifierParams.CLASS_COL) b2.setSelected(true);
setSettingsPane();
//set the parameters for colouring by prediction
setPredictionColParams(symbolOptions);
//set the class colour parameters
setClassColParams(symbolOptions);
//set the selected.
showOnlyBinary.setSelected(symbolOptions.showOnlyBinary);
setSettingsPane();
}
private int checkClassNamesBox(DLSymbolModifierParams symbolOptions, JComboBox<String> classNameBox) {
DLClassName[] classNames = dlSymbolModifier.getDLAnnotType().getDlControl().getDLModel().getClassNames();
// for (int i =0; i<classNames.length; i++) {
// System.out.println("DLSymbolOptionsPane: classNames: " + i + " " + classNames[i].className);
// }
int nClass = dlSymbolModifier.getDLAnnotType().getDlControl().getDLModel().getNumClasses();
classNameBox.removeAllItems();
for (int i=0; i<nClass; i++) {
if (classNames!=null && classNames.length>i) {
classNameBox.addItem(classNames[i].className);
}
else {
classNameBox.addItem("Class: " + i);
}
}
return nClass;
}
/**
* Set parameters for controls to change the colour gradient based on prediction.
* @param symbolOptions - the symbol options
*/
private void setPredictionColParams(DLSymbolModifierParams symbolOptions) {
//now set frequency parameters
colorRangeSlider.setValue((int) symbolOptions.clims[0]*100);
colorRangeSlider.setUpperValue((int) symbolOptions.clims[1]*100);
// colorRangeSlider.setColourArrayType( symbolOptions.colArray);
colorRangeSlider.setColourMap(PamUtilsFX.fxColArray2Swing(symbolOptions.colArray));
int nClass = checkClassNamesBox( symbolOptions, classNameBox);
symbolOptions.classIndex = Math.min(symbolOptions.classIndex, nClass-1);
classNameBox.setSelectedIndex(Math.max(symbolOptions.classIndex, 0));
//color box.
colorComboBox.setSelectedColourMap(PamUtilsFX.fxColArray2Swing(symbolOptions.colArray));
}
/**
* Set parameters for controls to change the colour gradient based on prediction.
* @param symbolOptions - the symbol options
*/
private void setClassColParams(DLSymbolModifierParams symbolOptions) {
//create a temporary array to save different class colours in - this needs to be
//before other params are set.
this.classColours = symbolOptions.classColors;
int nClass = checkClassNamesBox( symbolOptions, classNameBox2);
symbolOptions.classIndex = Math.min(symbolOptions.classIndex, nClass-1);
classNameBox2.setSelectedIndex(Math.max(symbolOptions.classIndex2, 0));
// int index = symbolOptions.classIndex2>=0 ? symbolOptions.classIndex2 : 0;
if (symbolOptions.classColors==null) {
symbolOptions.setDefaultClassColors(nClass);
}
if (classNameBox2.getSelectedIndex()>=0) {
colourButton.setBackground(PamAWTUtils.intToColor(classColours[classNameBox2.getSelectedIndex()]));
colourButton.repaint();
}
// //set the correct colour
// colorPicker.setColor(symbolOptions.classColors[index]);
}
/**
* get parameters for colouring by class.
* @param symbolOptions - the symbol options.
* @return
*/
public DLSymbolModifierParams getClassColParams(DLSymbolModifierParams symbolOptions ) {
// int index = classNameBox2.getSelectedIndex()>=0 ? classNameBox2.getSelectedIndex():0;
symbolOptions.classColors = classColours;
symbolOptions.classIndex2 = classNameBox2.getSelectedIndex();
return symbolOptions;
}
/**
*
* @param symbolOptions
* @return
*/
public DLSymbolModifierParams getPredictionColParams(DLSymbolModifierParams symbolOptions ) {
symbolOptions.clims=new double[] {((double) colorRangeSlider.getValue())/100., ((double) colorRangeSlider.getUpperValue())/100.};
symbolOptions.colArray = PamUtilsFX.swingColArray2FX(this.colorComboBox.getSelectedColourMap());
symbolOptions.classIndex = classNameBox.getSelectedIndex();
return symbolOptions;
}
@Override
public boolean getParams() {
//bit messy but works
DLSymbolModifierParams symbolOptions = dlSymbolModifier.getSymbolModifierParams().clone();
//need to check this here.
//checkClassNamesBox(symbolOptions);
if (b1.isSelected()) symbolOptions.colTypeSelection = DLSymbolModifierParams.PREDICITON_COL;
if (b2.isSelected()) symbolOptions.colTypeSelection = DLSymbolModifierParams.CLASS_COL;
//get parameters for colouring
symbolOptions = getClassColParams(symbolOptions);
//get parameters for colouring by prediction value
symbolOptions = getPredictionColParams(symbolOptions) ;
symbolOptions.showOnlyBinary = showOnlyBinary.isSelected();
dlSymbolModifier.checkColourArray();
//set the paratmers.
dlSymbolModifier.setSymbolModifierParams(symbolOptions);
return true;
}
private void setSettingsPane() {
holder.removeAll();
//holder.setLayout(new BorderLayout());
holder.validate();
if (b1.isSelected()) {
holder.add(probPane, BorderLayout.CENTER);
} else if (b2.isSelected()) {
holder.add(classPane, BorderLayout.CENTER);
}
holder.validate();
mainPanel.validate();
if (mainPanel.getRootPane()!=null) {
//pack the dialog because it is a different size
((GenericSwingDialog) mainPanel.getRootPane().getParent()).pack();
}
}
private JPanel createClassPane() {
classNameBox2 = new JComboBox<>();
classNameBox2.addActionListener((action)->{
//make sure the setting button shows the colour
if (classNameBox2.getSelectedIndex()>=0) {
colourButton.setBackground(PamAWTUtils.intToColor(classColours[classNameBox2.getSelectedIndex()]));
}
setSettingsPane();
});
classNameBox2.setPreferredSize(new Dimension((int) CLASS_NAME_BOX_WIDTH, 25));
// colorPicker.setPreferredSize(new Dimension(60, 25));
colourButton = new PamButton("Color");
colourButton.addActionListener((action)->{
Color color = JColorChooser.showDialog(colourButton, "Pick colour for class", PamAWTUtils.intToColor(classColours[classNameBox2.getSelectedIndex()]));
if (color!=null) {
colourButton.setBackground(color);
// colourButton.setForeground(color);
classColours[classNameBox2.getSelectedIndex()]=PamAWTUtils.colorToInt(color);
}
});
JPanel classHolder = new JPanel();
FlowLayout flowLayout = new FlowLayout();
classHolder.setLayout(flowLayout);
classHolder.add(classNameBox2);
classHolder.add(colourButton);
return classHolder;
}
private PamPanel createProbPane() {
PamPanel holder = new PamPanel();
holder.setLayout(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
c.gridx = 0;
c.gridy = 0;
holder.add(new JLabel("Select class"), c);
c.gridx++;
classNameBox = new JComboBox<String>();
holder.add(classNameBox, c);
c.gridx = 0;
c.gridwidth = 1;
c.gridy++;
holder.add(new JLabel("Color map"), c);
c.gridx++;
colorComboBox = new ColourComboBox();
colorComboBox.addActionListener((action)->{
colorRangeSlider.setColourMap(colorComboBox.getSelectedColourMap());
colorRangeSlider.repaint();
});
holder.add(colorComboBox, c);
c.gridx = 0;
c.gridy++;
c.gridwidth =2;
colorRangeSlider = new ColourRangeSlider(0, 100, JSlider.HORIZONTAL); // Min 0, Max 1 for probabilities
colorRangeSlider.setPaintTicks(true);
colorRangeSlider.setMinorTickSpacing(20);
holder.add(colorRangeSlider, c);
return holder;
}
@Override
public void actionPerformed(ActionEvent e) {
setSettingsPane();
}
}

11
src/rawDeepLearningClassifier/dataSelector/DLDataFilter.java
View File

@ -1,5 +1,6 @@
package rawDeepLearningClassifier.dataSelector;
import PamView.dialog.PamDialogPanel;
import PamguardMVC.PamDataUnit;
import PamguardMVC.dataSelector.DataSelectParams;
import pamViewFX.fxSettingsPanes.DynamicSettingsPane;
@ -33,10 +34,16 @@ public interface DLDataFilter {
public void setParams(DataSelectParams params);
/**
* Settings controls for this filter.
* @return the cotnrols for this filter.
* Settings controls for the deep learning filter.
* @return the controls for this filter.
*/
public DynamicSettingsPane<DataSelectParams> getSettingsPane();
/**
* Swing settings controls for the data deep learning filter.
* @return Swing dialog for the settings
*/
public PamDialogPanel getSettingsPanel();
}

15
src/rawDeepLearningClassifier/dataSelector/DLPredictionFilter.java
View File

@ -1,6 +1,7 @@
package rawDeepLearningClassifier.dataSelector;
import PamView.dialog.PamDialogPanel;
import PamguardMVC.PamDataUnit;
import PamguardMVC.dataSelector.DataSelectParams;
import pamViewFX.fxSettingsPanes.DynamicSettingsPane;
@ -27,7 +28,9 @@ public class DLPredictionFilter implements DLDataFilter {
*/
private DLPredictionFilterParams filterParams = new DLPredictionFilterParams();
private DLPredictonPane dlPredictonPane;
private DLPredictonPane dlPredictonPane;
private DLPredictionPanel dlPredictonPanel;
public DLPredictionFilter(DLControl dlcontrol) {
this.dlcontrol = dlcontrol;
@ -62,7 +65,7 @@ public class DLPredictionFilter implements DLDataFilter {
}
@Override
public DataSelectParams getParams() {
public DLPredictionFilterParams getParams() {
checkParamsClass() ;
return filterParams;
}
@ -96,6 +99,14 @@ public class DLPredictionFilter implements DLDataFilter {
}
return dlPredictonPane;
}
@Override
public PamDialogPanel getSettingsPanel() {
if (dlPredictonPanel ==null) {
dlPredictonPanel = new DLPredictionPanel(this);
}
return dlPredictonPanel;
}
public DLControl getDLControl() {

183
src/rawDeepLearningClassifier/dataSelector/DLPredictionPanel.java Normal file
View File

@ -0,0 +1,183 @@
package rawDeepLearningClassifier.dataSelector;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Label;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
import javax.swing.JSpinner;
import javax.swing.JToggleButton;
import javax.swing.SpinnerNumberModel;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import org.kordamp.ikonli.materialdesign2.MaterialDesignL;
import org.kordamp.ikonli.swing.FontIcon;
import PamView.dialog.PamDialogPanel;
import PamView.dialog.PamGridBagContraints;
import PamView.panel.PamPanel;
import rawDeepLearningClassifier.dlClassification.DLClassName;
/**
* Swing panel for Deep learning predicitons.
*/
public class DLPredictionPanel implements PamDialogPanel {
private DLPredictionFilter predicitonFilter;
private PamPanel contentPanel;
private JCheckBox[] enableClass;
private JSpinner[] spinnerClass;
private JToggleButton lockButton;
public DLPredictionPanel(DLPredictionFilter dlPredictionFilter) {
super();
this.predicitonFilter = dlPredictionFilter;
contentPanel = new PamPanel();
contentPanel.setLayout(new GridBagLayout());
lockButton = new JToggleButton();
FontIcon iconlock = FontIcon.of(MaterialDesignL.LOCK);
iconlock.setIconSize(20);
iconlock.setIconColor(Color.DARK_GRAY);
FontIcon iconlockopen = FontIcon.of(MaterialDesignL.LOCK_OPEN);
iconlockopen.setIconSize(20);
iconlockopen.setIconColor(Color.DARK_GRAY);
lockButton.setIcon(iconlockopen);
lockButton.addActionListener((action)->{
if (lockButton.isSelected()) {
lockButton.setIcon(iconlock);
}
else {
lockButton.setIcon(iconlockopen);
}
lockButton.validate();
});
}
@Override
public JComponent getDialogComponent() {
return contentPanel;
}
@Override
public void setParams() {
DLPredictionFilterParams params = predicitonFilter.getParams();
// TODO Auto-generated method stub
setClassPane(params);
for (int i=0; i<params.classSelect.length ; i++) {
//set the correct params
enableClass[i].setSelected(params.classSelect[i]);
spinnerClass[i].setValue(params.minClassPredicton[i]);
}
}
private void setClassPane(DLPredictionFilterParams input) {
DLClassName[] classNames = predicitonFilter.getDLControl().getDLModel().getClassNames();
contentPanel.removeAll();
enableClass = new JCheckBox[input.classSelect.length];
spinnerClass = new JSpinner[input.classSelect.length];
GridBagConstraints c = new PamGridBagContraints();
c.ipadx =5;
c.gridwidth=2;
contentPanel.add(new Label("Min. prediciton for each class"), c);
c.gridwidth=1;
c.gridy++;
for (int i=0; i<input.classSelect.length ; i++) {
//create the row
c.gridx = 0;
enableClass[i] = new JCheckBox(classNames[i].className);
final int ii = i;
enableClass[i].addActionListener((action)->{
spinnerClass[ii].setEnabled(enableClass[ii].isSelected());
});
enableClass[i].setToolTipText(classNames[i].className);
contentPanel.add(enableClass[i], c);
c.gridx = 1;
spinnerClass[i] = new JSpinner(new SpinnerNumberModel(0., 0., 1., 0.05));
Dimension prefSize = spinnerClass[i].getPreferredSize();
prefSize = new Dimension(60, prefSize.height);
spinnerClass[i] .setPreferredSize(prefSize);
spinnerClass[i].addChangeListener(new ChangeListener() {
@Override
public void stateChanged(ChangeEvent e) {
if (lockButton.isSelected()) {
for (int j=0; j<spinnerClass.length ; j++) {
if (j!=ii) {
spinnerClass[j].setValue(spinnerClass[ii].getValue());
}
}
}
}
});
spinnerClass[i].setToolTipText(classNames[i].className);
contentPanel.add(spinnerClass[i], c);
if (i==0 && input.classSelect.length>1) {
//set a lock button to
c.gridx=2;
contentPanel.add(lockButton, c);
//make the lock button the same height as the spinner
Dimension prefSizeB = lockButton.getPreferredSize();
lockButton.setPreferredSize(new Dimension(prefSizeB.width, prefSize.height));
}
c.gridy++;
}
contentPanel.validate();
}
@Override
public boolean getParams() {
DLPredictionFilterParams currParams = predicitonFilter.getParams();
for (int i=0; i<spinnerClass.length ; i++) {
currParams.classSelect[i] = enableClass[i].isSelected();
currParams.minClassPredicton[i] = (double) spinnerClass[i].getValue();
}
predicitonFilter.setParams(currParams);
return true;
}
}

12
src/rawDeepLearningClassifier/dataSelector/DLPredictonPane.java
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@ -9,14 +9,11 @@ import javafx.scene.control.Slider;
import javafx.scene.control.ToggleButton;
import javafx.scene.control.Tooltip;
import javafx.scene.layout.Priority;
import javafx.scene.text.TextAlignment;
import pamViewFX.PamGuiManagerFX;
import pamViewFX.fxGlyphs.PamGlyphDude;
import pamViewFX.fxNodes.PamBorderPane;
import pamViewFX.fxNodes.PamHBox;
import pamViewFX.fxNodes.PamSpinner;
import pamViewFX.fxNodes.PamVBox;
import pamViewFX.fxNodes.sliders.PamSlider;
import pamViewFX.fxSettingsPanes.DynamicSettingsPane;
import rawDeepLearningClassifier.dlClassification.DLClassName;
@ -47,7 +44,7 @@ public class DLPredictonPane extends DynamicSettingsPane<DLPredictionFilterParam
PamBorderPane topPane = new PamBorderPane();
Label label = new Label("Select classes to show");
Label label = new Label("Show classes above min. prediction");
PamBorderPane.setAlignment(label, Pos.BOTTOM_LEFT);
// label.setTextAlignment(TextAlignment.LEFT);
label.setAlignment(Pos.BOTTOM_LEFT);
@ -87,6 +84,8 @@ public class DLPredictonPane extends DynamicSettingsPane<DLPredictionFilterParam
Label valueLabel;
private boolean enableListener = true;
ClassDataSelector(String classType, int index) {
enable = new CheckBox(classType);
@ -110,10 +109,13 @@ public class DLPredictonPane extends DynamicSettingsPane<DLPredictionFilterParam
//if the lock button has been sleected then change all the sliders
//so that they are the same value as this slide (unless the class is disabled)
if (toggelButton.isSelected()) {
if (toggelButton.isSelected() && enableListener) {
for (int i=0; i<classPanes.length; i++) {
if (classPanes[i].enable.isSelected() && i!=index) {
classPanes[i].enableListener = false; //prevent needless calls to notify settings
classPanes[i].slider.setValue(newval.doubleValue());
classPanes[i].enableListener = true;
}
};
}

78
src/rawDeepLearningClassifier/dataSelector/DLSelectPanel.java
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@ -1,35 +1,83 @@
package rawDeepLearningClassifier.dataSelector;
import java.awt.BorderLayout;
import javax.swing.JComponent;
import javax.swing.JLabel;
import PamView.dialog.PamDialogPanel;
import PamView.panel.PamPanel;
import javafx.scene.Node;
import pamViewFX.fxNodes.PamBorderPane;
/**
* Swing panel for the deep learning data selector.
*/
public class DLSelectPanel implements PamDialogPanel {
private PamPanel mainPanel;
private DLDataSelector dlDataSelector;
private int currentIndex = 0;
public DLSelectPanel(DLDataSelector dlDataSelector) {
// TODO Auto-generated constructor stub
}
@Override
public JComponent getDialogComponent() {
// TODO Auto-generated method stub
return new JLabel("Hello Annotation DL");
}
@Override
public void setParams() {
// TODO Auto-generated method stub
super();
this.dlDataSelector=dlDataSelector;
mainPanel = new PamPanel();
mainPanel.setLayout(new BorderLayout());
}
@Override
public boolean getParams() {
// TODO Auto-generated method stub
return true;
public JComponent getDialogComponent() {
return mainPanel;
}
private void setDataFilterPane(int index) {
DLDataFilter dlFilter = dlDataSelector.getDataSelectors().get(index);
mainPanel.add(dlFilter.getSettingsPanel().getDialogComponent(), BorderLayout.CENTER);
}
@Override
public void setParams() {
DLDataSelectorParams currParams = dlDataSelector.getParams();
this.currentIndex = currParams.dataSelectorIndex;
//set the stored paramters for the deep learning filter
dlDataSelector.getDataSelectors().get(currentIndex).setParams(currParams.dataSelectorParams[currentIndex]);
//set the paramters in the dialog - note the dialog will have areference ot the filter and so can access the r
//set params above.
dlDataSelector.getDataSelectors().get(currentIndex).getSettingsPanel().setParams();
//set the
setDataFilterPane(currentIndex);
}
@Override
public boolean getParams() {
DLDataSelectorParams currParams = dlDataSelector.getParams();
//dialog has a reference to the data filter and will change params.
boolean dataFilterOK = dlDataSelector.getDataSelectors().get(currentIndex).getSettingsPanel().getParams();
if (dataFilterOK) {
//TODO - maybe should grab settings from all filters or just the selected one?
currParams.dataSelectorParams[currentIndex] = dlDataSelector.getDataSelectors().get(currentIndex).getParams();
dlDataSelector.setParams(currParams);
return true;
}
else {
return false;
}
}
}

26
src/rawDeepLearningClassifier/deep_learning_help.md
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@ -106,15 +106,15 @@ If using a deep learning model from a supported framework then all transforms ar
_An AnimalSpot, Ketos or other supported deep learning model will automatically create a list of transforms with the appropriate settings. These is no need to use the advanced pane but it is there in case users wish to change transform settings for some reason_
### Default Models
### Exanmple Models
Default models are selectable from the menu button in the Deep Learning Pane. Default models are deep learning classifiers which are open source, known to be effective and have have been published in open access academic litrature; they are downloaded directly from a GitHub repository and then all associated settings are automtically applied. The default model selection pane also contains hyperlinks to the papers descirbing each model which will take users directly to the relvent website.
Example models are selectable from the menu button in the Deep Learning Pane. Default models are deep learning classifiers which are open source, known to be effective and have have been published in open access academic litrature; they are downloaded directly from a GitHub repository and then all associated settings are automtically applied. The default model selection pane also contains hyperlinks to the papers descirbing each model which will take users directly to the relvent website.
<p align="center">
<img width="550" height="700" src = "resources/default_settings_humpback_1.png">
</p>
_Default models can be downloaded. Default models are models which are published, open and have been known to work well amongst the bioacoustics community. More will be added to PAMGaurd over time. If you you would like your model to become a defualt model then drop PAMGuard support an email._
_Example models can be downloaded. Example models are models which are published, open and have been known to work well amongst the bioacoustics community. More will be added to PAMGaurd over time. If you you would like your model to become a defualt model then drop PAMGuard support an email._
## Running
@ -144,6 +144,26 @@ _An example click detection module output coloured by deep learning annotations.
Other displays also show outputs from the deep learning module. Hovering over data units in the click display will, for example, show deep learning prediction values. The spectrogram will also show deep learning detections as translucent blue boxes (these must be selected in the right click menu).
### Symbol Manager
The deep learning classifier has a symbol manager that is used throughtout different PAMGuard displays. The symbol manager can either display deep learning detections by the prediction values of a particular class or colour the output class with the highest prediciton class. Colouring by a prediction value requires the user to select which output class they wish to display - all detections are then coloured by the output prediction values for that particular class via a selectable colour map. If colour by class is selected then each detection is coloured by the class with the maximum prediction value. The colours for each class are selectable.
<p align="center">
<img width="429" height="150" src = "resources/deep_learning_symbol_manager.png">
</p>
_The options for the deep learning symbol manager_
### Data selector
The deep learning classifier has a data selector which is utilsied thorughout PAMGuard (for example for exporting detections, generating clips, showing on displays). The data selector allows users to filter detections based on a minimum prediciton values for different output classes. Classifiers with multiple classes can have different minimum predicitons values assigned to each class. The user interface allows user to use a slider to dynimically change the minimum prediciton value. The lock button clamps the minimum prediction values of all enabled output classes together.
<p align="center">
<img width="190" height="170" src = "resources/deep_learning_data_selector.png">
</p>
_The options for the deep learning data selector_
### MATLAB
The easiest way to export to MATLAB is to select the desired units in the time base display, right click and select the MATLAB icon. Data units will be exported to a .mat file as list of structures which is then saved to the clipboard. This file can be saved and then dragged into MATLAB to open.

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33
src/test/export/ExportTest.java Normal file
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@ -0,0 +1,33 @@
package test.export;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
import clickDetector.ClickDetection;
/**
* Tests for export functionality.
*/
public class ExportTest {
/**
* Test exporting detections to mat files.
*/
@Test
public void matFileTest() {
System.out.println("Matched template classifier test: match corr");
//create a list of click detections.
ClickDetection clickDetection = new ClickDetection(0, 0, 0, null, null, 0);
//now open the mat file and check that we have all the data from these click detections.
}
}

5
src/test/matchedTemplateClassifier/MatchedTemplateClassifierTest.java
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@ -83,8 +83,9 @@ public class MatchedTemplateClassifierTest {
}
/**
* Test the match correlation algorithm combined with click length algorithm. Here we awant to test that
* a long waveform
* Test the match correlation algorithm combined with click length algorithm. Here we want to test that
* a long waveform can be processed properly - i.e the peak of the click can be found and cross correlation performed
* on a shortened section.
*/
@Test
public void testMatchCorrLen() {

3
src/tethys/dbxml/DBXMLConnect.java
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@ -150,8 +150,7 @@ public class DBXMLConnect {
*/
public boolean postAndLog(Object nilusObject, String documentName) throws TethysException
{
boolean ok = NilusChecker.warnEmptyFields(tethysControl.getGuiFrame(), nilusObject);
// boolean ok = NilusChecker.warnEmptyFields(tethysControl.getGuiFrame(), nilusObject);
TethysException e = null;
boolean success = false;

3
src/whistlesAndMoans/dataSelector/WMDDataSelector.java
View File

@ -39,6 +39,9 @@ public class WMDDataSelector extends DataSelector {
@Override
public double scoreData(PamDataUnit pamDataUnit) {
if (getParams().getCombinationFlag() == DataSelectParams.DATA_SELECT_DISABLE) {
return 1;
}
ConnectedRegionDataUnit crDataUnit = (ConnectedRegionDataUnit) pamDataUnit;
return (wantWhistle(crDataUnit) ? 1: 0);
}