Commit Graph

266 Commits

Author SHA1 Message Date
Douglas Gillespie
62b020b320 Add a new offlinefileslist function 2022-05-14 06:52:20 +01:00
Douglas Gillespie
3a9a5311aa Update .gitignore 2022-05-02 19:46:42 +01:00
Douglas Gillespie
9f998165ee
Updates to support ContactCollator plugin (#33)
* Change synchronization on RawDataTransforms soit uses the owner data
holder, not itself for synchronization. Otherwise you get thread locks.

* fix problem in SummaryComand

* Update command line options

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

* Update command line options

* Update DecimatorParams.java

* couple of updates to support new contact collator plugin

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

* FLAC Speed

Improve flac speed

* Update .gitignore

* Update .gitignore

* Updates to support new features in Contact Collator

* Small update to RawDatautils to handle null data
2022-05-02 19:40:24 +01:00
Douglas Gillespie
a0900a667e Small update to RawDatautils to handle null data 2022-05-02 19:38:14 +01:00
Douglas Gillespie
f9787a9633
Merge branch 'PAMGuard:main' into main 2022-04-28 13:48:41 +01:00
Jamie Mac
d85d9078a1
Bug fixes (#31)
* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Screenshots

* Updates and bug fixes to click train detector and CPOD importer

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Updates and bug fixes to click train detector and CPOD importer

* Fix standard classifier JSON logging

* Merge fixes to click train detector

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Screenshots

* Updates and bug fixes to click train detector and CPOD importer

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Screenshots

* Updates and bug fixes to click train detector and CPOD importer

* Fix standard classifier JSON logging

* Google humpback whale deep learning classifier

Google's humpback whale deep learning classifier can now be imported.
Updated TDisplayFX to make the data selection panes cleaner and clearer.
Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour.

* Bug fix to UI

* Updates to FX GUI

* Bug fixes

Click train detector now registers click train if there are no longer any click detections for a significant period of time.

Jitter in wrap spectrogram for TDisplayFX fixed

Deep learning module compatible with bearing localiser

Updates to FX GUI
2022-04-28 10:52:03 +01:00
Douglas Gillespie
c4ee5f389b
Contact Collator Updated (#30)
* Change synchronization on RawDataTransforms soit uses the owner data
holder, not itself for synchronization. Otherwise you get thread locks.

* fix problem in SummaryComand

* Update command line options

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

* Update command line options

* Update DecimatorParams.java

* couple of updates to support new contact collator plugin

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

* FLAC Speed

Improve flac speed

* Update .gitignore

* Update .gitignore

* Updates to support new features in Contact Collator
2022-04-27 09:34:27 +01:00
Douglas Gillespie
7a0b85f015 Merge branch 'main' of https://github.com/douggillespie/PAMGuard 2022-04-27 09:28:54 +01:00
Douglas Gillespie
50e3e86784 Updates to support new features in Contact Collator 2022-04-27 09:27:46 +01:00
Douglas Gillespie
35617c2571 Update .gitignore 2022-04-27 09:18:28 +01:00
Douglas Gillespie
f8cf8a72cb Update .gitignore 2022-04-27 09:17:00 +01:00
Douglas Gillespie
cba66b4ec9 FLAC Speed
Improve flac speed
2022-04-27 09:14:00 +01:00
Douglas Gillespie
2842143613 Sorting out sample rate info in clip display to support Contact Collator
plugin
2022-04-26 13:29:50 +01:00
Douglas Gillespie
a62cff4f11 couple of updates to support new contact collator plugin 2022-04-22 16:22:55 +01:00
Douglas Gillespie
add1be56ab Merge branch 'main' of https://github.com/douggillespie/PAMGuard 2022-04-20 12:35:04 +01:00
Douglas Gillespie
bc7e5b189c Update DecimatorParams.java 2022-04-20 12:34:50 +01:00
Douglas Gillespie
bfd93cb623 Update command line options 2022-04-20 12:34:35 +01:00
Douglas Gillespie
db28beb6da Change synchronization on RawDataTransforms soit uses the owner data
holder, not itself for synchronization. Otherwise you get thread locks.
2022-04-20 12:34:12 +01:00
Jamie Mac
da387005a3
Click train, CPOD, Time Base Display, Ishmael updates and Google deep learning integration (#28)
* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Create click_train_help.md

* Update click_train_help.md

* Screenshots

* Update click_train_help.md

* Update click_train_help.md

* Update click_train_help.md

* More screenshots

* Add screenshots

* Update click_train_help.md

* Add classifier screenshot

* Update click_train_help.md

* Update click_train_help.md

* Update click_train_help.md

* Updates and bug fixes to click train detector and CPOD importer

* Update click_train_help.md

* Update POM with latest jdl4pam

* Add screenshots for click train detector help

* Screenshots

* Update click_train_help.md

* Defult option for CPOD and porpoise to click train detector.

Also a minor

* Update pom.xml

* Bug fix for raw spectrogram in TDDisplayFX

* Update KetosClassifier.java

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Create click_train_help.md

* Update click_train_help.md

* Screenshots

* Update click_train_help.md

* More screenshots

* Update click_train_help.md

* Update click_train_help.md

* Add screenshots

* Add classifier screenshot

* Update click_train_help.md

* Updates and bug fixes to click train detector and CPOD importer

* Update click_train_help.md

* Update click_train_help.md

* Update click_train_help.md

* Update click_train_help.md

* Add screenshots for click train detector help

* Screenshots

* Update click_train_help.md

* Defult option for CPOD and porpoise to click train detector.

Also a minor

* Bug fix for raw spectrogram in TDDisplayFX

* Update KetosClassifier.java

* Fix standard classifier JSON logging

* Update click_train_help.md

* Fixed bug in sweep classifier when using SoundTrap click detections

* Added some colour averaging in the TFDisplayFX spectrgoram

* Bug fix for rainbow click bearings

Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup

* Google humpback whale deep learning classifier

Google's humpback whale deep learning classifier can now be imported.
Updated TDisplayFX to make the data selection panes cleaner and clearer.
Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour.

* Updated the prediction plots on time display

Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend.

* Updates to TDisplayFX

yFIshmael now owrks with TDisplayFX
TDisplayFX UI changes to make simpler.
Some abstraction for drawing lines on TDisplayFX

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Create click_train_help.md

* Update click_train_help.md

* Screenshots

* Update click_train_help.md

* More screenshots

* Update click_train_help.md

* Update click_train_help.md

* Add screenshots

* Add classifier screenshot

* Update click_train_help.md

* Updates and bug fixes to click train detector and CPOD importer

* Update click_train_help.md

* Update click_train_help.md

* Update click_train_help.md

* Update click_train_help.md

* Add screenshots for click train detector help

* Screenshots

* Update click_train_help.md

* Defult option for CPOD and porpoise to click train detector.

Also a minor

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Create click_train_help.md

* Update click_train_help.md

* Update click_train_help.md

* Updates and bug fixes to click train detector and CPOD importer

* Bug fix for raw spectrogram in TDDisplayFX

* Update KetosClassifier.java

* Fix standard classifier JSON logging

* Fixed bug in sweep classifier when using SoundTrap click detections

* Added some colour averaging in the TFDisplayFX spectrgoram

* Bug fix for rainbow click bearings

Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup

* Google humpback whale deep learning classifier

Google's humpback whale deep learning classifier can now be imported.
Updated TDisplayFX to make the data selection panes cleaner and clearer.
Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour.

* Updated the prediction plots on time display

Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend.

* Updates to TDisplayFX

yFIshmael now owrks with TDisplayFX
TDisplayFX UI changes to make simpler.
Some abstraction for drawing lines on TDisplayFX

* Merge fixes to click train detector

* Bug fix to UI
2022-04-20 12:27:21 +01:00
Douglas Gillespie
81fd9f5481 Update command line options 2022-04-13 17:03:44 +01:00
Douglas Gillespie
54f789eead Merge branch 'main' of https://github.com/douggillespie/PAMGuard 2022-03-29 14:48:48 +01:00
Douglas Gillespie
07752f3dd3 push correct jdk in classpath 2022-03-29 14:47:38 +01:00
Douglas Gillespie
db32b280d1 fix problem in SummaryComand 2022-03-29 14:25:31 +01:00
Douglas Gillespie
a13522f69e Fix error in summarycommand 2022-03-29 14:07:24 +01:00
Douglas Gillespie
f1d0268ec5
Change synchronization on RawDataTransforms soit uses the owner data (#26)
holder, not itself for synchronization. Otherwise you get thread locks.
2022-03-29 11:42:05 +01:00
Douglas Gillespie
7fefb38620 Change synchronization on RawDataTransforms soit uses the owner data
holder, not itself for synchronization. Otherwise you get thread locks.
2022-03-29 11:39:26 +01:00
Douglas Gillespie
aec4a44213
Merge pull request #2 from PAMGuard/main
merging with dev branch
2022-03-25 11:18:13 +00:00
Douglas Gillespie
d49d204a8a
Merge branch 'main' into main 2022-03-25 11:18:05 +00:00
Douglas Gillespie
f365695b4f Feature fix for reading flac files offline, where it was getting a bit
confused about load start times and attempting to reload for too much
data, causing out of memory errors.
2022-03-22 11:46:30 +00:00
Douglas Gillespie
8d6aeb735a
updates to PAMGuard command line options and UDP control (#25)
* Fix network sender since it was hopelessly out of date and did not send
data in the correct format. OK now, though only tested on NARW.

* Mods to support command line and Network control of PAMGuard and to
retrieve summary information from some modules.
2022-03-18 14:52:47 +00:00
Douglas Gillespie
f48579ff22
Improvements to udp PAMGuard control (#24)
* comment changes in graphics

* Mods to enable getting and setting parameters for individual modules via
xml i/o via udp commands.
2022-03-15 14:26:38 +00:00
Douglas Gillespie
7ee8bdbe2c Mods to enable getting and setting parameters for individual modules via
xml i/o via udp commands.
2022-03-15 14:22:48 +00:00
Douglas Gillespie
c539943680 comment changes in graphics 2022-03-14 14:44:14 +00:00
Douglas Gillespie
e3f83071ae
Merge pull request #1 from PAMGuard/main
Fixes to NoGUI, Network send and spectrogram graphics.  (#23)
2022-02-27 14:20:31 +00:00
Douglas Gillespie
178275939c
Merge branch 'main' into main 2022-02-27 14:20:07 +00:00
Douglas Gillespie
ff048eed9f
Fixes to NoGUI, Network send and spectrogram graphics. (#23)
* Update .project

* Terminal commands

* Fix network sender since it was hopelessly out of date and did not send
data in the correct format. OK now, though only tested on NARW.

* Fix NoGui operatoin and Network sender
2022-02-27 14:06:26 +00:00
Douglas Gillespie
a03a29e772 Update .project 2022-02-23 10:17:29 +00:00
Douglas Gillespie
a4be692d29
Daqbinary (#22)
* Make a couple o fthings private

Code tidy in VR Range Panel

* Remove binary from Acquisition since it messes up database
2022-02-23 09:57:04 +00:00
Douglas Gillespie
01c41a2896 Simple fix to amplitude calculations which were not thread safe. Not
constants are stored per channel rather than a single constant, so will
be fine.
2022-02-23 09:54:34 +00:00
Douglas Gillespie
027a854084
Fix viewer problems (#21)
* Update .project

* Two little problems. 1. Packing of navigation dialog in Viewer mode; 2.
stopping limits of viewer scroll bar extending to present, which was
annoying with old data since data were in tiny fraction of scroll.

* Revert "Update .project"

This reverts commit ba2f15c088.

* Revert "Revert "Update .project""

This reverts commit bffd413cfa.

* Revert "Revert "Revert "Update .project"""

This reverts commit c8f2f2a1be.
2022-02-22 13:03:05 +00:00
Douglas Gillespie
4ef27e0944
Keep old project name 2022-02-22 12:23:15 +00:00
Douglas Gillespie
b3cb30c512
Viewer updates (#19)
* Update .project

* Two little problems. 1. Packing of navigation dialog in Viewer mode; 2.
stopping limits of viewer scroll bar extending to present, which was
annoying with old data since data were in tiny fraction of scroll.

* Revert "Update .project"

This reverts commit ba2f15c088.

* Revert "Revert "Update .project""

This reverts commit bffd413cfa.

* Revert "Revert "Revert "Update .project"""

This reverts commit c8f2f2a1be.
2022-02-22 12:22:19 +00:00
Douglas Gillespie
642080d8db
Daqbinary (#20)
* Make a couple o fthings private

Code tidy in VR Range Panel

* Remove binary from Acquisition since it messes up database
2022-02-22 12:14:32 +00:00
Douglas Gillespie
081514f9d2
Update .project (#17) 2022-02-18 17:10:49 +00:00
Douglas Gillespie
e0c9abcc3d
Rw improvement (#16)
* Update .project

* RWE imporvement to peak detection and dealing with smoothing.

* Make improvements to MARW edge detector so that it doesn't merge
harmonics, by using a threshold down from the peak as well as up from
the noise
2022-02-18 17:05:51 +00:00
Douglas Gillespie
591d3157b6 Updates to readme and version info for release of V2.02.03 2022-02-08 17:32:13 +00:00
Douglas Gillespie
be4a5a8816 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into pr/10 2022-02-08 17:00:17 +00:00
Jamie Mac
7bbd6918c4
Add template names to matched click classifier. (#12)
* Bug fix for matched click classifier

Some of the alarm stuff in the click detector was throwing an exception because the matched click classifier adds a click ID that is not in the click ID module's list...now fixed and test with porpoises.

* Matched click classifier now has template names

The name field of the imported templates is now the file name of the template.
2022-02-08 16:08:14 +00:00
Douglas Gillespie
1a59d7c08c Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into pr/10 2022-02-08 11:58:25 +00:00
Jamie Mac
6ef5adcad2
Bug fix for matched click classifier (#10)
* Bug fix for matched click classifier

Some of the alarm stuff in the click detector was throwing an exception because the matched click classifier adds a click ID that is not in the click ID module's list...now fixed and test with porpoises.

* Matched click classifier now has template names

The name field of the imported templates is now the file name of the template.
2022-02-08 10:56:46 +00:00