From 5d83af1d4283f1628cdec1350580c2aef915d4bd Mon Sep 17 00:00:00 2001
From: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date: Wed, 17 Jan 2024 21:11:31 +0000
Subject: [PATCH 1/2] updating Tethys help (#122)
---
README.html | 127 +++++++++---------
pom.xml | 1 +
src/help/JavaHelpSearch/DOCS | Bin 77908 -> 78059 bytes
src/help/JavaHelpSearch/DOCS.TAB | Bin 5945 -> 5960 bytes
src/help/JavaHelpSearch/OFFSETS | Bin 1677 -> 1681 bytes
src/help/JavaHelpSearch/POSITIONS | Bin 538483 -> 538852 bytes
src/help/JavaHelpSearch/SCHEMA | 2 +-
src/help/JavaHelpSearch/TMAP | Bin 73728 -> 73728 bytes
src/help/Map.jhm | 2 +
src/help/PAMGUARDTOC.xml | 2 +
.../tethys/docs/images/TethysGUI_1.png | Bin 0 -> 83853 bytes
.../docs/images/calibration_information.png | Bin 0 -> 5998 bytes
.../tethys/docs/images/deploymentspanel.png | Bin 0 -> 32892 bytes
.../tethys/docs/tethys_overview.html | 8 +-
.../tethys/docs/tethys_quickstart.html | 80 +++++++++++
.../utilities/tethys/docs/tethys_server.html | 2 +-
16 files changed, 154 insertions(+), 70 deletions(-)
create mode 100644 src/help/utilities/tethys/docs/images/TethysGUI_1.png
create mode 100644 src/help/utilities/tethys/docs/images/calibration_information.png
create mode 100644 src/help/utilities/tethys/docs/images/deploymentspanel.png
create mode 100644 src/help/utilities/tethys/docs/tethys_quickstart.html
diff --git a/README.html b/README.html
index ca3211e9..26da7a1a 100644
--- a/README.html
+++ b/README.html
@@ -466,9 +466,9 @@ name="_Version_2.02.10_January">Version 2.02.10 January 2024
New Features
Importing modules from other configurations: New options from file menu allowing
-import of specific modules, or module settings from other configurations. E.g.
-if you had three similar configurations and had set one of them up with a new
+lang=EN-US> from other configurations: New options from file menu allowing import
+of specific modules, or module settings from other configurations. E.g. if you
+had three similar configurations and had set one of them up with a new
detector, or got the click classifier settings set up just right in one of
those configurations, you can import the additional modules or the click
detector settings easily into the other configurations.
@@ -478,9 +478,8 @@ files) file performance when scrolling through
audio data in Viewer mode.
Viewer Launch by right clicking on sqlite database and selecting open with / Pamguard
-ViewerMode launcher menu option.
-
+lang=EN-US> by right clicking on sqlite database and selecting �open with / Pamguard
+ViewerMode launcher� menu option.
Bug Fixes
Logger Forms
@@ -496,9 +495,9 @@ correctly saving updated bearings to the database. Now fixed.
ROCCA Classifier fixes
-Allow Rocca to run without classifiers: Fixed
-bug that threw an error if no classifier files were specified in Rocca Params
-dialog
+Allow Rocca to run without classifiers:
+Fixed bug that threw an error if no classifier files were specified in
+Rocca Params dialog
Fix memory issue with
RoccaContourDataBlocks not being released for garbage collection
@@ -563,9 +562,9 @@ handlers to handle corrupt map files.
New Features
Restart Options: When you restart
-processing of offline files, if output data already exist (binary data of within
-database tables) you will be asked if you want to overwrite the data, cancel,
-or try to continue from where to left off.
+processing of offline files, if output data already exist (binary data of
+within database tables) you will be asked if you want to overwrite the data,
+cancel, or try to continue from where to left off.
Updated SoundTrap sud file interface so
that PAMGuard now extracts and stores the Click Detector settings from the sud
@@ -759,8 +758,9 @@ the TF FX display to crash if no data were displayed.
See major release notes for V 2.02.01
below.
-Bug 495: TD FX display throws NullPointerException
-if user has removed all data units and then moves mouse over display area.
+Bug 495: TD FX display throws
+NullPointerException if user has removed all data units and then moves mouse
+over display area.
Version 2.02.01
October 2021
@@ -1369,8 +1369,8 @@ Implemented a simple UDP output for PAMGuard alarms.
7.
-Changes to Spectrogram Mark Observers, to allow individual channels to be selected
-instead of the spectrogram panel as a whole.
+Changes to Spectrogram Mark Observers, to allow individual channels to be
+selected instead of the spectrogram panel as a whole.
8.
2.
-Java 12 is better at handling Windows scaling issues on high-DPI displays. Beyond
-that, users should not notice much of a difference between this version and
-previous beta releases.
+Java 12 is better at handling Windows scaling issues on high-DPI displays.
+Beyond that, users should not notice much of a difference between this version
+and previous beta releases.
@@ -1472,8 +1472,8 @@ lang=EN-US> Updates to the Ishmael detectors.
Beta Version
2.00.16 May 2019
-PAMGuard Version 2 contains major updates. You
-should read and understand the notes listed for PAMGuard Version 2 contains major updates.
+You should read and understand the notes listed for Beta Version 2.00.10 before proceeding
with installation and use of this version.
@@ -1772,10 +1772,10 @@ settings even when user tries to cancel or discard changes
6.
-Bug 387. Map was stopping displaying data based on the start time of data
-units. Have changed this to last updated time so that click events will display
-if they have been recently modified. Otherwise, long events get lost from the
-display.
+Bug 387. Map was stopping displaying data based on the start time of
+data units. Have changed this to last updated time so that click events will
+display if they have been recently modified. Otherwise, long events get lost
+from the display.
7.
@@ -2111,9 +2111,9 @@ showing.
2.
-Bug 323. Difar module. Fixed a couple of small bugs
-in the DIFAR system which caused it to not work if old configuratins were used.
-
+Bug 323. Difar module. Fixed a couple of small
+bugs in the DIFAR system which caused it to not work if old configuratins were
+used.
3.
@@ -2262,10 +2262,10 @@ so they will no longer work with older PAMGuard versions.
2.
-Display colour options will be lost and most data displayed
-on the map may default to black. This is due to the above changes to how
-colours are managed. Changing back to the colours of your choice is relatively
-simple through the PAMGuard GUI.
+Display colour options will be lost and most data
+displayed on the map may default to black. This is due to the above changes to
+how colours are managed. Changing back to the colours of your choice is
+relatively simple through the PAMGuard GUI.
@@ -2697,11 +2697,11 @@ planned file format changes and that this is purely a future proofing exercise.<
7.
-Bug 279. GUI Resizing: The whole PAMGuard GUI would suddenly resize to something
-very small when a dialog is opened. This has been traced to improper use of a
-common dialog component SourcePanel which tries to repack its parent Window.
-Some programmers had inadvertently set it to repack the main PAMGuard GUI
-instead. This has been Fixed.
+Bug 279. GUI Resizing: The whole PAMGuard GUI would suddenly resize to
+something very small when a dialog is opened. This has been traced to improper
+use of a common dialog component SourcePanel which tries to repack its parent
+Window. Some programmers had inadvertently set it to repack the main PAMGuard
+GUI instead. This has been Fixed.
8.
@@ -3256,10 +3256,11 @@ sonobuoys. See online help for details.
MEAL Localiser (Localisation Group)
This module, developed by Jamie Macaulay of St Andrews
-University estimates the 3D localisation of clicks using a variety of algorithms.
-It's primarily been developed to track harbour porpoise in three dimensions
-over scales of 10's of metres. While currently only working with output from
-the click detector, we hope eventually to extend its use to whistles as well.
+University estimates the 3D localisation of clicks using a variety of
+algorithms. It's primarily been developed to track harbour porpoise in three
+dimensions over scales of 10's of metres. While currently only working with
+output from the click detector, we hope eventually to extend its use to
+whistles as well.
Accelerometer Readout (Sensors group)
@@ -3442,9 +3443,9 @@ whistle.
New Modules
-Clip Generator: Saves and displays
-short waveform clips around detections. Can work with any detector (or indeed
-any other data stream within PAMGuard).
+Clip Generator: Saves and
+displays short waveform clips around detections. Can work with any detector (or
+indeed any other data stream within PAMGuard).
Local time display: displays the
computers local time on the main display panel.
@@ -3520,9 +3521,9 @@ information correctly in the binary files.
Logger Forms
-A substantial amount of work has been
-carried out on Logger forms, funded by the South West fisheries Science Center.
-
+A substantial amount of work has
+been carried out on Logger forms, funded by the South West fisheries Science
+Center.
Click Detector
@@ -3973,9 +3974,9 @@ more displays are set up for offline data viewing in future releases.
Viewer data map
-When using the PAMGUARD viewer an additional panel will be displayed
-showing an overview of data quantity (per hour) from the various database
-tables connected to PAMGUARD.
+When using the PAMGUARD viewer an additional panel will be
+displayed showing an overview of data quantity (per hour) from the various
+database tables connected to PAMGUARD.
Spectrogram Display overlays
@@ -4185,9 +4186,9 @@ display correctly and amplitude scale updates after scale parameter changes. Speed improvement.
-PAMGAURD FFT calculations now use the JTransforms FFT library
-which gives a factor 2 speed improvement compared to previous FFT methods used
-in PAMGUARD
+PAMGAURD FFT calculations now use the JTransforms FFT
+library which gives a factor 2 speed improvement compared to previous FFT
+methods used in PAMGUARD
New Modules
@@ -4543,9 +4544,9 @@ localiser (affects stability of click train localiser and whistle localiser in <
1.2.0 Beta December 2008
-This release contains many bug fixes from the PAMGUARD industry
-field trial which took place in the Gulf of Mexico on the RV New Venture in
-November 2008.
+This release contains many bug fixes from the PAMGUARD
+industry field trial which took place in the Gulf of Mexico on the RV New
+Venture in November 2008.
Bug Fixes
@@ -4650,8 +4651,8 @@ mouse is moved over the display. Choice of colour maps for display.
'
Sound playback. Now supported in ASIO sound cards, so you can have sound
-coming in through the ASIO card and back out through its headphone socket (after
-passing through PAMGUARD filters and other modules) at the same time.
+coming in through the ASIO card and back out through its headphone socket
+(after passing through PAMGUARD filters and other modules) at the same time.
'
@@ -4671,11 +4672,11 @@ Symbol'>'
+ The Tethys database is only used in
+ PAMGUard Viewer mode and is only used to archive project data to a single
+ centralised database.
+ It is NOT a replacement for the existing PAMGuard database.
+
+ PAMGuard Tethys Module
+ Launch PAMGuard in Viewer Mode with an existing set of data.
+ Add a Tethys module to PAMGuard from the File / Add Modules / Utilities menu.
+ A new tab panel will show the Tethys interface
+ 
+ The tab shows a number of panels for the connection to the server and the various types
+ of data that will be output to the database. Some of these should summary information on what's in the
+ current PAMGuard dataset (consisting of your PAMGuard database and binary store), others may be empty until you start to
+ export to Tethys.
+
+
+
+ Tethys Server
+ Make sure you have a Tethys Server running. The PAMGuard interface will
+ only work with Tethys 3.
+ Check the server connection. If PAMGuard has correctly connected to the Tethys server, the top panel of the display will be a normal
+ grey colour. If the connection cannot be made, the panel will be orange.
+ If required, change the server settings using the "Select Sever" button
+
+
+ Project and Instrument Information
+ Either select an existing "Project", or create a new one.
+ You also need to give Tethys more information about the instrument(s) or arrays you've deployed than in previous PAMGuard versions. Again, select an
+ existing instrument, or set up a new one. You'll notice that this information is held with the rest of the PAMGuard array management information.
+
+ Data Export
+ It's best to export data in the sequence the panels are laid out in on the PAMGuard display, i.e. Calibrations, then Deployments, and finally Detections.
+
+ Calibrations
+ To export the calibration data, press the "Export..." button at the top of the "Instrument Calibration Information" panel.
+
Most of the calibration data is taken from the array manager and from the sound acquisition module. However, PAMGuard will ask a few questions about
+ HOW the instrument was calibrated, when it was done and who is responsible. Fill in as much information as you can!
+ IF the export is successful, a record will show for each hydrophone (or sensor) in your instrument array in the calibration information table:
+
+ 
+
+ Deployments
+ PAMGuard will have done it's best to work out the temporal extent of your data by looking in the
+ PAMGuard database and
+ binary Store. Where data were collected on a regular duty
+ cycle, or continuously, there should be a single record in the table of recording periods. If data were collected on a more
+ "ad-hoc" basis, for instance during a boat based survey, there might be many different records in the table.
+ Occasionally, there may be short recording periods (e.g. while you were testing kit on deck) that you don't want to export. Either select
+ individual rows that you want to export, or right click on the table and "Select All".
+
+ Press the "Export..." button and work through the questions to provide additional information about your data, why it was collected, etc.
+ Once the document(s) have been exported, the document names will be shown alongside each PAMGuard deployment period
+ 
+
+ Detections
+ The bottom left panel shows a list of different types of PAMGuard data that can be exported and should also show the total numbers of each type of data that are available
+ within the PAMGuard storage systems. Select the datablock you want to export from and press "Export...".
+ You really don't want to try to export zillions of data to Tethys , in the options that will appear you can opt to just export certain types of detections
+ or summary counts.
+
+
+
+ Previous: Overview
+ Next: Tethys Server
+
+
+
+
+