All Classes and Interfaces
Class
Description
The class AbstractCellEditor serves as the base class for the TreeTable's
table cell editor.
Abstract implementation of Filter interface to
provide common functionality for two of the main
function calls for processing arrays of data.
Class for localisation information.
Abstract Localiser class.
A scroller UI interfacing with PAMGUARD programmed using JavaFX.
Deprecated.
Reinstated Target motion add-in as used by the click detector.
Reinstated Target motion add-in as used by the click detector.
Contains more generic nodes for JavaFX implementation of video range GUI.
AbstractVRMethod provides a significant amount of the basic functionality required to determine the range of an animal from an image.
A class containing a
TableCell implementation that draws a
TextField node inside the cell.Class for all PAMGAURD data based on acoustic types of data, i.e.
Implementation of AcousticScrollerGraphics which uses the existing datagram of a PamDataBlock to
show information in the acoustic scroll bar graphics.
Used as a flag to indicate that the data unit implementing this interface holds
some type of acoustic data.
The acoustic scroll pane shows a summary of all the acoustic data available in a particular scroll period.
Handles the graphics for an acopustic scroller.
Main data acquisition control to get audio data from sound cards,
NI cards (via UDP), files, directories of files, etc.
Very simplified version of the Acquisition parameters
to be passed over the JNI to the C backend.
Main dialog for acquisition control.
Very simple concrete implementation of SQLLogging to log the starts
and stops of PAMGUARD in the database.
Settings pane for the sound acquisition parameters.
Data acquisition process for all types of input device.
The AcquisitionSettings class provides a module-local storage object for holding
on to the properties of the audio data source (acquisition module) upon which the
module is depending.
Base class for action settings.
Add Then Multiply then Add is a calibration method in it that has
some unnecessary, but useful redundancy.
Pane with controls to change advanced settings of the electrical noise pane.
Pane with a few more advanced settings for the MHT variables.
Read in some AIS data which caused AIS to crash on certain strings.
A set of AIS data strings which can combined with simulated NMEA data for
testing purposes.
AIS Position report data
BAse class for any alarm data source which is returning
some kind of data measured in dB, which needs
to be added in a different way to normal.
Set of params for an individual alarm output.
Alarm action for serial port output.
Singleton class for all alarm actions to share a single serial port, it's settings
etc.
Experimental java based demultiplexer.
Chi^2 value for dB amplitude of tracks.
Construct a dialog panel with range information for a list of named channels
Descriptions of a module that will use analog data.
Anchors for localization effort coordinate system.
Class to sort out angle calibration data.
Data unit for storing angular information, often used to store data from imu intruments (inertial measurement unit) and heading data from compass sensors.
Data for a single angle veto.
Dialog to get data for a single angle veto.
Dispaly for angle veto.
Class to support functions to handle vetoes on angles to clicks
Dialog to manage multiple angle vetoes.
PArameters controlling angle vetoes for a particular detector.
Functions used by a specific DataAnnotationType to read and write binary data
settings and retrieving that information in PamDataUnits.
Annotation handler that provides functionality for the programmer to set things
up so that the user can chose which types of annotation to use.
Class to handle choice of annotator and any other
associated options.
General dialog that can be used with any annotation type.
General interface for dialog panels which get incorporated into other
dialog panels for editing one or more annotations of a data unit.
Manage annotation options for a datablock
Annotation options.
Settings panel for configuring annotation types
Display summary information about a data unit and it's annotations.
Symbol options for annotations.
Writer to convert an annotation into XML.
FX GUI for the SoundAquisition module.
A Tensorflow or PyTorch model zipped with a PAMGuard settings file.
Runs a Ketos deep learning model and performs feature extraction.
Create a 3D visualisation of the array.
Main dialog for hydrophone array configuration
Array display panel showing tilt, roll, etc.
Parameters for all of the three display - pitchroll, heading and depth
JavaFX UI bits of the Array Manager.
Manager for different array configurations.
Parameters wrapper for array data.
Types of value which might occur in streamer data for height, head, pitch and roll
where values can be fixed, default or from a sensor
default not applicable to depth, 0 for pitch and roll, GPS head for heading
HPR on a user display.
Label for a datablock that has sensor data.
this is nominally an add on to data units, but we do also add it to GpsData so
that GpsData and StremerDataUnits can both be passed to array graphics.
The main settings pane for settings up a hydrophone array.
Utilities for converting data to and from an Ascii 6 bit format.
This currently doens't seem to need to do anything.
Everything and everything to do with controlling and reading ASIO
sound cards.
Attenuation model.
Generates a little ARFF file with different attribute types.
Better management of new data list.
Automatically provides Tethys data for a PAMGuard datablock.
This is the data type produced by the linearAverageSpectra
Create average waveform and FFT spectrum.
Class to schedule SwingWorker tasks so that they execute one
at a time.
Deprecated.
Module that implements the Azigram algorithm from Thode et al 2019 J.
Just a dirty hack for testing.
Module that implements the Azigram algorithm from Thode et al 2019 J.
Azigram process will take FFT data from a DIFAR sonobuoy source, demux, and
then compute Azigram (Thode et al 2019 JASA).
Trying to standardise measures of background noise for detectors.
Catalogue data that are already backed up.
Main panel for handling, configuring and displaying backup progress.
Exception thrown when a backup operation fails.
Base interface for all BackupStream, BackupAction and BackupDecision items
to facilitate dialog creation and display.
Class that can be returned by a PAMControlled unit which gives backup information
which is mostly a list of BackupStream objects (or just one of, but some modules may
have multiple streams which do not necessarily relate directly to the datablocks.
PAMGuard module to automatically back up files.
Observers of backup progress.
Class to send progress data to backup observers.
This is the central management class for each datastream that's going to get automatically backed up.
Class to assess the performance of a bank of filters and decimators.
Class to create a set of octave or third octave bands
using base-two exact steps according to the standard
ANSI S1.11-2004.
Contains data on the performance of a single filter band.
Whitens data in time using the methods provided by Gerald d'Spain and used in
Tyler Helbles paper.
Basic checks of one or more processes in a module.
Property set for all
A basic frequency-domain beamformer
Dialog for the basic frequency domain beam former parameters
Pane for the basic click classifier.
Simple layout for side bar components.
Container for batch processing results
Command to get PAMGuard to send back the batch processing status.
A set of functions to handle importing and overriding settings imported from a psfx during
batch mode processing in viewer mode.
Unpacked contents of a line of BCL data.
Reader for BCL files.
Provider of beam former algorithms - may need > 1 algorithm object if
channels are grouped into separate array sections, e.g.
Class to wrap the beam former control system and extract from it
the algorithms that can create beamograms and then wrap each of those
up so that they become available to the more generic bearing localiser.
This module requires audio from a DIFAR sonobuoy and will output
directional audio by using simple beamforming algorithms.
Beam former annotation that can be added to any data unit as an annotation.
Base process for both continuous and detect-then-localise beam forming.
Main beam forming process.
This process doesn't calculate continuous beams, but when data do arrive,
it calculates a beam'O'Gram for data in that time-frequency box and estimates
a best location based on that time interval.
The DIFAR SidePanel contains the list of DIFAR classifications, to allow
the user to choose which classification is assigned by default.
Handle channel groupings so that the actual algorithm
gets called with a complete array of all channels in
it's group in one call.
Information about a specific beam
Temporary data used during beam forming, e.g.
Observe things like updated graphics on beam former.
Data output for the BaemOGram.
Can plot lines or scaled images or both.
An advanced pane for bearing measurements.
Chi2 value for changing bearing.
Measures the difference in change between three bearing measurements.
Subclass of parameters for bearing.
Simple Enum indicating the direction the jump can be.
Classification result from the bearing classifier.
A bearing based classifier for click train.
Manager for UI stuff for the bearing classifier.
JSON string logging for the bearing classifier.
The Bearing classifier settings pane.
The bearing classifier parameters.
Display component interface for one bearing channel group.
Class to estimate bearings, with errors from a closely spaced
hydrophone array
Class to automatically select / create the most appropriate type of
bearing localiser.
Calculate the mean of a load of angles in degrees.
Manages classification flags and/or any bespoke alteration to specific types of data units
after an MT Classification has been processed.
Can back up anything, PAMGuard or not.
Bespoke drawing on datamap.
This class can be used within a detector that may or may not be
attached to a beam former (alternative is probably raw fft data).
Parameters for beam former localiser
Connection node for the binary storage module.
Interface for users of binary data as it's being read from a file.
Not just a source, but also a sink for binary data from the
binary store.
Match data based on binary file information.
Used to read data back from a binary data file and either send
it off to the associated PamDataBlock or hand it back to the
BinaryStore controller, e.g.
Not really a dialog, but displayed by BinaryStore while its making maps
of stored data during Viewer operation.
Class to temporarily hold an objected data that has just been read from
a binary file.
A binary offline data map is a datamap for a single data stream (i.e.
Handles writing of an actual binary data file.
Manage storage and retrieval of PAMGUARD serialised settings storage in
binary files.
The binary store will work very much like the database in that it
monitors the output of data streams and when data is added to them
it writes it to the binary store.
The JavaFX GUI for the binary store module.
Set of functions used at restarts to determine the status of the binary store.
Class to handle basic UID functions related to the binary store
Binned granularity
Will have to collect different counts for each type of call for each datablock (if there
are such things) so a little more complicated than might be expected.
Possible blocking modes, none, always blocked, each processed independently,
block the first block to get the background then continue as normal, or
reverse the first block, then continue as normal.
This is a convenience class which stores the critical non-static information about the
data blocks being processed.
DIFAR Calculations, based on the Matlab bScanNew functions
Class to sort indexes, leaving original data intact.
Version of SQLLogging which buffers up the data units for a few seconds before writing them
so that other parts of PAMguard get a chance to modify them before they go into the
database.
used to store and process information about each buoy.
Clas for saving buoystatus data into the serialised settings.
Separate out from BuoyStatusDataunit so that it can be serialized
Class for collecting data to do with individual buoys receiving data
over the network.
Classes to convert between various wav and aif stream formats and
double data scaled from -1 to +1 for PAMGUARD.
Really simple calibration data class - may change at later date to
be a lot more sophisticated.
Contains data for a Difar calibration histogram.
Information for a specific calibration type.
Handle the calibration process for a single channel
Calibrations Process card attempts to fill in the
calibration data for the Quality Assurance and Process fields.
Wizard card to select call types (species) to export.
Class for controlling everything to do with the FX Camera observing the scene.
Observer to use with Pamdialog which is called whenever the cancel button is pressed.
Deprecated.
Replaced by new 3D group localiser.
Information on the Sound Trap CDET detector configuration
Sub form control is a button which sits within the layout of a normal
form and creates an additional Popup form when it's pressed, with appropriate
cross referencing between the two form types.
Singleton centralised annotations types list.
AIS Data recorded in the English Channel
by Richard McLanaghan of IFAW.
An iterator that has a bit more functionality than a basic iterator.
Functions to convert between
Interface allowing individual devices to provide their
own channel list panel.
Calculates a Chebychev window for use in FOR filter design.
This class provides a custom renderer for a JTree that displays a
check box before the standard open/closed subtree icon, and a text string
for the node content.
Class for checking a storage folder exists and optionally creating it
Pane with controls to fix wave file headers.
Minimisation functions which is based on bearings rather than time delay measurements.
Class to hold basic classification data for a click train.
Paramters for the time delay based minimisation function.
Simple classifier which has a chi2 threshold
Simple chi^2 classifier parameters
Minimisation function for a localisation performed using time delay calculations.
Simple table with a check box column that only allows one check box column for
single or multiple selection of table rows.
Used in conjuction with the Choice table.
Interface for fragment classification.
Type of probability that will be returned by this classifier.
Provides a history window for classification results.
dialog panel to show basic information from a fragemtn classifier and to load
up new classifier files.
String logging for classifier for the click train detector.
Some offline functions / functionality.
in an attempt to generalise the classifiers and keep them
separate from anything whistle specific, use this
abstract class to hold classifier specific parameters
and cast it into something more concrete when it's used
by a particular class;
Class to serve up classifier types to the Whistle classifier
Class to serve up classifier types to the Whistle classifier
Click Classifiers all now share a common dialog and need to provide
a common component to it.
Alarm object for the Click Alarm
Write a click classification annotation to a binary file
Save classification information to the database.
Class for storing clicks to binary store.
Class for managing extra binary info for click
detector binary files.
This is the main bearing time display for the click detector.
Annotation type for showing which click classifiers in the click detector
passed the clicks detection, not just the first one.
Annotation for click classification
Pane which allows users to select click classifiers.
Simple panel to offer the three basic colour options for clicks -
colour by species, train or both.
Main Controller for click detection.
Get the FX GUI for the click control
Pane for changing click detections display properties.
dialog to wrap around clickDelayPanel for making a stand alone dialog
Pane to chnage click delay settings.
Class for Click Detector clicks.
Main click detector process.
Symbol chooser for the click detector.
Common functionality for all display windows in the click
detector panel
Dialog for basic click display parameters
Parameters for displaying clicks in the TDDisplayFX.
Model from Thomas webber which is a good way to test the click based stuff is working in PAMGUard.
Pane containing controls to change echo detection parameters in the click detector.
Handles efficiently plotting click FFT's on the frequency axis.
Click Train data block deletes old data in a slightly
different way to PamDataBlock.
A localiser implemented for groups of clicks.
Class for holding classification information.
Calculates the click length.
Dialog to allow users to select which type of localisation algorithm to use.
Dialog panel for click localisation, and probably some
other types of localisation too ...
Databse logging information for Clicks.
Deprecated.
Graphics for drawing clikc detections and classification on the data map.
Dialog for click detection parameters.
Handles the plotting of click data in the TDDisplayFX.
The click raw plot manager.
Menu items for manually classifying selected clicks in a TDGraph.
Function to remove clicks from blocks of data.
Usually a
ButtonBase only fires once per mouse click, namely when the mouse is released.Convert a group of clicks to an average spectrum.
Pane which allows selection of different click types.
A pane to change click detector settings.
Functions for handling offline data display
and processing.
Generate short click like sounds.
Creates and stores a spectrogram image for a wave file snippet.
The implementation of DisplayPanelProvider should be created
as a single instance (or one for each instance of the detector
which has this display).
The edit template dialog allows users to create mean spectrums from marked out events.
Deprecated.
Chooses which symbols should be displayed by the click detector
Clikc symbol options which contain a few more settings tghan standard symbol options.
Class for storing click templates.
Deprecated.
Interface for a click train detection algorithm.
Main settings pane for the click train detector.
A click train detector.
Deprecated.
The click train detector data block.
Data selector which makes it possible to select events based on their type.
The DetectionDisplay information for ClickTrain detections.
Automatic click train's from the click train detector.
Functions for saving a click train.
Logs the the children of the click train detection.
Click train id params (separated out from main click params).
Offline processes for the click detector.
Run the click train detector in viewer mode, including the click train classifier.
Settings for the click train detector.
The core of the click train detector.
Manages colours of symbols.
Temporary data block for click trains.
Class which deals with click train warnings.
Graph which shows a click and associated trigger functions
Superclass for click parameters, including the ClickTypeParms and
SweepClassifierSet classes.
The click type manager manages click types within the click detector.
Pane for changing basic click classifier settings.
A property wrapper for a basic click with JavaFX properties.
An object which provides info on and can change click types.
Display which shows the raw click waveform.
Updates click waveform from raw audio data.
Class to Copy graphics content to the clipboard and the printer
The clip generator is used to generate short sound clips around detections.
Class for calculating clip delays when clip has
multiple channels of data.
Really basic class for clip data blocks, which can be used by the
Clip display (which is now incorporated into other modules, such as the
DIFAR module).
Clip display panel.
A set of functions that can be used to add additional items to a
clip display unit.
Dummy projector to use with the clip display which is needed as a way of passing a referecne
via this projector, to the clipDisplayPanel through to the symbolchooser.
Graphic component for a single clip display.
Settings for a clip generator - which can be triggered by any AcousticDataUnit.
Use the same localisation information as for whistles.
Some static functions to playback sound clips.
The clip data info.
The clip plot provider.
Process for making short clips of audio data.
General clip gen settings (file location, etc.
Creates and stores a spectrogram image for a wave file snippet.
This is just a dummy datablock to fool the Clips dialog into showing
options for the clips from spectrogram marks.
Looking into making a symbol modifier that will work with the DIFAR ClipDecorations, but its
too complicated since the decorations are only added to the individual clips.
Parameters controlling tests of a single cluster type
Make a panel which allows you to select a load of clusters.
Used in the sweep classifier dialog to get and set the code
value from the text field.
Names of Tethys Collections.
Creates a combo box which shows a selection of colours or colour gradients.
Interface that enables the colour manager (PamColors) to change the
colour of any swing component.
A series of functions for creating arrays of colours
A colour map contains information to create a colour map and the correct CSS to colour components.
The colour range slider shows a linear colour gradient between two thumbs
with the rest of the slider coloured by the minimum and maximum of the colour
gradient.
A range slider which shows a colour gradient between two thumbs.
This UI is designed to allow a user slide to thumbs defining the max and min amplitude for a colour scale.
Deprecated.
Interpret commands which may have come either from a terminal or from a Network
(e.g.
Interface for PAMGuard plugins.
Draws a compass given the rotation of the map in degrees.
Class definition for a Complex number type.
Class for handling arrays of Complex data.
Comparator to compare complex numbers first by real part, then by imaginary part.
shows multiple data selectors in a pane.
A hiding dialog panel for use with multiple display overlays.
A tabbedhidingpane which includes a settings button on the tab.
The Class ConfigurationDialogSettings holds parameters about the
configuration dialog box that are persistent from one invocation
to the next.
The main rectangle nose for the ConnectionGroupNode.
A node which holds other connection nodes, minimising the space they use in
the data model.
A sub connection pane with a single plug.
Line which connects a plug or socket to a ConnectionRectangle or other ConnectionLine.
Listener for connection events with ConnectionShapes within a ConnectionNode.
A connection node is a node that has a parent and children
The main body of the connection node, i.e.
Creates connection nodes from both saved parameters and when new modules and/or
as structures are added manually.
Information on structures used in the data model.
Useful functions for connection nodes.
A pane which allows users to drag rectangles around and connect them
together.
This is how you start a JavaFX 9+ application if you are not using modules.
A connection structure is a connection node which is a utility rather than a node.
Connection structure types.
A ConnectionNode which holds other connection nodes.
Simple application to test a connectionPane;
Interface for any interactive shape in a
ConnectionPane.Listener for node connector events such as dragging, being detected etc.
What to do when multiple contour patches are found in a single detection.
Data select creator for a single logger control.
Data selector for a single logger control.
Main editor for a particular control.
Convenience class.
Sheet of control properties for a particular control title.
Title panel for the control editor.
Class definition for a x,y coordinate number type.
Interface for algorithms that can provide a coordinate choice.
Enumeration of the Name field in nilus.Localize.Effort.CoordinateReferenceSystem
Within Tethys, these are only ever used in their String form.
Within Tethys, these are only ever used in their String form.
Class definition for a x,y coordinate number type.
Copy a file from one location to another, trying to preserve any sub folder stucture
from the source to the destination directories.
Imports or exports data from an external database.
Advanced settings pane for correlation
Calculates the correlation value between subsequent clicks.
Parameters for correlation MHT variable
Manages correlation values and ensures correlation calculation between
two data units is stored and not calculated multiple times.
Holds the UID of a click and the correlation value.
Holds the maximum value for the correlation function and lag value.
Wrapper class for an input stream which counts the number of bytes
read, skipped etc.
Options for improved display coupling and inter-display zooming.
Binary storage for CPOD data.
Holds CPOD click train classification.
Enum for species classiifcation from CPOD/FPOD click train detector.
CPOD or FPOD click.
Data block which holds CPOD and FPOD detections.
The click train detector data block.
Base class for a click train data unit.
Deprecated.
CPOD control.
Basic filter for CPOD data.
Data selector for CPOD data.
Creates CPOD data selectors.
Pane for changing the CPOD data selector settings.
Swing data selector
Parameters for the CPOD data data selectors.
Data info for showing a CPOD waveform.
Deprecated.
A CP1 along with it's CP3 file
Imports FPOD and CPOD data and converts into binary files.
Deprecated.
Deprecated.
CPOD plot info.
The plot provider for CPOD data.
Read CPOD data.
Holds an CPOD header information
CPOD FX based settings pane.
Logs the the children of the click train detection.
The settings pane for CPOD detections on the TDGraphFX.
Some useful utility function for CPOD and FPOD data
CPOD file types
Class to monitor Thread CPU usage over multiple calls.
simple class for passing information about data map making
from swing worker to dialog.
Log error strings based on information coming back from the cRio through
the SSH window.
A List of strings returned by the cRio which indicate an error of some sort.
A set of cross reference items that may need to be updated.
Functions for cross reference updating.
Base class for CSV data unit export.
Export to CSV files which are RAVEN compatible.
Export data units as .csv file
Extra results or information for each CTDataUnit from the click train algorithm.
Logging for CTAlgorithmInfo.
Handles algorithm info logging.
A classification results for a single click train.
Process which classifies click trains.
A classifier which is used to classify groups of detections
Handles GUI for the classifier algorithms.
The classification manager for the click train detector.
Runs only the click train classifier on the data (does not recalculate click trains)
The basic classifier pane.
Classifier params class.
Pane which allows users to create and change settings for multiple click train classifiers.
Types of click train classifier that the click train detector can use.
The click train data selector.
Data selector for the click train detector.
The click train select pane in JavaFX
Specific data selector parameters panel for the click train detector.
Data unit for a click train which holds a series of data units grouped into a click train.
Swing based graphics for drawing click trains on the map.
Base class for a click train data unit.
Handles GUI interactions with each click train detection algorithm.
The JavaFX GUI for the click train detector
Basic localisation info for the CTDataUnit.
Process which, if conditions are met, attempts to localise a click train.
Parameters for Click Train Localisation
Sub class of TM annotation type which has some extra functionality for
filtering click trains before target motion localisation.
Settings panel with some additional settings.
Process check for the click train detector.
A click train offline dialog which ensure that the click train offline
tasks cannot be run at the same time because they have different parent data blocks..
Class to add to a window in order to intercept and interpret Ctrl key
strokes.
Parameters for click train data selection.
Swing holder for the CT side panel
Average spectrum plot for click trains.
The PAMControlled unit GUI bits when using Swing.
A template classifier which uses a click template to essentially cross correlate
the spectrums.
The main click train classifier graphics.
Manages warning for the click train detector
Class for managing PamCurosrs - returns the previous one
if at all possible, but creates a new one if the connection
has changed.
This class is used to track the time (both sample and milliseconds since 01-01-1970), and the value
of a curve.
Class that makes files of any type from
a single starting point - strips of the bit
after the .
Class to hold various types of information about a sensor.
Class for unpacking XML metadata files created from Mark Johnson's D3 software
Class for converting channel indexes and numbers to hydrophones
for the main PAMGAURD DAQ.
DaqDeviceDescriptor class mirroring the C version for use with JNA.
Settings pane for a DAQ specific nodes.
Data unit containing information on run starts and stops.
Abstraction to multiple data acquisition devices.
Interface for External DAQ Systems
Odd little class that tries to stop all of the settings for every possible
daq system being output to xml by only accepting them if they are the selected
system type of at least one daq module.
Some kind of data annotation, i.e.
Something that can tell us a little more about
a type of DataAnnotation, such as how to store and display
and edit the data in that annotation.
Returned by datablocks, though default is null, to give information on how
automatic the process was.
Run some tests to try to work out why it's so much slower to load
data when the query is based on a non indexed column compared
to an index one, even though the actual query execution time
is a small fraction of the total time.
Works with a DataUnitFinder to match PamDataUnits by
database index.
Table of Detections documents for a single PAMGuard datablock.
Compare two datablocks by name so that they can be easily sorted.
Class to return lists of species codes or names for a datablock.
Dialog to edit ITIS species codes for a datablock.
Manage species conversion for a single datablock.
Species map for a specified data block
Data about a PAMDataBlock.
Generic class for copying data from binary data files to database files.
Class for counting events - e.g.
A datagram is a set of data which summarises the real data content in quite course bins
of about 10 minutes (though this may vary).
Generally, Datagram data look a bit like very course spectrogram data, except that they are designed to show data density as a function of frequency instead of energy density as a function of frequency.
They can be calculated automatically from many types of data and are stored in the binary index files for easy access when mapping data.
Generally, Datagram data look a bit like very course spectrogram data, except that they are designed to show data density as a function of frequency instead of energy density as a function of frequency.
They can be calculated automatically from many types of data and are stored in the binary index files for easy access when mapping data.
DatagramManager needs to return more than just an image - it also needs
the start and end times of the data, which will have been extended out to
interval boundaries.
Interface to add to OfflineDataMapPoints so that they can serve up
a datagram.
Progress data on datagram creation
Interface implemented on a PamDataBlock which is able to provide
Datagram type data.
Class to pass around a few bits of information about a datagrams scale
This class is used to define what data to import and how to import it.
Functions for a data input store.
Provides a set of functions that can check and repair data.
Class to manage minimum data storage times for all datablocks.
Info about a specific data line within a TDDataInfo.
TDDataInfo objects can't be serialised since they contain
references back into datablocks and everything else in PAMguard,
so have to hold a summary of what's in each one to save into psf files.
A pane which shows progress bars bars for various data load tasks in PAMGuard.
Used in a simple store of datablocks queues for loading.
The data map appears only during PAMGUARD viewer mode and is the root of
a navigation system allowing the operator to scroll easily through large
amounts of data.
Interface for additional functions of the datamap GUI.
Interface for module specific data map drawing.
Effort provider for most types of datablock that bases itself off one of the
datamaps, binary (preferred) or database.
The GUI for the data map.
Holds information whcih can identify a data map.
Layout the DataMap giving less space to the hidden components
Class to allow datamaps to update and notify the data map viewer each time
they get additional data added (or even removed) as we start to use datamaps
in real time.
Pane which shows users all data currently stored in binary files and
databases within PAMGuard.
The main panel managed by DataMapControl
In reality, this does most of the actual controlling.
A scroll bar which shows a summary of the data.
Settings pane which allows users to change settings for data maps.
No real idea what this is for, but it's going to get passed to DataBlocks along with a list
of selected data units, so that they can return data unit bespoke menu items
Sub class of ConnectionPane to deal with modules being dragged from
module list to pane.
A pane which shows a list of all the available modules.
The data model pane allows users to change PAMGuard's data model.
The primary function of the setting class is to save the positions of the
modules nodes.
The data model setting manager handles building and saving the data model
connection nodes and structure based on saved data and the current PAMGuard
data model.
Controls the colour of lines.
Functions for a data output store.
Standard classed which are attached to a datablock and can be
used to select certain types of data unit (e.g.
Called when a data selector changes.
Something that creates data selectors.
Dialog panel to wrap around a standard dialog panel from a data selector.
Dialog panel to wrap around a standard dialog panel from a data selector.
Data select parameters.
Panelette to go into the main DataPanel to show the data for a single data
stream
Interface to set / control limits on data times.
Generates settings panes for different data transforms.
Simple class to hold a data type and a data unit.
Data units that can be plotted on the FX 2D displays, such as FFT data, beam former
output, etc.
Class for data unit basic data.
Little bit of data to add to all PamDataUnits
when they are read back from a file which will
be used to say which file they were from, whether they
need updating, etc.
Class for finding data units in a reasonably controlled and
organised way.
Class for matching data units to a set of other
criteria.
Swing based information panel giving information about a data unit
which can be incorporated into a larger dialog.
Pane which allows users to select a data and time using various spinner.
Class to handle regular commits of the data when Auto Commit is not
set.
ConnectionNode for database module.
Database system for accessing data in just about any type of odbc database.
Version of DBControl for loading settings at program startup.
Version of DBControl for normal use while PAMGUARD is running
- reading and writing of data
Simple FX implementation of the database GUI.
Display panel for dBHt data - can be incorporated into a spectrogram
plug in or a stand alone display window.
Dialog which shows the progress in data map making.
Pane which shows progress in mapping the database.
Pane for selecting a database.
Functions for writing database table schema in a format
compatible with the Tethys schemas.
Load all of the settings from a database and store in a single class.
simple abstract class for any extra database functions which
do not easily work with PamDataUnits and PamDatablocks
Text area with a character limit
Class containing functions for managing the database connection.
Some standard queries we're going to want to make from various
parts of the system as the user interacts with the GUI.
Class to remove DC offset from audio data.
Information on the data a detection can display.
Information on the type of data that can be displayed
The different types of graphs that can be displayed
Pane which allows users to select parent data blocks.
ComboBox which holds the options for different plots to be displayed.
Provider class for detection display data.
Extends the standard plot pane;
Holds information on the scale (e.g.
This class implements the decaying average normalizer/estimator for the likelihoodDetectionModule.
This class is used to convert signal and background time constants to ExponentialAverager alpha values.
Deprecated.
New decimator processe, based on the DecimatorWorker class
which can be use to upsample as well as decimate.
Settings for the decimator.
FX GUI for the SoundAquisition module.
Job to run the actual decimation.
Test the defualt models.
Default hydrophone parameters.
Default parameters for different species for the MHT click train detector.
Pane which allows users to view and select default models.
Default label format for range slider.
Some default click templates for the classifier.
Default data unit matcher for use with
DataUnitFinder
Matches clicks on time and possibly also channel/sequence number
depending on the number of arguments supplied.
Default templates for the template click train classifier.
The default spectrum templates.
Functions for attempting to efficiently prep data for correlation using a variety of
pre-processing methods.
Generic parameters associated with delay measurement.
A classifier based on the delphinID method which uses whistle contours to predict
dolphin species.
Settings pane for delphin ID.
Allowed data input types for DelphinID.
Handles transforming whistles or clicks into whichever transform is required by delphinID.
A bunch of utility functions that a re useful for testing and running
DelphinID models
Subclass of Abstract whsitle data unit for loading whistle contours from .mat files.
Holds a whistle group and some extra information on sample rate, fft length and hop and the start of the processed file.
Subclass of Abstract whsitle data unit for loading whistle contours from .mat files.
A delphinID test suite.
The delphinID worker.
DelphinID user interface components.
Observer interface for DIfar demultiplexing.
options for Deployment export collected by the export Wizard.
Deprecated.
Functions to gather data for the deployment document from all around PAMGuard.
Class to give a general overview of all the effort in PAMGuard which will form the
basis for Deployment Documents.
Hydrophone depth may be read out in a number of different ways and may
arrive from a number of different sources.
Panel containing the three test entry fields for nilus.DescriptionType
Class to handle warnings from deserialisations which occurr when classes no longer exist.
Deprecated.
Detection plot which can display single or groups of detections.
This class filters events on a channel if the time passed since the last detection on the same channel
is less than a minimum interval.
Class for grouping any type of data together.
A detection plot display with convenience functions to set any type of data unit.
A group detection display with all the bits added to allow the display to be used in the FX GUI as
a stand-alone user display.
Receives detections, which may come from multiple channel groups, which in
the case of the click detector means they may not be in order (or for
any other detector in fact) and may have come out of multiple threads,
so can get dead messy.
Listener for detection group.
Deprecated.
Localiser which deals with detections in which one or more groups of
detections are being localised.
Options that get passed into a detection group localiser.
A summary of information associated with some marked data units.
Panel to show a table of data on all DetectionGroup data units.
Basic paramter for whistle group transforms.
This class is used to uniquely identify detections.
Interface to allow a bit of flexibility as to how different 'detector' outputs are
matched with generated QA sounds.
This is intended to be overridden by any class which wants to monitor the progress of a detection match.
An interface to satisfy basic plots.
A detection display plot usually plots a single detection.
Parameters class for the Detection Plot Display
The detection plot projector deals with all co-ordinate conversion from screen to the pixels
and vice versa.
Deprecated.
Functions for handling output of Detections documents.
This class is used to track statistics about a running detection.
This class is responsible for writing ThresholdDetectorDataUnits to the database (if configured).
General interface for components which are going to get included in alarge dialogs
Reinstated Target motion add-in as used by the click detector.
Modified version of the map panel so that some of it's drawing can be enhanced / reduced
to suit the needs ot the target motion dialog.
Scroll pane for which we can set a maximum height in characters for the standard font.
Sits at the top of the DIFAR queue panel
Some small changes to the generic class for copying data from binary data files to database files.
Data selector for DIFAR data units (displayed on the map)
Initially just a copy of the Whistle invalid input: '&' Moan Data Selector.
This is a main panel which will hold as many other panels as
we need for the DIFAR display system.
Display window for viewing and selecting bearings from difarDataUnits
Contains a spectrogram, the DIFARGram (i.e.
Localisations from a single sonobuoy are bearings originating from the
sonobuoy.
has a case block at bottom of class to copy/paste into methods
Structure to hold data returned from the native C call
The DIFAR SidePanel contains the list of DIFAR classifications, to allow
the user to choose which classification is assigned by default.
Database storage of DIFAR information.
Set the symbols for DIFAR Time-Data plots.
A control panel which will most likely sit in the right hand
edge of the DifarGram display, but keep separate in case
we decide to put it somewhere else at a later date.
Spectrgoram projector for drawing directly onto the spectrogram display.
Whistle fragmenter which completely discards all regions
which have more than one peak in any slice.
Functions to get and display disk space in sensible units.
The display connection node changes the colour of connection lines which
connect from parent nodes.
Panel to go in the top of a clipDisplayPanel which has all the controls needed
to set contrast, colour, etc.
This is a simple interface which should be implemented in the controlled unit of a localiser.
Singleton class to manage display names and make sure they are unique
across the entirety of PAMGuard .
Standard layout for the queue part of the display
A standard display panel that can be incorporated into other displays, eg.
DisplayPanelContainer is an interface implemented by graphics components
which have the ability to incorporate DisplayPanels from other Pamguard
modules.
Plug in panels for the display.
DisplayProviderList is used to manage a list of possible providers
of display panels that may be incorporated into other displays.
Data stored in a list for each component of a User Display Panel.
Deep learning results annotation.
Saves deep learning annotations in binary files.
Log deep learning annotation to the database
The DL annotation symbol chooser
Annotation type for data from the matched click classifier.
The classifier model.
Model specific GUI components.
Selects which type of DL classifier to use.
The deep learning classification process.
A class name along with a unique identifier number.
Manages assigning class names and unique identifier numbers for each class type.
Module which uses an external deep learning classifier to identify any data
unit containing raw data.
The JavaFX GUI for the DLControl...
Score a data unit with a deep learning annotation.
Creates a data selector for the deep learning module.
Data selector of DL data units.
Paramters for the DL data seelctor
A data unit created from classification results of DL model.
Datagram showing the raw model outputs form the classifier.
Manages default models.
A detected DL data unit.
Saves and loads binary data for classified Deep Learning data units.
Holds classified data units from deep learning model.
The datagram provider for classified data deep learning units.
Graphics for the detected data units
Allows the deep learning results to be plotted on the TD display.
The DL detection plot provider.
Listener for downloading files.
Manages the downloading and unzipping of models.
The detection graphics for the DL localiser.
Data block which holds deep learning detections derived from groups of data units.
Plot results from deep learning group detections.
Logging for deep learning detection groups.
Logs the the children of the deep learning detection group.
Symbol modifier for DL groups
Contains both a list of transforms and preview image of the waveform, spectrogram or other visualisation of
the transform.
The localisation for a DL data unit.
A default model that can be loaded from a file or a URL.
Holds classified data units from deep learning model.
A pane which allows users to select a model and then loads the model on
on a different thread, showing a progress indicator.
Runs the deep learning model and performs feature extraction.
The offline process.
The parameters for the deep learning prediction plot.
Decides whether a prediction has passed a threshold to be used to create a new
data unit.
A data filter which filters data by the maximum prediction value
for different classes.
Parameters for filtering by the minimum prediciton value.
Swing panel for Deep learning predicitons.
Plot the raw probability information.
The DL detection plot provider.
Settings pane for filtering deep learning results by class prediciton.
Binary storage for the all the model results, i.e.
Saves the classified DL data units to a database.
JavaFX pane for the deep learning data selector.
Swing panel for the deep learning data selector.
The settings pane.
The DL side panel for the Swing GUI.
Status reporting for the deep learning module.
The DL symbol modifier.
Parameters for colouring symbols by deep learning probability.
Swing symbol options for the annotation pane.
Creates a que for grouped data units for classiifcation.
Shows preview spectrogram or waveform for a DL transforms
Settings pane for all DLTransforms
Pane which allows users to create a series of transforms for
raw data before inputting into a deep learning model.
DL transforms pane launcher - HACK to get JavaFX to work in Eclipse for some reason.
Test the dl transfroms pane.
Basic information about a document that can be used to
make document lists.
Map of all documents, with links or labels of Documents associated with this project.
information about a document AND the nilus object to go with it.
Generate short click like sounds which consist of an unwindowed single
cycle sin wave.
Class for filtering double of float values in a database table
A mouse adapter which allows panning of the display.
DragResizer can be used to add mouse listeners to a Region
and make it resizable by the user by clicking and dragging the border in the
same way as a window.Control field with two spinner.
Classifier which returns a random results.
Converts a string into a time.
Status information on how far conversion progress has gone.
Information about dwv files extracted from
Sound TRap xml log files.
Reader for dwv files.
Interface for implementing dynamic settings panes.
A dynamic settings is a settings pane which allows users to change settings instantly.
An echo detection system can provide everything there that is needed to decide whether clicks
are echoes or not.
Interface to classes which do the actual work of detecting echoes.
Left hand side of the dialog which displays all the components which can be
added / removed.
Record scroll effort.
functions for working out total effort and periods of recording from a variety of sources, which may be
the recordings database, binary files, etc.
Singleton class to provide management for all types of Effort in PAMGuard.
Handle problems when binary and raw effort don't add up
Set of functions that can be returned from any datablock which can
give information about effort.
Filter which checks whether possible track might be electrical noise.
Draws an elliptical error.
A 3D elliptical error.
A totally empty table definition.
Class to hold new emulated data
Handles generation of a single buoy emulation.
As with the binned Detections, this may generate multiple encounters
at the same time for different types of sounds.
Window that only scales the ends of a waveform - suitable for calls such as whistles
where we want to leave most of it alone.
Settings pane for the Ishmael detector.
Parameters for the energy sum detectors.
interface which can be added to an enum so that it provides tooltips as well as toString.
Class for calculating errors from localisation data.
Functions for putting together an event, similar to functionality within
the click detector.
Event check repair task, so it can be called from batch processor
since events are probably all in memory, ignore normal ways of
accessing data and do own things.
Reinstated Target motion add-in as used by the click detector.
Deprecated.
Reinstated Target motion add-in as used by the click detector.
Deprecated.
Reinstated class to rotate and transform an event so that it's track lies as close
as possible to the x axis.
Simulates some clicks to test the MHT algorithm on.
Create an example sound.
The example sound factory
An example sound type.
Quick test of how long exception handling really takes.
Exits PAMGuard.
This is a simple exponential (decaying) average.
Detections handler already has a very system for looping through
data which is a bit different to the standard one in offline task,
so an going to override the main background function and do it our
own way!
Create a pane to export data.
Manages opening settings dialog and saving settings for both FX and Swing GUI's
Some functions useful for exporting manually annotated files.
Allows files to be copied to clipboard.
Parameter for the exporter.
Handles an offline dialog for processing offline data and exporting to bespoke file types.
Export data to a file type.
Tests for export functionality.
Slightly standardised panels to put into the export wizard
so that it's easy to work out which 'card' we're on, etc.
An extension structure is a structure which allows users to clean up connection nodes.
Handle data from multiple external mouse handlers returning
an OR of their response to the various functions.
This is an external mouse adapter class which should work with both Swing and Fx
Mouse events.
Interface for showing a pop up menu on a mouse action within an ExtMouseHandler.
Simple implementation of a JavaFX pop up menu for a an ExtMapMouseHandler.
Fancy button which has a normal button AND a drop down
for other web client pages.
FFT Wrapper which uses the edu.emory.mathcs.jtransforms.fft
transforms library for the actual FFT calculations.
This has the same functionality as IirfFilterm.
Deprecated.
Class to better handle Complex FFT Data, including the FFT length along with the
Complex data - this is important since FFT length cannot be extracted from the
length of the Complex array since it's sometimes only stored half the fft length
not the entire thing.
Exception thrown by the FFTDataOrganiser.
Interface to indicate that a data unit can provide it's own FFT data.
Interface to indicate that the data units contained within this datablock
can provide their own FFT data.
List of FFT Data provided by the FFTDataOrganiser.
Functions to create blocks of FFT data for multiple channels as needed by
various localisation algorithms in PAMGuard (e.g.
The FX GUI for the FFT module.
List of possible input types for the FFTData Organiser:
FFT Data from an FFTDataBlock
RAW Data from a PAMRawDataBlock
FFT Data from within a data unit (e.g.
FFT Data from an FFTDataBlock
RAW Data from a PAMRawDataBlock
FFT Data from within a data unit (e.g.
Settings pane for the FFT module.
Plots the spectrogram of a detection which already has a calculated spectrgram, e.g.
Plots spectrogram data.
Handles efficiently plotting click FFT's on the frequency axis.
Settings for displaying raw data clips on a frequency time display.
The settings pane for the FFT plot.
Transform pane for Fourier transform
Shows the file date.
This was WavFileDataMapPoint, but can be used for any file types with OfflineFileServer.
Extract file dates from the file name
Simpel dialog component which can interact with a file date.
Pane which allows settings for a FileDate to be changes.
Functions connected with storing data files.
Used by FileInputSystem
Implementation of DaqSystem for reading data from audio files.
Create a list of files of a given type within a folder structure.
Information about a list of files.
Has a single callback to get the results of a file list worker.
Class to list files in one or more directories.
Information on a file path or folder path that can be used with the
backup system
Swing component that can be used to set a file location for source or destination files.
This is generally used as a temporary class for calling Copy and move actions since
by necessity the source and destination locations are held in different places.
Parser which calculate the time from a file's name.
Class for breaking a file name down into it's constituent
parts.
Playback of sound from wav files.
Interface to device types that can be used to play
back sound when acquisition is reading audio files.
The settings pane for file playback.
information added to a FileDataMapPoint when only part of the file
is associated with this map point.
Filters raw data using a specified filter.
Create a more generic dialog panel for the PAMGuard
filters which can be incorporated into larger panels
if desired.
This interface abstracts the consumer of filtered event objects.
This class tracks detections (after the DetectionFilter has done its business) when they are active, collecting statistics such as
startTime, duration, and the peak time/energy values.
FilterPArameters for use when the filter is on it's own (within a FilterController)
rather than combined into some other detector.
A panel that can be included in various places which displays a list
of filter properties.
Settings pane for filter module.
Slider for the high pass filter sound out process.
Pane for a waveform filter.
Arbitrary response filters.
FIR filter method, filter design uses a Cheychev window function.
Single list of detections, all in the same list so that
they can easily be sorted prior to final grouping....
Common interface for the results of fit tests, e.g.
A modification of JLabel which can only grow, i.e.
Symbol modifier which cannot modify anything....
Opens a Flac compressed audio files.
User: hansolo
Date: 16.04.14
Time: 22:07
Pane which flips to show "back" and "front"
User: hansolo
Date: 16.04.14
Time: 22:06
A pane which can flip to show another pane (referred to as the advanced settings pane).
Read out a Fluxgate World 3030 shaft encoder.
JavaFX pane for the folder input of the sound acquisition.
Control parameters for FolderInputSystem
Read multiple files in sequence.
Description of the Class
used to make sure counters are unique based on table name
Layer that sits between the form description and the actual edit
dialog for altering a form.
Class to hold plot options for a single form.
Class to provide a panel of plot options for a single Logger form.
Manage a bit of persistent data for a single Logger form description.
Controls the settings for a single Logger form description.
Functions for handling hotkey events.
Easy class to allow other parts of PAMGuard to monitor some or all
Logger forms.
Some general parameters for PAMGuard Viewer mode
The top-level Logger GUI element -- a Tab in the swing GUI.
Utility class to return details of a data unit found on a graph.
Utility class to return details of a data unit found on a graph.
Wrapper class to hold a data unit and some click information.
Functions for importing FPOD files.
Holds an FPOD detection.
Holds an FPOD header information
Holds FPOD wav data.
Parameters class for fragmented whistle classification.
interface for classes which are able to parameterise a whistle fragment
Store for lots of whistle fragments during whistle classification
A simple control which has a high and low pass editiable frequency spinner.
Creates a standard panel to display frequency resolution information
A set of static functions for formatting frequency values in a common way,
i.e.
Format frequency string converter.
A
Graphics2D implementation that writes to a JavaFX Canvas.A graphics configuration for the
FXGraphics2D class.A graphics device for FXGraphics2D.
Utility functions to load image files into Canvases to use as icons in
displays, etc.
Class to get called early on which will initialise FX
so that it can be used within the Swing GUI.
The advanced pane for the generic classifier.
Generic dialog for the backup system that can take any
number of BackupFunction items, be they streams, decisions, actions, etc.
Generic data plot info which can work for a wide variety of data types.
A very generic data plot provider.
A generic model - can be load any model but requires manually setting model
*
Test the generic classifier.
Import and export settings files for the generic classifier
A Data Info which plots 1D line data i.e.
Settings pane for the generic pane.
Parameters for the deep learning module.
Functions for saving and loading generic model metadata information.
UI components for the generic model UI.
Generic model worker.
Settings pane which holds the symbol options from the data block of the plot info.
Generic TOAD calculator which does it's best by any type of sound.
Dialog panel for a generic TOAD calculator.
General parameters for detection TOAD measurement.
Get XML settings from one or more modules.
Global parameter pairs set at startup time.
These are the arguments passed to the command line.
These are the arguments passed to the command line.
Defines the assumed medium that sound is propogating through i.e.
The type of medium
Manages the global medium @see GlobalMedium
Stores parameters for the current medium.
Some global management of PAM symbols, in particular needed for superdetection
symbol options when a supdet symbol manager says to use colour by superdetection.
Class owned by PamController which manages time corrections from NMEA sources and / or NTP servers, etc.
Recreate functionality of SIO function GPL_Quiet.
Note on times for GPS data ...
Add a bit of extra functionality to GPSDataBlock so
that it can check new GPS data are 'reasonable'
and flag bad ones.
Class of utilities to help match times to GPS locations.
This is more complicated than the stramerDataIterator since it needs to
combine data from two sources.
Terminal component: Use bitmap font to render
3D grid for localisation.
Parameter control for all 3D grids.
Deprecated.
Deprecated.
Deprecated.
Listeners for changing selected detection in the GroupDetectionDisplay.
A ComboBox which shows a selectable list of channel groups.
The grouping part of a grouped source pane which can be used
separately from the entire grouped source pane.
Interface to add to datablocks which have channel grouped data.
Temporary holder for raw data with a pre defined size.
Pane which shows a combo box to select a parent data block and has channel
check boxes which can be grouped.
Specific parameters which always to with a GroupedSourcePanel
Information about a channel group used by the DetectionGrouper
Used to store localisation results if a group of PamDetections (rather than one) is used.
Provides information useful for localisation from groups of detections.
Result class for the a group localiser.
Many classification functions need the mean values of
each parameter from a group of training data.
Represents the parameters that make up a guard band, used as
input to the Likelihood detection algorithm.
The GuiFrameManager manages multiple PamGui frames, each
of which may contain multiple tabs of module information
and a side panel.
Information about GUI frames.
information from one point in a harp header.
Enum of heading types (mostly for track output in Deployment documents)
Can be used to get notifications into any bit of pamguard when things are changed in
one of the sliding dialogs.
Something similar to the hiding panel, but doesn't get put into an existing
panel, but rather floats over the top.
Hiding pane which can be added to any node.
Class for a hiding, possibly sliding panel to hold things like
the side bar, top control panel of the clip display, etc.
More sophisticated side panel container which can
close itself down to a very small strip to make
more room for main display items.
A hiding tab is is used in a HidingTabPane
The hiding tab pane has tabs which collapse in size rather than the tradition tab panes in which switching a tab simply
removes the current tab from the pane.
Functions to calculate the Hilbert transform of data.
Doesnt' store fragemnts individually - just adds their data to a series of
histograms and whenever the parameters are requried, it estimates those
parameters based on the contents of the histograms.
Provide a basic display panel for showing data from any number of
PamHistograms, either in a single panel, or as a series of sub panels.
Holds hover data.
Atlantic version of Google's humpback whale network.
Panel for the ArrayDialog to show a diagram of the array
Panel for the ArrayDialog to show a selection of hydrophone arrays and
listed details of the currently selected array
Dialog for adding / editing the details of individual hydrophone
elements in the array.
Class for importing hydrophone data from external file and saving to database.
HydrophoneLocator is an interface for objects that can work out the true positions of
hydrophones based on any or all of the following information
Class for handling different hydrophone locators.
Methods for getting streamer origins.
Property class for a hydrophone object.
The settings pane for a single hydrophones.
Table which allows users to add and edit hydrophones.
Hyperbolic localisation attempts to localise using the INVERSE problem.
Keeps a copy of the raw position vector for hyperbolic localisation.
Hyperbolic localisation using methods described in Gillette, M.
Holds settings for hyperbolic loclaiser.
Holds settings for hyperbolic loclaiser.
Hyperbolic settings pane.
Adv IDI chi2 pane allows.
A data acquisition system that uses an Ocean Sonics icListen to acquire the data
to be streamed to and used by PAMGUARD.
Creates a click ICI histogram display add-in
Parameters for the IDI Display
Calculate the chi2 value based on slowly changing inter-click-interval.
The IDI Chi2 Pane.
The IDIChi2Parmas.
Classification result from the bearing classifier.
An inter-detection interval based classifier for click trains.
The IDI classifier graphics.
Holds IDI data.
Holds some basic IDI info on the click train.
Calculates the inter-detection interval (IDI) (usually clicks) interval for a set of data
units based either on the time stamp or a more complex sample rate and cross
correlation calculation.
Pan which allows users to select IDI measurement limits for click trains.
A panel which allows users to manually add a heading and roll angle.
Pane which shows image angles and animal bearing and distance.
Time offset for PamImages.
Interface for reading image timr from filename.
Text field which can immediately respond to text being entered and
update a corresponding value in a PAMGurd control structure.
Generic Dialog for opening a file.
This class brings together the abstract classes and display componwenets which create a data import system for PAMGUARD.
General PAMguard class for managing import and export of specific Java object types.
Pane for importing an exporting .pgtf settings files.
Simple dialog asking the user to input a date for GGA string input.
Class to take external GPS data and record in a database table.
Simple dialog which returns a path to get GPS data from;
Import a template from a csv file.
Import a .mat file of a click template.
The IMU module may have multiple ways of aquiring IMU data.
Dialog box for IMU calibration values.
Sets up a thread to import .csv files and save data units to a database.
Import IMU data from .csv.
Uses sensor information, heading, pitch and roll, plus GPS co-ordinates and height to calculated the position of an animal.
The Inferno colourmap
Class to conduct an infinite sort of data.
Wraps multiple Infinitesorts to provide something akin to
Matrix sorting.
Extension of InfiniteSort to also keep a running total of mean squared
values.
Panel of information near top of main frame.
Instrument identity panel, contrians additional fields required by Tethys.
Integer symbol modifier.
Choice box which allows selection of interpolation options.
Dialog component used by both the streamer and the hydrophone dialogs
Interface for an interpolator.
Radio buttons which allow selection of interpolation options.
Class for filtering integer values in a database table
Plots the raw Ishmael data (i.e the detection values and noise)
Brings together groups of IshDetWrappers
Beginning of a binary data source for the Ishameal detector to save the
Ishmael data so new peaks can be picked out.
Control for the Ishmael Detector modules.
Basic detection on a single channel for the Ishmael det/loc.
This has information for a single IshDetection that indicates (1) whether
the detection is an 'anchor' detection within this channel, i.e., whether
it is the principal one of a group of multipath detections, and (2)
whether the detection is an anchor detection across channels, i.e.,
whether it is the anchor detection on a specially-designated reference
channel.
Standard data unit for Ishmael detector output.
This is the abstract superclass for all the "Ishmael detectors", i.e., the
detection PamProcesses that use a detection function and threshold in the
course of doing making detections.
IshDetGraphics displays a detection function from an Ishmael-type
detector (EnergySum, MatchFilt, SgramCorr).
Groups togetehr a series of IshDeections.
Dialog to change Ishmael display settings on the spectrogram plugin.
Ishamel display parameters for the Spectrogram plug in.
Energy sum pane.
Plots a whistle contour over.
Binary data for peak binary data source.
Whenever one of the IshLoc routines calculates a location
(bearing, X-Y position, etc.) it generates an IshLocation,
which is then passed to the rest of PAMGUARD via
IshLocProcess.outputDataBlock.
This implements the two locators from Ishmael.
Two-hydrophone bearing calculation.
Two-hydrophone bearing calculation.
This is a superclass to a "real" localization class.
Plots Ishmael detections on the TDdisplayFX
The plot provider for Ishmael detection data.
Plots the raw Ishmael detection output.
The Ishmael raw detection output plot provider.
Process for choosing a symbol to represent IshLocalizations on the
map (and elsewhere).
FX implementation of the Ishmael detector.
Generic process which picks a peak from any of the Ishmael detectors, e.g.
Spectrogram correlation pane.
IshTrack may not need to hold any location information itself - it mainly
holds a list of IshAnchorGroups, each of which has a PamLocation object, the
contents of which will make up a track.
Functions associated with pulling ITIS information from the databsae.
Some MR defined ITIS codes for non animal sounds.
Global flag set at runtime for Jamies development flags.
The
JFontChooser class is a swing component
for font selection.Converts arrays of numbers into string representations which are a little
bit, but not entirely json like for writing to text fields in the database.
Class to hold data that will be converted into a json-formatted string.
Dialog for smoothing kernel options.
Classifier which uses deep learning models from Meridian's Ketos framework.
Classifier which uses deep learning models from Meridian's Ketos framework.
Paramters for Ketos classifiers.
Settings pane for a Ketos classifier.
Test the Ketos models in PAMGuard.
Result from a Ketos classifier.
UI components for the generic model UI.
Runs a Ketos deep learning model and performs feature extraction.
Class to generate standard panels for plot keys.
Kills PAMGuard, not attempting to stop it first.
Classifier which uses deep learning models from Koogus' framework.
The Koogu model worker.
Dialog for adding and removing clicks to and from
offline events.
Class for storing Landmark information.
Imports landmarks.
List for storing landmarks.
Pane to edit a group of landmarks
Contains GUI components for the landmark method.
Contains GUI components for the landmark method.
Pane which allows users to create a land mark.
Stores a set of latest data units, only one per data block and can
retreive them in various ways.
Class for handling and formatting latitude and longitude data.
holds gps stamp, both lat and lon will save separately in the data base but
will display in between 1 to 3(if time too) fields on the form and in one in
the data table.
Set of functions to set up reading and writing of
latitude longitude and depth data to a database table.
Shows the value of a latitude or longitude in various standard formats.
A better Lat Long editable dialog strip, containing
the functionality developed for the new Array Manager.
Pane with controls to to set the values for a Latitude and Longitude.
A pane which shows a latitude or longitude.
A least squares algorithm for solving particular localisation problems.
Least squares localisation for Target motion analysis.
Implmentation of the least squares locaiser.
The length of a click.
The Class LikelihoodDetectionParameters provides the standard PamGuard
abstraction of system-save-able settings for a module.
The class LikelihoodDetectionParametersDialog is created by the LikelihoodDetectionUnit to
integrate configuration of the likelihood detection module into the configuration menus
of PamGuard.
The class LikelihoodDetectionUnit implements that standard PamControlledUnit functionality
required by PamGuard for a plug-in module.
The class LikelihoodFFTController manages the automatic creation of any
FFT processes that are required to support the target configurations.
The LikelihoodFFTParameters class represents Likelihood Detector-specific FFT
parameters and calculations that support the auto-creation of processing streams
for the target configurations.
Errors are generated from the curvature of a Chi2 surface.
This is the PamProcess implementing the Linear Averaged Spectra processing block for the likelihoodDetectionModule.
Train and run linear classification
Wrapper to make a linear localisation into a group localisation
Deprecated.
The line info.
Observe a line of text
Functions for updating data in a linked database table, i.e.
Class for issuing commands directly to the linux shell on the cRio
Copied from https://www.peterfranza.com/2008/09/26/little-endian-input-stream/
LM: The Levenberg-Marquardt algorithm for least-squares minimization
Monitor class for multi thread data loading in viewer mode.
Keeps a record of the last load postion if a load thread is cancelled.
Interface to attach to localisation algorithms which can provide basic information
(primarily for better book keeping and Tethys output)
Holds information about a localisation.
This is a wrapper around any type of algorithm parameters so that
they can be easily serialised into a single hash table in the main
group localiser parameters section.
Control for the localiser display.
Main pane for the localiser display.
~
Creates AWT instance of the localiser embedded with a swing container.
Interface for loclaiser error.
All localisers in PAMGuard should satisfy this interface.
Class to build a single localisation document during export.
Creator thingy that Localisation algorithms can use to overwrite any standard
behaviour in LocalizatinBuilder.
Handler for localizations.
Enumeration of the ReferenceFrame field in nilus.Localize.Effort.CoordinateReferenceSystem.Subtype
Within Tethys, these are only ever used in their String form.
Within Tethys, these are only ever used in their String form.
Enumeration of the ReferenceFrame field in nilus.Localize.Effort.CoordinateReferenceSystem.Subtype
Within Tethys, these are only ever used in their String form.
Within Tethys, these are only ever used in their String form.
Manage location options for the different clusters and tests.
When taking photos users may have been at one location, on a boat, or at multiple different static locations.
Class for settings to be optionally held by hydrophone locators
Class for holding information on what a type of information a localisation has.
Class for drawing localisation errors.
The loc info pane.
Utilities associated with log files.
A LoggerForm is the central component of all form types, inclucing normal forms
popup forms and subtab forms.
Handler for sub tab commands for sub tab forms.
Adaptation of TabbedPane to provide a bit of extra support for logger forms,
such as mouse click actions on the tabs themselves, etc.
Functions for writing a list of modules into any database as character data
Runs at DAQ start, goes through the settings manager list and for each
set of settings, it serialises the settings data into a binary array, this
is then converted from binary data to 6 bit ascii data (using the character set
from the AIS standard, which should be compatible with any DBMS).
Performs a multinomial logistic regression using WEKA library
Functions for writing serialised Pamguard Settings into any database as character data
Runs at DAQ start, goes through the settings manager list and for each
set of settings, it serialises the settings data into a binary array, this
is then converted from binary data to 6 bit ascii data (using the character set
from the AIS standard, which should be compatible with any DBMS).
simple data unit for use with the LogXMLSettings class
2022 Additional way of saving settings for each module into the database in more human readable
XML format.
Change listener for PAMGuard Lookup items.
Lookup component to go in dialogs, Logger forms, etc.
dialog for editing the contents of the lookup table.
hold data for a single item from the lookup list.
Handles information for a single list from the look up table
Singleton class for managing a common lookup table for
many PAMGUARD modules (following from Logger format)
Wrapper class around other available magnetic variation models so that I can switch
to other models easily should the need arise.
SSH Terminal frame
Interface to add to any configuration settings object which
will contain / generate / allow creation of descriptors
of what's within that parameter set.
Node which handles data input for a ManagedSettings parameter.
Wrapper around a SettingsPane to provide simpler
functionality for including panes from one part of PAMGuard in
another part.
This contains absolutely nothing since individual SimpleMap displays handle their
own settings.
Holds information about all things plotted on the map,
primarily how long they should plot for and whether they
are currently enabled or not.
PArameters for MapDetectionsManager which
can be easily serialised and stored in pamsettings
Settings for Map Grouper.
This is the actual map display, with the bluebackground, the gps track, etc.
Convenience extension of Point3D to easily get 2D points.
The map needs a process since it now produces data units to go into a data block.
The Map Rectangle Projector.
A layer which is added to a 3D map.
Class that helps to chose whether a data unit within a given mark is
actually wanted or not.
PArameter set for handling mark overlays selections.
Extra information for OverlayMarks which can be provided from
the mark source.
Simple panel of checkboxes which can be used by an overlay marker
(i.e.
the idea is to visually represent each localisation three dimensional space to allow easy manual analysis of the likely location of a cetecean location.
standard panel that can select mark providers
of particular types.
Singleton class to handle mark relationships.
Centralised location where all relationships between markers
and the marked are stored.
Database logging for stand alone Annotation data.
Master PAMGuard array localiser.
Master reference point for PAMGAURD.
System for master references used by various bits of PAMGuard.
Annotation for the matched click classifier.
Annotation for the matched click classifier which adds the match and reject correlation values for each template pair
to the binary files.
Writes a matched click classifier annotation to the database.
Annotation type for data from the matched click classifier.
Tests for the matched click classifier.
Matched template classifier parameters.
Class to hold results from the matched click classifier
Deprecated.
Manage detection matchers and their settings.
Stores information for a click template
Work out confidence intervals for an
array of matrixes.
Dialog for showing the content of a matrix.
Get the mean and eventually some other parameters from a list of
matrixes.
Matrix operations for arrays of Complex data
Really need to write these for ComplexArray rather than Complex[] since
it's a lot faster.
Information about an MCCboard
Measurement Computing constants copied from the cbw.h header file.
JNA interface for Measurement Computing acquisition boards.
Interface to the MCCLibrary JNA calls.
Interface to Measurement Computing data acquisition boards.
Dialog panel for MCC boards.
Useful functions that use the JNI but use some PAMGuard specific
structures, so don't want them in the JNA class in order that that
can be used with other software.
Markov chain Monte Carlo (MCMC) is a minimisation technique used widely in a variety of field, from finding exo planets,
to solving complex intergals.
Elliptical error for MCMC.
Plots some point son the map
An MCMCHM (Markov Chain Monte Carlo Hydrophoe Movement) algorithm adds hydrophone positions as a parameter in the MCMC localiser.
Deprecated.
Paramters for running a Marklov chain Monte Carlo algorithm.
Median Filter for a finite amount of data.
Now that there are many menus, there will several instances of each
menu item.
Holds info allowing a swing menu item to be converted to JavaFX nodes.
Class to handle Project MetaData.
Time Parser which uses image metadat.
Grid search using Matched field Processing
Not completed - will take far too long and need too much memory
to process at resolution required for NNHF clicks.
AlgorithmInfo for the MHT algorithm.
Class for unpacking algorithm strings.
An MHT algorithm with all the hooks required for running in MATLAB.
Any variable used by the MHT algorithm
Parameters class must extend this.
The MHTChi2 provider manages the mhtchi2 algorithms for each track possibility.
Handles which type of chi2 algorithm is being used and
what settings pane to create.
A variable which is used to calculate chi2 value.
MHT classifiers for the Java / MATLAB interface.
A click train algorithm based on a multi-hypothesis tracker (MHT) which groups data based
on a minimisation function.
Handles removing garbage tracks from an MHT algorithm's probability mix.
Graphics for the click train detector.
Core functions for a multi-hypothesis tracking (MHT) algorithm which groups
data based on a minimisation function.
Options for the MHT algorithm
Parameters for the MHT algorithm, contains two serializable parameter
classes, one for the MHTKernel and one for the MHTCHi2Provider.
The main settings pane for changing settings of the MHT algorithm.
Basic side pane which shows the MHT metrics.
Swing version of the side pane.
Simple implementation of click train detector which tests the MHT kernel and a simple chi^2 algorithm.
MHTTestGraph for testing the MHT algorithm
Testing of some of the algorithms
The settings pane for a MHT chi2 variable
An MCMC pane with a few extra options for Mimplex localisation.
Pane which shows all the different.
Minimisation algorithm.
Class which must be populated for various minimisation algorithms
Pane which allows users to set minimum and maximum value of a variable
the number type e.g.
Adds annotations to data units.
Export a click to a MATLAB structure.
Export data for any data unit which implements raw data holder.
Export a detection to MATLAB
Handles the conversion of data units into MATLAB structures.
Export to MATLAB .mat files menu.
Deprecated.
Revamp of the earlier MLGridBearingLocaliser but with a more sensible
coordinate frame.
Export a noise measurement to MATLAB
Export data for any data unit which implements raw data holder.
Exports super detections.
A component that looks very much like a normal popup menu, but the
show(...) function doesn't return until any menu actions are complete.
Generic pane which shows a list of localisation algorithms
Handles the saving and loading of Model results from binary files.
Data unit which stores classification results from a classifier model
Reinstated Target motion add-in as used by the click detector.
A connection node which represents a PAMGuard PamControlledUnit.
Class to contain module specific information
which will be stored at the end of a binary
data file, just before the BinaryFooter.
Class to contain module specific information
which will be stored at the end of a binary
data file, just before the BinaryFooter.
Handles module icons in PAMGuard.
Enum for module icons.
Object which holds the type and name of a PAMGUARD module
and can read and or write it from file.
information on a module node read from a settings xml file.
Holds seriliazbale informations on a ModuleConnectionNode.
A node which shows the internal structure of a PamControlledUnit
Used to control menu groups for the main PAMGUARD File/Add Modules ...
Class for dealing with sleecting individual data units with a Mouse.
Almost identical to copy file.
Model of movement of a simulated object.
Manage a list of movement models for the simulator.
Moving average filter.
A matrix for moving average calculations, initially designed to
replicate some functionality in SIO GPL_Quiet function.
Parameters and useful functions for a single MT classifier.
Classifier which classifies clicks.
Offline task for reclassifying clicks.
A pane with controls to set a single matched click classifier.
Test for the MTClassifier.
A classification for a click train.
The JavaFX GUI for the Matched click classifier control...
Offline processes for the matched click classifier.
Calculates a correlation difference coefficient between a match and reject click template
and classifies a data unit based on a threshold value for the coefficient.
Settings Pane for matched template parameters.
Simple test of multiport communication.
Atlantic version of Google's humpback whale network.
Launch several terminal a place them on the screen
The algorithm class for the Minimum Variance Distortionless Response beamformer.
MVDR (minimum variance distortionless response) beamformer provider
Calculate the nanosecond time from the sample number.
Utility to measure execution times of various parts of PAMGuard.
A 'global' synch object that can be used by both the GPS data block
AND the streamer data block since they are often working together
with dual iterators, so can lock / concurrently modify, etc if
not carefully synchronised together.
A pane which is somewhat related to a tab pane but where the tabs are on the
left or right and horizontal instead of vertical.
Class of functions to help interpret incoming audio data - put
into a separate class to keep functions separate from rest of NetworkREciever class.
Class to handle remote control of PAMGuard.
Buoy data names in the hashtable of paired values can be any string type, but am setting
a load of them here, so that constants can be used wherever possible to improve
programmer reliability.
Interface for classes using the NetworkReceiveThread.
Class for drawing buoy positions on the map.
Class for handling Network data, will reduce number of parameters in
Network calls and be a LOT more flexible.
Functions to pack up data for sending over the network.
Receive near real time data over the network in the form of packaged PamDataUnits.
Send near real time data over the network to another PAMGUARD configuration.
this uses jAsioHost for acquisition.
The NewBandNameDialog is used by the LikelihoodDetectionParametersDialog to allow the
operator to specify a band name.
The Enum BandType specifies whether the band name will be for a signal band or a
guard band.
Deprecated.
Pane which shows hardware channels on a National Instruments device mapped to PAMGuard software channels.
Constants from NIDAQmx.h
Nidaq is is a wrapper style class, which makes calls to native C++ functions
within in a .dll library.
PArt of the system for playback from wav files.
A few static checks of some nilus classes to see if it's
worth writing them or not.
Wrapper for Nilus data objects.
Class to wrap up a nilus object so that it can be saved using Java serialization.
Functions to automatically unpack a document from Tethys into a nilus object.
DAQ system to receive data from remote NI Compact Rio chassis in compressed
or uncompressed data formats.
Playback system to use when acquiring data from NI cards.
UDP commands to and from the NI CRio chassis.
Intermediate class for all NMEA data types.
Special type of data block, just for NMEA data.
Interface to assist a datablock in setting up emulated NMEA data.
Class which provided an editable ComboBNox for selecting
NMEA string.
Extract noise statistics from acoustic data.
Where to store data for detectors which have a specific noise measured output
i.e.
A wrapper around non scrollable cursors to make them behave in the same
way as a scrollable cursor.
This is a data type for normalizer output.
The data type generated by the normalizer PamProcess.
Interface to abstract the various normalizers for the likelihood detector
It is OK to return a null DataUnit if you cannot yet produce data based on
the input given.
This PamProcess implements the normalizer of the likelihood detector.
A simple convenience class to pair signal and background time constants together.
Very simple panel to force a component to be at the north end
of a panel.
Not really a beam former.
Provider for the null beam former.
Null data selector that doesn't actually create a data selector.
the Null fragmenter doesn't break Connected Regions at all.
slightly fudged contour which doesnt' have any points for situations where
no contour was found within a GPL detection.
Null GUI controller which will get used with the -nogui options.
The number spinner allows users to select a number by spinning through a range of numbers.
The default skin for the NumberSpinner control.
Contains information required to load data from a file or other source into a datablock.
Handles the loading of offline data from a PamDataBlock.
Class which get's held within a PamDataBlock which
provides summary information on data within that
block when operating in viewer mode.
Map points to go into an OfflineDataMap.
Interface implemented by PamControlledUnits which
are capable of reloading and restoring data when operating in
Viewer mode.
PamDataBlock for offline events.
OfflineEventDataUnit replicates the RainbowClick functionality in
OfflineRCEvent.
List of offline events which can be included in various dialogs
associated with offline event creation and management.
Generic data store for offline files.
An extra panel that appears in the DAQ control when offline
so that user can point the DAQ at a set of wav of aif files
to use with the offline viewer.
Make a list of files with the given file filter.
Functionality for handling data from files offline.
Deprecated.
Processes that run offline.
Super detection filter for offline tasks.
An offline task, such as click species id.
Some global management of offline tasks / task groups.
Deprecated.
This has been split off from OfflineFileServer so that OfflineFileServer can be used with
other file types.
Converts old angle pairs, which used system a below to new angle pairs which
used angle system b.
Dialog for offline processing of a particular data type.
Will offer the user choices in how to select data (e.g.
Will offer the user choices in how to select data (e.g.
Display panel for dBHt data - can be incorporated into a spectrogram
plug in or a stand alone display window.
Annotation manager that should be able to do absolutely everything (almost) self contained
within itself without having to add about 4 different functions to it's parent controller or process
Panel of options for different operational states.
Deprecated.
The user interface for OrcaSpot classifier.
Stores results from an OrcaSpot classification
Contains OrcaSpot specific settings fields.
Stored settings for the OrcaSpot module.
Stored settings for the OrcaSpot module.
Side panel showing how many OrcaSpot detections are in the buffer and the last values of the detections.
Executes the Orca Spot deep learning classifier from a python.exe file and
python scripts.
Executes the Orca Spot deep learning classifier from a python.exe file and
python scripts.
Class to hold settings for the different origin methods.
Special checkbox for overlay drawing.
Provides functions for managing lists of overlays which might
be used with a specific GeneralProjector, i.e.
Observer for when a checkbox menu item associated with an OverlayDataManager is changed.
A detection display which can display group data units and
their super detections in a tab pane if applicable.
Receive mouse actions made on the map, turn them into regions
displayed as an overlay on the map and send the region information
off to any observers who might be interested in those data.
Handles user mouse and touch interactions with the display.
Interface used by something that is observing a spectrogram mark.
Static list of overlay mark observers.
List of all available overlay mark providers.
Interface for menu items which are TD Display specific.
Manages all menu items which are specific to the TDDisplay.
Standard swing panel for selecting overlay mark information.
Deprecated.
Really simple BearingLocaliser which works with two element closely
spaced arrays.
functions for sorting paired arrays, i.e.
Information for additional paired values that will get displayed in the main
RXTable view.
Some math and utility functions for arrays and Lists.
Class defining the default CSS Style sheets to use for JavaFX displays.
Interface for PAMGuard opening a sound file.
The file filter for audio files compatible with PAMGuard.
Interface for PAMGuard opening a sound file.
Central class for opening sound files.
Implementation of RecorderStorage specific to audio files.
User controls to change bespoke settings for audio loaders.
Deprecated.
Useful functions for swing.
Draws an axis on a Java Component.
Draws an axis on a JavaFX Node.
Pane which contains two or more axis and a plot panel.
Axis which utilises the javafx number axis instead of the graphics inside pamaxis.
A list of PamDataUnits, set as a data unit itself so that it can be
passed through a threaded observer.
Parameters for controlling a PamBlockProcess
Modified PamProcess which can block data for analysis in chunks rather than a continuous data stream.
Class defining standard borders for PAMGaurd displays.
Class primarily aimed at making little panels for the
side panel
PAMGuard implementation of JavaFX Button.
Base class for PAMGurad chart, which can be projected into a graphics object -
either a bitmap or a screen component.
Series data for PAmChart.
Color picket which allows users to set a default opacity for the default colours selected by a user.
Class to take all of the configuration information out of PamController.
Slightly modified connection object to pass around - contains not
only the database connection, but also an sqlTypes object which can
get's used to make a few slightly non standard mods to some column
and data formats to keep the various dbms's happy together.
Any connection node node used in the PAMGuard data model must satisfy this interface.
Some constants to be used throughout PAMGuard
The PamControlled unit for modules based on JavaFX.
Provides Swing GUI components for a PAMControlledUnit.
The GUI for a PAMControlled unit.
Basic interface for the primary UI and UI manager showing the PAMGuard GUI.
Helper to initialize a headless
PamController from unit tests.Interface to put behind several existing PAM objects so that
they can start working in a common way without having
to totally rewrite everything.
Class to generate Cursors for databases which can directly support
scrollable cursors and ones which cannot.
holds a single row of data for a non-scrollable result set
wrapped up with NonScrollablePamCursor.
Manages the exporting of data units to a particular type of file e.g.
An iterator that has a bit more functionality than a basic iterator.
Default number formatter for DateAxis, this stays in sync with auto-ranging and formats values appropriately.
Edit box for entering datetimes.
Class defining the default CSS Style sheets to use for JavaFX displays.
Dependency information if this module can ony work if some other module is
providing appropriate data.
Interface to describe dependencies.
Wrapper and functions associated with the Tethys Deployment object which can
exchange these with the PAMGuard database and display Everything is just held
within a list, in no particular order, which getContent public
This is from the Deployment JavaDoc.
Standard logging class for any PamDetection, but you'll want to extend it for any
additional information your detector outputs.
General functionality for PamGuard dialogs.
Creates a dialog with some useful PAMGUARD customisation.
Creates a swing dialog which holds an FXPane.
General class for dialog panels which will be incorporated into one or
more actual dialogs.
Creates a VBox where the children and can be dragged to reorder.
An exception handler intended to catch Run-time exceptions.
Exports data to external files.
PAM extension structure.
Some useful functions to open up a File Browser
Modified file/folder chooser for use throughout PAMGuard which by default will open
in the folder containing the psfx or database file, rather than user.documents
Flip pane which has is supposed to be used for advanced settings.
Flow layout with a standard gap for consisten appearance througout PAMGUARD
Chooser for selecting folders, which can show the files in the folder, but will only
save if the folder is selected not a file.
Some static functions to handle PAMGuad default folder and
to create them as and when necessary.
Handles glyphs from various libraries.
Class to layout PamFramePlots
Standard grid bag contraints to use as a default in
dialogs.
Structure which groups together connection nodes.
Parameters for the group structure.
Pamguard main class.
Table view of PAMGuard deployments.
Pamguard main class.
Meta data for a PAMGuard data set.
Class to hold static license and release information for PAMGUARD.
Class for writing XML configuration output to a file.
A pane which holds a set of tabs.
Holds settings for the FX GUI.
Manages references which indicate which GUI PAMGuard is using.
Handles the FX based GUI.
Extends the PAMTabFX class so that a new stage with PamGui nodes appears when
tab is dragged out of frame, rather than just a new tabPane as the primary
pane.
The PamDataPane contains a pane with two hiding panes, a left pane and a right pane.
class for collecting data into a 1-D histogram.
Class for collecting two dimensional histogram data.
Get the PAMGuard icon.
Class which holds photos or other images and reads metadata.
Similar to PAMProcess, but always subscribes itself to upstream
datablocks using the instant options to this process always get's called
in the same thread as data were collected in and before data units are sent for
storage.
A dialog which has no modal
Called whenever the dialog is closed.
A PamInternalNode is a resizable node which can be resized within another node.
Interpolation library.
Static classes to perform interpolation tasks
Daft panel that takes it's content out of a scene and then puts it pack in again which
somehow convinces the scene to resize.
Interface for passing information from overlay graphics to plots to give information to include in
keys for the various displays.
Extension of JLabel to use standard PAMGUARD colours
Shows a launcher pane which allows a user to open a real time or viewer configuration.
A
SpinnerValueFactory implementation designed to
iterate through a list of values.Pane which shows users load progress from ALL PAMGuard loading tasks.
Was thinking of putting funcitonality in here to link PAMGuard to log4j or some such, but ran
out of time.
Convenience class with a log scale on the y axis.
Some functions to compliment those of the Jamma
Matrix class
Interface for anything that can add menu items to a Swing menu
Deprecated.
Holds information about available PAMGUARD modules.
Class for measuring the time difference between the PC clock and an NTP server.
Make a diagram of the overall PAM process layout.
Adapter class for PamObserver so not necessary to implement
absolutely everything.
Class to manage symbols for various PAMGAURD displays.
Class to lay out windows within a JDesktopPane
Description of data within a field in a class
Parameter description which can use a single parameterless getter
to retrieve a field from a class.
Description of the parameters within a class.
This is a class created to deal with the problem of text fields having a zero length.
Interface for PAMGuard plugins.
Pop over which has some extra functionality including the ability to resize.
Basically a quaternion is a vector which can encode three dimensional
orientation information (e.g.
An extension of JSlider to select a range of values using two thumb controls.
A range slider with some extra functionality such as changing the track colour and
text labels for the thumbs.
UI delegate for the RangeSlider component.
Extension of RecyclingDataBlock that is used for Raw audio data.
A simple dialog which allows the user to select which mode to run PAMGuard in.
Parameters for choosing pAMGuard run mode.
Sub class of the standard scroll bar
Creates a scroll bar system that allows users to navigate through data in real time and viewer mode.
Interface to define modules which can be considered as sensors of some sort.
Create a dialog to show module settings pane.
Deprecated.
Stores a group of PAMGUARD settings read back from the database
or some other store (e.g.
Pane which holds settings menu.
Added to a PamControlledUnit which can save and reload PamSettings
information from files, databases, etc.
Allows users to pick a specific shape
PamSidePanels provide support for additional display units for each
PamControlledUnit displayed in a vertical column to the left of the main
tabbed display.
PamSidePanels provide support for additional display units for each
PamControlledUnit displayed in a vertical column to the left of the main
tabbed display.
Methods for changing the scale of sliders.
Spinner with some bug fixes from raw JavaFX versions.
Implementation of the split pane that can remember it's position.
Class to handle some temporary disabling of the PAMGuard start button during
creating of objects at startup.
Parameters for the extension structure.
This class is used as temporary storage for subtable data of PamDataBlocks being loaded from a database.
Parameters for sud file extraction.
Load SVG icons.
Standard symbols for Pamguard graphics.
Base class for both FX and Swing PamSymbols
Manage symbol choices for a single display and datablock.
Dialog for user control of PamSymbols
PAMSymbolManagers are attached to a single datablock and control the type
of symbol and line that get's used to plot data on the variety of
PAMGUard displays.
Symbol options base class to be used by everything.
Component for including in dialogs.
Class to show a PamSymbol alongside a button which allows the
user to change it.
Creates tabs in Pamguard.
A draggable tab that can optionally be detached from its tab pane and shown
in a separate window.
Defines a database table for use with the Pamguard database
The Pamguard database can query this table definition to
see what columns should be present and to create appropriate
tables.
Defines a single item (column) for a Pamguard database table
These are listed in PamTableDefinition for each table.
Tab pane which allows for detachable tabs.
The PamTabPane skin adds a few extra features to the standard TabPane:
Class for passing information from loading tasks to the FX GUI.
Stores information for a single tip of the day
Viewer dialog for PAMGUARD tip of the day
A JavaFX class to emulate the Swing TitledBorder
taken from https://stackoverflow.com/questions/14860960/groupbox-titledborder-in-javafx-2
The bordered-titled style can be found in style sheet pamDefaultDialogCSS.css.
Toggle switch with a label to the right of the switch, not the default left.
Tooltip with some extra functionality, such as setting HTML text
Useful classes for JavaFX library.
Extension of the validator class to add PAMGuard specific functions.
A set of variables for loading a section of data from the viewer mode database.
This class, when enabled within a JLayer will grey out a JPanel and show a circular rotating animation.
A warning message to put into the warning system displayed in the title area
Base class for PAMGuard wizard cards.
A simple dialog with a progress bar, and potentially also some
lines of text that can be used in conjunction with a SwingWorker to
show progress of a task that's taking some time to execute.
Wrapper around a SwingWorker so it's easy to launch a background thread that will
update a modal dialog with a progress bar and some text
Worker update message with property to allow FX bindings (e.g.
Wrapper with two callback functions to use with a PamWorker
Test models that are zipped with a PMAGuard pgdl settings file.
Loads a zip file and checks for a saved model alongside a pamguard settings file
Simple pane with everything setup for 3D viewing.
Store parameters from a managed parameter set in the PAMGuard database.
Just about everything giving overall control of some managed parameters.
A parameter validator for checking whether an input value for a field is valid.
Single class to hold everything we need to know about sample
rates.
Interface for anything that is capable of making estimates of PC time corrections
e.g.
Wrapper around a nilus Deployment object to provide a bit of extra bookkeeping
and functionality for PAMGuard.
WhistlePeakUnits contain information
from a single FFT slice.
Really simple detector, looking for peaks rising above some
threshold.
Peak frequency symbol modifier.
Option pane for the PeakFreqSymbolChooser.
Swing panel for changing parameters for the peak frequency symbol chooser.
Options for peak frequency.
Peak frequency variable for click train detector.
Pane for peak picking parameters
Information about a peak found by PeakSearch algorithms.
Peak position in a 2D array.
Peak search algorithms which can find a peak in an array of real numbers.
Pane for a peak search trim transform.
Interface for all performance tests.
Simple (but reasonably pleasant) graphics window for drawing
in during performance tests.
Decorate GranularityType
Pink noise source - that's noise that has roughly the same amount
of energy in each octave band.
Class to handle instrument information
Calculations associated with a piston model.
Make a graphics component showing pitch and roll.
PAMGuard wrapper around some of the jserialcomm functionality in order to make it slightly
easier to use in the PAMGuard swing environment.
Main Pam Controller for sound playback modules.
Provide data for sound playback in a suitable format.
Options for sound playback
Class for playback systems to add a system specific dialog component
to the sound playback dialog.
High pass filters for playback system.
The FX GUI for the playback pane.
FX settings pane for the sound sound playback.
Parameters controlling sound playback
Pam Process for sound playback (controls data from multiple channels
and then passes it on to the PlaybackSystem.
Receives notificaitons from the playback system detailing how
far playback has got in viewer mode.
Th eplay back side pane.
Slight modifications to sourcePanel so that only the correct number of
channels can be selected.
Slight modifications to sourcePanel so that only the correct number of
channels can be selected.
Interface for soundplayback systems.
Class to hold basic information about the state of a playback device.
Play gain slider.
Generic component that can be used for sliders
in play control side panel bits
Default slider pane for the sound output sliders.
slider to control playback rate.
Define colours for spectrogram
The plot pane contains 4 axis.
A quick implementation of a chart/plot.
This is a class designed to act as an adapter between the zoomer class and the TDGraph class.
Created by IntelliJ IDEA.
Polpred tide file
PolPred parser which uses the standard dating system with day, month, year time stamps.
Slightly different behaviour to MasterReference.
Find a Position Reference, based on a preferred order.
Class to detect and manage PPS information from GPS.
The pre-classifier pane holds settings for the pre-classifier.
Model results for the classifier.
A node for a pre-process pane.
Abstract instance of PamParameterDataInterface which implements everything
apart from the getData() function
Process NMEA data to extract AIS information
Class for passing information around with Datablocks giving a record of
what has happened to the data within them throughout the whole processing chain.
Class for providing annotations.
Process data selector can be used by any process monitoring one or
more data blocks.
Modeless dialog showing all project deployments.
Panel for entering project information including
project name, region, cruise, and site.
Options that can be added to the GeneralProjector class so that whatever draws
the data units can pick up this additional information.
Really simple propagation models.
Base class for strips of information to go with each
property of a form
Pane for settings some basic environmental variables.
Read and write psfx type configuration files.
Used for loading in and analysing test data sets.
Create a chart showing missed detections as bars along the bottom, found detections as
bars along the top (inverted), and a probability line graph through the middle (overlayed
on top of everything).
A cluster contains all the information required to generate a sound or a sequence of
sounds.
Make a correlated sequence of values with a given width and mean.
Dialog type panel to match detectors with QA sound types.
Deprecated.
Generic class for QA Tests, Sequences and Sounds so that they
can hold their operational status data.
Class for generating locations at which sequences should be created.
Process to monitor output of all other detector data blocks.
Get notifications when something in QA changes.
Handle QA Operations status information including possibility
of editing ops data times and values.
Use a re-threaded data unit list to manage analysis tasks.
Abstract class to generate sound sequences
Interface for all QA module sounds.
SIDE logging class is going to have to do something a bit fancy to work out which sounds have
been detected and by which detectors.
Class to conduct and hold results of an analysis of test data.
Panel to control immediate tests and possibly also some of the
longer term tests.
Processed and summarised detection data for a single or group of tests and a single detector
should contain enough data and functionality to provide everything needed for reporting.
Basic three parameters from a whistle fragment from
a quadratic fit.
Class for importing streamer data from external file and saving to database.
The DIFAR SidePanel contains the list of DIFAR classifications, to allow
the user to choose which classification is assigned by default.
Quick remedial action.
Class to provide a quick single warning that can be easily removed without having
to handle all the references in the owning class.
Data output from GPL_Quiet
Converts Radians to degrees and vice versa.
Does the work of converting a RainbowClick databse.
Planning to keep one random test per cluster type.
Whistle generator makes random whistles using a 2nd order polynomial shape
derived from three equally spaced points in time.
Spinner control used to set display ranges which can
be added to a PamScroller.
Adds data unit annotation to RData frame.
Algorithm which simply looks at the ration of one click type to another.
Click train algorithm which is very simple.
Information on a Raven table non standard column.
System for importing and displaying data from Raven selection tables.
Raw clip data info.
The plot manager for data units that contains raw clips of data.
The clip plot pane.
TH symbol chooser for raw clips.
Plots clips waveforms.
Data source for Raw acoustic data.
RawDataDisplay is used to create plug in panels that can be used at the
bottom of spectrogram windows (and eventually other displays).
Interface to be used by PamDataUnits which contain raw data which
might get used by other processes.
Used to load data for any display in which raw data is required to be loaded for detections.
Holds transforms for raw wave data such as spectrum, spectrogram, cepstrum etc.
Exception thrown by PamRawDataBlock when raw data are requested.
Holds raw data from a sound file.
A few useful functions for handling raw data which are better off in a simple
class rather than linked to a data unit, such as the functions in RawDataTransforms.
This was copied from the ClipBinaryStorage class so cannot easily be changed without breaking backwards compatibility.
This was copied from the ClipBinaryStorage class so cannot easily be changed without breaking backwards compatibility.
Detection Display dataInfo for any rawdata holder.
Making this a plugin.
Data info for the raw data info.
Basic parameters for deep learning module.
Plots FFT data as background if raw data is available.
Plots the FFT of stored acoustic data.
Exports click detections to a .wav file.
Parameters to use when a data source can be either raw or fft data.
Graphics for raw data for the acoustic scroll bar.
Raw sound data is by default not stored in memory.
Implementation of the spectrum plot for any data unit that impleements raw data holder.
Plot for any RawDataHolder to show a waveform.
Manages plotting raw data.
Shows a Wigner plot of a click
Exports a data unit to a List in R.
This is a helper class to compute block averages.
Stuff for re-running whistle classification offline.
Control a sound file recorder.
Process raw audio data prior to storage.
Control parameters for sound recorders.
Writes audio data into a file.
RecorderTriggers are used to automatically make sound file
recordings in response to detections, or any other PamGuard event.
Information for triggered recordings to tell each recorder how long
a recording it should make.
dialog accessed from corner of Deployments panel that controls duty cycles, merging, and
potentially even discarding (of short) of effort periods in the data for both evenly duty cycled
and also for more adhoc data collection.
Information about periods of effort that might come from either the raw data recordings or
an analysis of binary data maps.
Enumeration of the ReferenceFrame field in nilus.Localize.Effort.CoordinateReferenceSystem
Within Tethys, these are only ever used in their String form.
Within Tethys, these are only ever used in their String form.
Created with IntelliJ IDEA.
Pane for changing settings of the refraction method
Method for breaking up connected regions which contain multiple
crossing whistles into sensible parts.
Class for performing various regressions.
Join fragmented shapes back together again.
Actions that can be attached to a status message.
Used when something might repeat a lot.
Top level Report object.
Static class containing all of the processing necessary to generate a docx report from a Report object.
A section in the report.
Class of a load of static text to include in various parts of report.
Class that tests out the report generation
Set of functions to help decide what to do when reprocessing.
Choices on what to do when re-processing data and finding that output data already exist.
Used to cancel data requests when calling to load data in multiple threads.
Check data resolution to be sure that it really is being digitised at the resolution it claims.
Creates a standard panel to display frequency resolution information
Simple Swing panel for responsibleparty fields.
Converts results to values.
Iterator for going backwards through a datablock, but only selecting data untits that
have a specific channel.
Handles exporting pam data units into an rdata.
Using Munger SL distribution of 178/176.
Right whale model from Shiu et al.
Export noise data to RData
Valid orientations of the axis
Rocca/Weka interface for classifying a contour
Short script to load the data from an existing contour stats file (Rocca output), classify each row and save
the data into a new summary file.
Short script to load the data from an existing parameter stats file, classify each row and save
the data into a new summary file.
Short script to load the data from an existing event (school) stats file, classify each row and save
the data into a new summary file.
Creates a modal dialog box containing the current Click Events, and allows the user
to select which events are analyzed by Rocca.
Use this modal dialog to let the user choose one string from a long
list.
A field mapping the sweep direction to the nominal index used to train
the classifier
A field mapping the sweep direction to the nominal index used to train
the classifier
An EnumMap linking the parameter names to the values measured/calculated from
the contour.
Enum class with the names of the contour parameters
Main controller for Rocca
Rocca data unit
code copied from WorkshopDataUnit.java
Databse logging information for Rocca statistics.
Global flag set at runtime for Rocca development flags.
Short script to load an existing contour file (Rocca output), recalculate the parameters and save
the data into a new summary file.
Data unit containing the RoccaContourDataBlock to save to the database
Parameters for Rocca
modified contour calculations to better match original Matlab routine
modified contour calculations to better match original Matlab routine
code copied from WorkshopParametersDialog.java
Main Rocca process
Class to hold information about the random forest classifier.
Container to hold all the sighting data
Container holding information about the current sighting, including pointers
to the contours already measured
Databse logging information for Rocca statistics.
Single-stage classifier creation.
Data unit containing messages that have been sent to the local RockBlock.
Data unit for incoming/outgoing RockBlock messages.
Databse logging information for Outgoing RockBlock Messages
Data unit containing messages that are being sent from the local RockBlock.
This version of RockBlockProcess uses the jSerialComm library instead of RXTX
Gathers data from multiple threads unpacking Rona flac files
and put them in order and sends off to a datablock.
Bespoke system for handling data from the Rona hydrophone array which
consists of sets of seven files, each with different ends in th ename.
Functions to automatically bring together and load sections of
raw data from the single channel Rona FLAC files.
Symbol modifier that rotates through standard colours, usually based on the
data's UID.
Exact implementation of the 2003 Right Whale detector I developed when I was
working for IFAW and is now implemented in the Cornell right whale buoys.
Temporary holder of data about spectral peaks.
Export whisltes to RData
Standard classifier which does exactly the same as the old edge detector
classifier.
Deprecated.
A layout container who lays out its children in a row or column arrangement
(as specified by the orientation) and places a Sash between each child.
Class which can tell a data store what type of work is
needed to re-save the data.
Class to launch a thread which will get the screen size
(including the bounds of multiple monitors)
A custom scroll bar.
A class for coupling two or more scrollers.
Contains the spectrogram data for a single channel.
Wrapper for the FFT data block allowing it to be plot as a spectrogram on a TDGraphFX.
A method to quickly plot data units on the display
A method to quickly plot data units on the display
Scroll jumper allows the use of arrow keys to move to the next data unit.
Small set of scroll controls which can be inserted into any window for
controlling the loading of data in viewer mode.
Seconds to milliseconds
Holds raw data segments which will be classified.
A group of detection which are within a particular segment.
Acquires raw sound data and then sends off to a deep learning classifier.
Test the segmenter on a chunk of sound data.
Makes a dialog panel for selecting a folder
typically for file output.
Creates a pane which allows users to select a folder.
Information to be passed from a user of analogue sensor data
options for separating deployments.
An iterator that has a bit more functionality than a basic iterator.
Summary of sequence data for a test report
Selects groups of fragments into training / test groups
simply by concatenating all the files together from some random start point.
Constants copied from the RXTX library gnu.io.SerialPortInterface.
Standard panel for entering serial port settings.
Create locations for the source at a preset list of distances from the receiver reference.
Didn't work.
Standard settings button with the little cogwheel for use throughout Swing components.
Create a dialog to show module settings pane.
Convenience class for opening a settings file dialog.
Pne which allows a user to select a .psfx settings file.
Class to handle the import of settings from other psf files.
Slightly more than a standard settings.
Listener used with a SettingsFilePane to check for settings that have changed.
To improve complex module loading where settings may be saved by multiple sub-modules, in
July 2015 many modules which had fixed settings had their settings names and types changed !
Therefore these modules won't have found their settings on the first go, so need to also check
against the alternate names defined for each class.
Realising that we often just need to pass around the name of a module or group of settings, have
split this off from the main PamSettings interface so that it can be passed on it's own.
All settings objects must implements both Cloneable and Serializable
to make an interface that has both and use for settings (a bit after the
horse has bolted this, but may be able to apply retrospectively).
Functions needed for module settings pane
Display a simple strip along the top of the Scrolling data panel
which shows a little arrow or something for each set of PAMGAURD settings
This implements the spectrogram correlation detector.
Example class to go with WslPeak to show how WslPeaks, WslShapes and
WslEvents all go together.
Class to draw a simple ship, to show the layout of the standard AIS
dimensions.
Separate class to manage shore functions for the video range, all this could
go in the controller, but might as well keep it separate.
GUI Components for the shore method
Represents the parameters that make up a signal band, used as
input to the Likelihood detection algorithm.
Information on a single simulated object
SimObjectDataUnit is one per sound source, i.e.
Parameters for all simulated objects
Class for a simple 2D plot which can hold both
a data array and a related image.
A Tensorflow model packaged with a jar file.
Calculate the ICI value of amplitude.
Chi2 variable which compares the difference between the two three values.
Parameters class for a simple chi2 variable.
Simple data block for clicks
class to extend- to be used for any control with only one data input field
A holder class which is convenient for sub classing.
Simple classifier graphics.
The simple chi^2 classifier pane.
Simple data observer which gets a notification when a
data unit is selected
Make a decision based on a simple binary threshold for a prediction.
Very simple echo detection system which uses a single test of time
between the previous click and this click to determine if it's an echo or not.
A simple electrical noise check which checks how low the chi2 value is.
Parameters for the electrical noise.
Simple error class.
Simple example sound loaded from a file.
A much simpler filter pane with just few options
Some abstract class function for hydrophone location that are used by
more concrete locators, in particular the StaticHydrophoneLocator
and StraightHydrophoneLocators
Class to hold information for plotting a line on top of
the simple2Dplot.
Stores the last load point in millis.
Mainly a container for map objects, holding the main MapPanel and the right
hand control items.
Simple Pane to change MHT settings.
Simple observerbale class which can pass on a single object to observables.
Simple parameter description which can work with a public
field.
Simple implementation of PAMTaskUpdate which returns 100% by default.
Simple parameter validator which return OK for all values.
Pane for a simple transform.
Time delay based simplex method for localisation.
Time delay based simplex method for localisation.
Deprecated.
Simulation of simulated sound.
Class to hold information and generate a signal
of a specific type
Class to list and manage different types of signals.
Class to hold information on a single sound.
One of these will be created for every sound produced
by a SimObjectDataUnit.
Quick test of NBHF click simulation test.
Version of pamdatablock that always keeps one and only one dataUnit.
Class to format SI units adding appropriate millis, micros, kilos, etc.
A simple sliding block averager.
Smart location tester which processes previous sequences to see how many hits
they got and then dynamically tries to chose a sensible place for the next set.
Smoothing filter which is basically a moving abstract filter
but it operates once on a finite amount of data
and does not insert any delays (unlike MovingAveragefilter which
handles infinite streams, but adds a delay)
Functions to interface with the SAIL Ltd DAQ card C code via JNI
Some extra functions for SMRU development team
Holder of array geometry for a group of data units and an
instant in time.
SNR annotation type.
SonobuoyManager should contain all of the Sonobuoy related functions in the
DIFAR module.
Contains table of sonobuoy deployments and calibrations
SpundCard settings controls for the DAQ pane.
Used by SoundCardSystem
Base sound card playback to use in the SoundCardPlayback and
the SoundCardFilePlayback classes.
e
Settings pane for sound cards.
Everything and everything to do with controlling and reading sound cards.
Some functions for the File and Folder input systems to give a bit of
extra functionality / help for different file types.
List of SoundFileType objects.
Handles play back in the TDisplayFX
Information about a sequence of sounds.
A deep learning classifier running models wihc have been created using the
AnimalSpot framework .
Result from the SoundSpotClassifier.
UI components for the SoundSpot deep learning model.
Runs the deep learning model and performs feature extraction.
Window function for sounds, always operate in place on a waveform
Standard panel for dialogs that shows a list of
available data sources and, optionally a list of data channels.
Standard panel for dialogs that shows a list of
available data sources and, optionally a list of data channels.
Interface for objects requiring notifications when
channel selections in a GroupedSourcePanel change
Data for a species to include in things heard data
Observe changes in a spcies managers options.
dialog to select which species maps to import / export.
Information linking a name within a PAMGuard datablock to a ITIS species code and call type.
Master manager for species maps which will eventually allow for export and import from XML
documents, databases and other things ...
Might be a problem for some batch task management having these so global and having datablocks in the external config that are not in the main model.
Might be a problem for some batch task management having these so global and having datablocks in the external config that are not in the main model.
Interface for multiple plugins to the spectrogram noise
reduction system.
A class which sums energy across a spectrum from a start frequency to an end frequency
The data type for the output of the spectralEti module.
The PamProcess which implements the spectralEti signal processing.
contains the spectrgram data for a single channel.
A general pane with a frequency slider, colour bar slider and colour combo
box.
Wrap up the spectrogram display so that it can be displayed
using the more modern UserDisplayComponent system.
Side panel for the spectrogram which allows users to quickly change spectrogram settings
Draws the image of a spectrogram on a canvas.
Class to convert the new style OverlayMark's into old style spectrogram marks.
Class to receive notifications when the mouse is dragged across the spectrogram display
Get's called on mouse down and mouse up.
Class for registration of classes that will observer
spectrgram displays.
Standard process for any PamControlled unit observing marks made manually
on spectrogram displays.
JavaFX pane for changing SpectrogramNosie settings.
Creates a graphical representation from a matrix.
These are the parameter settings for a single
spectrogram window, note tha a single spectrogram tab may have
multiple windows
Spectrogram for the dataDisplayFX.
Spectrogram projector for overlaying data onto the spectrogram bitmap
which will always be scaled 1:1 with regard to pixels per frequency or
time bin.
Extend ScrollJumper to get data selectors and selected datablocks from
a single spectrogram panel.
The Spectrogram Zoomer acts as the class which handles all zoomer functionality.
Simple background measure for a channel of complex or real FFT data
Uses a dead simple decaying mean measurement
Plot for the spectrum of a waveform.
A data unit wrapper for a spectrum template.
Parameters class for the spectrum template.
Simple spherical grid.
Simple spherical propagation model to use with the simulated acquisition model.
SPL annotation type.
Splash screen
Class that will remember and reset the position of a split pane.
A Split Window normalizer implementation.
This class is used to convert signal and background estimator times in seconds into window widths in samples
suitable for use with the SplitWindowNorm class.
Data selector params for a single species.
PAMGuard database system to make use of Sqlite databases: https://www.sqlite.org/
Specifically, this database system makes use of the xerial sqlite-jdbc library,
https://github.com/xerial/sqlite-jdbc.
SQLLogging performs basic SQL actions to write and read data from a database.
common functionality to add on to an existing SQL logging object.
Utilities for converting between java.sql.types numeric
and text formats.
SSH session
Advanced settings for models - allows the users to define which transfroms to use.
Create a standard set of bearing information that can be used with any data block
capable of generating bearing information.
Allows users to map hardware channels to software channels in PAMGUARD.
A classification object for a standard classification
Standard classification JSON logging
Combines the IDI, CHI2, BEARING and TEMPLATE classifier into one.
Handles the GUI for the standard click train classifier.
A useful abstract class for standard models which are a file or URL that is loaded, have a UI and
utilise PAMSettings to save settings state.
Pane for the standard classifier.
Standard classifier parameters.
Holds all elements of a connection node together.
Plug connected to a collision rectangle.
A socket which allows connections to parent nodes.
Basic data fitler for a CPOD
Implementation of FileDate to read the standard file
date format that I use in Logger.
Settings pane for a standard file date.
The chi^2 calculator for the MHTKernal.
Pane which has advanced settings for standard MHT chi^2 calculator
Some extra info on the chi2 algorithms
Logging for the StandardMHTChi2Info used with an MHT algorithm.
The settings pane for the chi2 value.
Parameters for the PamMHTChi2 class.
Standard MHT Chi2 provider manages the StandardMHTChi2 calculators associated with each possible track.
Settings pane for SoundSpot
Parameters for the SoundSpot model.
A TDMarker which uses the standard PamGuard behaviours from OverlayMarker;
Converts a MenuItem to an OverlayMenuItem.
Colours for a 2D surface plot between two z limits.
Result from the SoundSpot classifier.
A standard sound that has a duration and sweeps between two
frequencies.
A symbol modifier pane that allows users to select a colour for symbol, symbol line and symbol shape.
Deprecated.
A symbol options pane which allows users to select a list of symbol modifiers.
Fixed properties of a beam forming algorithm.
JavaFX settings pane for a static hydrophones.
Get the status of PAMGuard 0 = idle, 1 = running
Calculate the mean and standard deviation of
an double array.
Summary information about the data stores.
Class to hold a whole load of PamScrollerData objects between runs.
Class to carry information about an OfflineDataStore.
Straight Hydrophone Locator, uses GPS heading information from
GPS and assumes that the hydrophones are just sticking straight out
the back of the boat as though on a rigid stick.
Simplest movement model - is the one that's in there at the
moment, i.e.
Summary information on all Detections documents for a Stream for this
PAMGuard dataset.
Contains information on an individual streamer -a Streamer is loosely defined
as a group of hydrophones who's positions are fixed relative to the streamer.
Iterator for moving through streamer data.
Class for importing streamer data from external file and saving to database.
Property class for a Streamer.
Functions to manage streamer sensor data.
A JavaFX settings pane for a streamer.
A pane for setting up hydrophones.
Parameters controlling export of a single stream.
Simple annotation type that does nothing by add a string text to
a datat unit.
Contains saveable information for connection structures.
A list of these is held within a SuperDetection data unit.
Opens a .sud audio file.
Audio file reader for a .sud file.
Some Swing and FX controls to allow a user to change sud parameters.
Class to handle BCL and DWV data from a SUD file during sud file processing.
Class to handle appropriate notifications for SUD files, which go a bit
beyond what's handled in the chunk notifications.
Display ST detection parameters.
Gets a summary string made up of strings from
multiple modules.
Display for summary data inserted at top of DataMap
Display for summary data inserted at top of DataMap
Class added to a PAMDataunit which can be a SuperDetection.
Extensions to SQLLogging to be used with datablocks that log sub detections.
Deprecated.
Wraps a symbol modifier stolen from a super detection in order to pass the super
detection into the symbol modifier rather than the original sub detection.
An improvements on the BasicClickIdentifier based on work by
Gillespie and Caillat in 2009.
The dialog for the sweep click classifier.
Slightly different pane for the sweep classifier.
Parameters for the sweep click classifier.
Pane which contains controls to change a SweepClassifierSet.
Do the actual work of the click seep classifier
Separated into a separate class for clarity and to keep
Separate from all the control functions.
Extension of canvas which allows Swing Graphics2D code to be used in JavaFX
A user display which is based on a swing component.
Set of dialog warnings which can be called on either the AWT of the FX thread.
Listener called when symbol data changes with a symbol maanger.
Class to hold symbol data for both FX and Swing types
of PAMSymbols.
A symbol modifier modifies a PamSymbol.
Pane which allows the changing the settings of a symbol modifier.
Panel to include in a dialog with options to select and activate a variety of symbol modifiers.
Version of the standard symbol manager that only has the optoin on the main
symbol type and no modifiers whatsoever.
Gets a callback when a symbol has been modified so that
it can repaint.
Different db systems can proide a system specific dialog panel
by implementing this interface
Different db systems can proide a system specific dialog panel
by implementing this interface
Doesn't actually do anything, but does collate some system information
Class for some system based time functions, primarily to get
CPU time for the process and to set the system time.
This is similar to a tabbed pane but instead of tabs overlapping each other as in a JTabbedPane they expand and contract.
Settings information for a PamGuiTabFX.
Create a VBox or HBox with create (+ icon), edit (settings icon) and delete (- icon) buttons.
Pane which holds data within a table and has add, settings and delete buttons.
Some general functions to do with table checks which I want to use outside of the
normal dattabse interface.
Simple pane to select a tab and create a new tab if neeeded.
The Class TargetConfiguration represents a single configuration
for the likelihood detector, which can run multiple configurations
simultaneously.
The State enumeration represents the current activity state of the
TargetConfiguration, that is, whether is is currently requested to
be active by the user (or, alternately inactive), or whether there
is an error in one of the parameters of the configuration.
The Class TargetConfigurationExporter.
The TargetConfigurationImporter is used to import a target configuration from an ASCII
file that have been saved by the TargetConfigurationExporter.
The TargetConfigurationNameDialog is used by the LikelihoodDetectionParametersDialog to
allow the user to enter in a new target configuration name.
Target motion module.
The targetMotionControl Panel allows the user to select a GROUP of pamDetections which can be passed to the localisation algorithms and used in target motion analysis.
Reinstated Target motion add-in as used by the click detector.
The control panel will return a list of pamDetections.
Deprecated.
Reinstated Target motion add-in as used by the click detector.
Reinstated Target motion add-in as used by the click detector.
Reinstated Target motion add-in as used by the click detector.
Parameter control for offline task groups.
Handles logging of tasks to the database.
Wee class for holding the latest data on each task, most importantly the
database index which is needed for updates.
Dummy datablock to use with some dummy SQLLogging classes in TaskLogging.
Interface to receive notifications about the
task progress (which will be running in a
different SwingWorker thread).
Class used to transfer status and progress
information out of the OfflienTaskGroup worker thread.
Subclass for the td display.
Wrapper which holds a list of time delays and the corresponding detections used to calculate those delays.
The axis panel forms the main Component of the display, The time
scroller and various other components get added and controlled
from TDControl though.
The main class for the TDDisplay.
TDControlFX acts as a wrapper class for a time base display programmed in JavaFX.
The controller for the display if the main PAMGuard GUI is in JavaFX mode.
Top pane.
Information about a type of data that can be displayed on any of the plots.
Information about a type of data that can be displayed on any of the plots.
A plugin is used to display extra data for a TDDataInfo.
TDDataInfo objects can't be serialised since they contain
references back into datablocks and everything else in PAMguard,
so have to hold a summary of what's in each one to save into psf files.
Provider class from TD data.
Provider class for TD data.
Static holder of information about plottable data.
Static holder of information about plottable data.
A pane which allows users to;
The controller for the TD display.
The main display node for showing tdGraphs.
Panel for a data graph.
Contains a set of split panes or
a box layout for all the actual graphs.
A TDGraph allows users to plot multiple types of data on a single time based
graph.
The settings for an individual graph.
Pane with control to change generic settings of a TDGraphFX.
A basic zoomer class for the tdgraph.
Contains functions required to calculate a hyperboloid using time delays.
Contains functions required to calculate a hyperboloid using time delays.
Gets callbacks from the registry menu when a
particular provider is selected.
Default symbol chooser for the display.
Adapter which converts the OverlayMark class within PAMGuard to the TDOverlayMarker used in the dataPlotsFX display.
Handle mouse events from an FX display and send them off into the
main panel marking thingamagig.
The pane for the adv.
An overlay adapter allows user mouse and touch interactions with the display.
Subclass for the td display.
Stores parameters for a TDDisplay.
A more complex pop up menu for the display.
Projector which handles all time to pixel conversions for the display.
Information about the scale requirements
of a set of plotable data.
Data for the TDScaleInfo which can be serialised and saved.
SettingsPane for acosutic scroller.
A wrapper for the hiding panes which allow users to change display settings for each different data block
Associated with a TDGraphFX.
Pane which quickly allows users to change spectrogram settings
Interface allowing things getting drawn on the plots to chose their won symbol
Interface allowing things getting drawn on the plots to chose their won
symbol
Temporary data unit for unconfirmed click trains.
Temp data units for bearing localiser and crossed bearing localisation ...
Temp data units for bearing localiser and crossed bearing localisation ...
Classification result for the template classifier.
Pane which allows users set classification parameters for a template classifier.
Parameters for the template classifier
Interface fro importing a template
Shows and allows users to import a spectrum template.
Terminal component super class
Handle events
Implements the FilteredConsumer interface.
Runs a simple GUI and tests the MHT click train algorithm on a bunch
of simulated clicks.
Test how BitSets work
Quick program which performs some simple tests the standard chi^2
algorithm.
Contains the main list of clusters as well as three smaller panels for test range, quick tests and random tests.
Possible document actions
Top strip of main Tethys GUI for connection and project information
Quick play with a simple system for outputting data to Tethys.
Any PAMGuard data stream which can provide Detection data to PAMGuard will
be able to return one of these.
Table view of a collection of Tethys documents.
Common panel used by Calibrations, Deployments and Detections to show an export button and other
common components, such as help, a table, etc..
Parameters for controlling export of Tethys data.
Class to hold and unpack a XML string returned from the ITIS_ranks document
in a Tethys database.
Static formatting (rounding and range checking) functions for latlong values.
Summary of localisation info in a datablock, specific to Tethys needs.
Function(s) to get location information for Tethys in the required format.
Logging everything we put into Tethys in our own database.
Functions to pack up a PAMGuard parameters object into the correct format
for Tethys.
Set of functions to provide mesage reports on Tethys output.
Deprecated.
Basis for a message system which will get passed around whenever something happens in
Tethys, whether it be a new connection, progress during data output, etc.
Base class for offline tasks in Tethys.
Manager for offline tasks in Tethys.
Hold settings for all Tethys tasks.
Settings controlling output of a Tethys stream.
Class to make it easy to find tooltips for a given nilus class and field nams.
Wizard card with a few extra functions for Tethys.
Text terminal: Use Java font to render
Data returned by a TFContourProvider.
Interface to add to data units that hold a time-frequency contour.
This is a decorator class for PamObservers which intercepts any
data being sent to that observer and puts the data into a list
which will then be re-read in a separate thread, rather than
sending if for direct execution.
A threading hydrophone is one that exactly follows the track of the ship.
This class performs the actual max likelihood detector logic.
This is the Threshold Detectors output data unit.
This PamProcess is the main maximum likelihood threshold detector logic.
Vasic data block for tide data
Stores data on the tide at a specific location at a specific time.
The tide manager open tide data and holds it in memory.
Converts a string to tide data
Class to hold time correction information
Chi^2 value for time delays.
Class to pass round time delay data.
Time delay parameters.
Converts a tiome to another time.
Class to format time ranges, particularly when they get quite large and doing them
in seconds no longer makes sense.
Want something along the lines of
if an integer number of days, then just days,
if an integer number of hours, then days and hours
if an integer numeber of minutes, then days, hours, minutes
if an integer number of seconds, then days, hours, minutes, seconds
etc.
Want something along the lines of
if an integer number of days, then just days,
if an integer number of hours, then days and hours
if an integer numeber of minutes, then days, hours, minutes
if an integer number of seconds, then days, hours, minutes, seconds
etc.
A time range spinner which allows integration with a PAMGUARD time scroll bar.
Spinner which cycles through various time ranges.
Enumeration of the ReferenceFrame field in nilus.Localize.Effort.TimeReference
Within Tethys, these are only ever used in their String form.
Within Tethys, these are only ever used in their String form.
Simple annotation type that does nothing by add a string text to
a datat unit.
Class for filtering double of float values in a database table
Simple decorator class to add a titled border to any settings pane.
Options for target motion analysis.
Annotation type for target motion analysis.
Reinstated Target motion add-in as used by the click detector.
Takes a PamDetection with sub detections and has functions to generate various types of information for a localiser.
This class handles the loading for data for the target motion module.
Reinstated Target motion add-in as used by the click detector.
This class deals with processes in the target Motion localiser which ONLY occur in offline mode.
Parameters that apply to all TOAD based localisers.
Class to handle TOAD (Time of Arrival Difference) calculations for a particular type of data.
Class to tell a TOAD calculator how to filter data during a cross correlation
measurement.
Class holding information about TOAD delays, channels, etc.
The Mimplex localiser is similar to MCMC but it localises multiple possible combinations using fast algorithms then uses MCMC to localiser the final combination.
The TOAD options pane.
Deprecated.
use older DelayMeasurementParams instead.
Holds information on a track possibility
Simple class for holding a few bits of information on the track
Something similar to ClickTrainDetector, but working on the output of tracked clicks so that
accurate positions for groups of tracked clicks are calculated and can be displayed / stored.
Data block contains summary statistics for tracked groups of difar bearings
Summary statistics are calculated not only on an individual channel, but
individually for each sonobuoy deployment.
Hold localisation information for Difar TrackedGroups.
TrackedGroupOverlayGraphics show a summary of all the bearings
to each tracked group (on the map)
Subscribe to DifarDataBlocks and assign new bearings to groups of whales
Database storage of DIFAR information.
Some general information about the track: whether it exists and
the frequency of GPS points.
A collection of training data for multiple species.
A collection of training data for multiple species.
A group of training data from a single species
A group of training data from a single species
Training contours from a single file, each contour representing
one whistle.
Training contours from a single file, each contour representing
one whistle.
Storage for whistle classifier training data.
Storage for whistle classifier training data.
Class containing functions to randomly select suitable groups of
training and test data from a TrainingDataCollection
Stores a shape and a transform, if it has one.
The TreeTable class provides a widget that is not native to the standard
Swing UI library - the Tree Table.
The TreeTableModel represents a LikelihoodDetectionParameters object
(which contains module parameters and an ArrayList of TargetConfiguration objects)
as a node-based tree for use with a JTree.
The class TreeTableModelAdapter is a necessary part of the TreeTable implementation
because it serves as a bridge between the JTable that forms part of the widget and
the JTree that forms another part (the table cell renderer).
Class to stack up blocks of data about the trigger background level and store them
into sensible sized data units, i.e.
Basic recorder trigger which can be re-implemented in many guises.
Last updated on May 26, 2015
This class is almost identical to the simple exponential (decaying) average.
Some functions to load and import data stored in text files (includes .csv files)
Type modifications for ucanacces.
Thread for receiving and responding to UDP commands and requests over
the network
Interface which can take data unit or information
from either a binary file or from a database and
find the corresponding data in the other type of store.
Class for managing UID's during real time operations.
Params needed for the UID repair.
Class to store UID information about the database tables.
Modification of PAMViewParameters to work using a list of UID's rather than
a between times type string.
Task manager for a PamControlledUnit.
The unit test for Signal and Guard Bands.
Dialog to update the PC clock from GPRMC data.
Generic class for copying data from binary data files to database files.
Very simple class used in an ArrayList of used modules that
get's saved between runs.
Class to hold information about and send notifications to open user display components.
Adapter class for UserDisplayComponent which manages
some of the functions which may not be needed to all
display components.
Class which acts as a plug in for a display in PAMGUARDFX.
Frames for general purpose user displays.
Any display which sits inside PAMGuard must be an instance of UserDisplayNodeFX.
Parameters for a display node.
Provider of displays for the main display panel.
User form data selector for use with annotations.
This is a wrapper around a standard forms data selector.
SQL Logging addon for Logger form annotations.
User form symbol modifier for use in user form annotations.
A symbol modifier which allows the user to manually change settings.
Override standard Timestamp class and stop it making UTC corrections as it writes to database
Created by pedro_000 on 6/28/2014.
Filter class for use with multiple data types in filtering
database table data.
Abstract class for ValueFilters for filtering database data tables.
UI for rotating text in VerticalLabel
A vertical layout manager similar to java.awt.FlowLayout.
Provide a graphics planel, or panels that can be added to the bottom of spectrogram
displays.
Class for passing around data on how the load of
data from the databsae is going.
Class for tansfering data about adata load precess.
The videoRange module determines location information based on photographs of objects (photogrammetry).
The main display.
A wrapper to allow an FX pane to be become part of the tab p[ane.
The horizon method allows a user to click two points to define a horizon and then click an animal to define a RANGE.
Method for measuring the distance to an animal based on the pitch and height of an observer.
Pane which holds some type of visual media e.g.
Pane for editing an image or video
This panel control image editing.
Pane for showing an image or video.
Holds the image and can be used to PAN and zoom
The LandMark uses landmarks at known positions or at known angles from the
position the image was taken to calculate an animal's position.
Class to store information on loclaisations using an image.
Basic media player to watch videos in the video range module.
Pane which shows the metadata for an image or video.
The Method to localise animals from an image.
Main pane to hold image and controls.
Pane for changing the main video range settings class.
AbstractVRMethod contains many useful functions to create panels, update methods ,
Holds side controls.
Create a JavaFX GUI within the current swing framework.
Some useful functions for the video range module.
Interface for warning displays.
System for handling and displaying warnings and errors from various parts of PAMguard.
Show a dialog which can display a warning message and can be told to
never show again.
Part of a managed warning system.
A warning dialog in JavaFX with a "do not show again" dialog box.
Serializable list of which warnings should be hidden.
Class to manage more sophisticated communications with PAMDog.
Waterfall spectrogram plot for super detections detections which have sub detections
that can provide FFT data.
Settings pane for a waterfall spectrogram.
Quick constructor for 16 bit wav file audio formats.
Wav annotation type.
Wav audio file - opens any raw audio file.
Handles writing of .wav files.
Writes data units and/or ordered raw data to a wav file.
Class to provide clip functions to a pam data unit.
Functions to plot a waveform on a plot panel.
Waveform plot.
Options for exporting wav files
Export a .wav clip.
Wav file input stream which will work for large wav files (>2 Gigabytes) which
fail with the standard JAva classes since the data chunk size gets read as a
signed integer which then ends up invalid input: '<' 0.
Bespoke system for storing wav files.
Chunk information from a wav file header.
Worker which extracts acoustic files from a folder.
Panel to west align components witin other components.
Controls the appearance of whistles on a TDGraphFX.
Whistle Classifier control class.
Whistle Classifier process
Interface to get the basic information out of a
whistle object.
Class containing functions to calulate the delay between
a detected whistle on one channel and the signal on
an adjacent channel.
Class for estimating whistle delays from a whistle shape.
Plots a whistle contour over a spectrgram if one is available.
Break a whistle up into fragments.
Whistle group detection is initially designed to take just one whistle from each
of many hydrophone pairs.
Whistles/Moans are long (relatively) tonal sounds which can be plotted on a bearing/amplitude display and/or spectrogram.
Transform whistles to an image.
Plot which shows FFT settings controls and a colour box to change whistle colour.
dDefines colours and symbols for whistles on the TD display
Functions to convert a group fo whistle contours to an average spectrum.
Plots a Wigner transform of a detection.
Called whenever a wigner calculation is updated.
Window function for use with FFT.
Default data selector for the whsitle and moan detector.
JavaFX settings pane for the whsitle and moan detector data selector.
Notes on ManagedParameters
- the superclass RecorderTriggerData extends ManagedParameters and manually adds in a few fields
in the getParameterSet method that would otherwise be missed (because they are protected and
do not have getters).
Wrapper class which returns Swing GUI functions from the soon to be
deprecated functions within the PamControlledUnit class.
Species selector for whistle classifier.
dialog for whistle classifier data selector
Copyright (c) 2013, 2014 Oracle and/or its affiliates.
A utility class to cover up the rough bits of xml parsing
From http://www.java2s.com/Code/Java/XML/Returnsaniteratoroverthechildrenofthegivenelementwiththegiventagname.htm
Some Swing dialogs n stuff for managing module settings in and out of
XML.
control options for when to save XML data and also
have buttons for preview and output.
Property form for a cross reference sontrol.
Simple container for a few zero crossing parameters.
Functions to unpack gzip files of PAMBuoy data.
http://www.crazysquirrel.com/computing/java/basics/java-directory-zipping.jspx
To be implemented by any display working with the
Zoomer class.
A scroll pane which allows the user to zoom the content node with scroll bars acting accordingly.
Class for handling multiple zoom and marked areas on a
display.
A zoom polygon created by the zoomer.
Interface to support a variety of zoomable shapes.