clickDetector

Class ClickSpectrumTemplateEditDialog

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

javax.swing.JDialog

PamView.PamDialog

clickDetector.ClickSpectrumTemplateEditDialog

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class ClickSpectrumTemplateEditDialog
extends PamDialog

The edit template dialog allows users to create mean spectrums from marked out events. A created mean spectrum can be exported as .csv file and displayed on the Click Spectrum window. Templates contain data on species ,sample rate, and standard deviation of each frequency bin along with the mean FFT. The idea behind these templates is that they can be used to help the user identify dolphin clicks and perhaps highlight common features over multiple clicks. The problem of classifying dolphin clicks is a difficult one. Different clicks from the same animal often have highly different spectral properties. For some species the average spectrum of multiple clicks does contain peaks and features which can be useful. The aim of this class is to allow the user to gain some kind of handle on these features. Further development must look at some sort of statistical analysis to quantify the similarity between a template and click/click event.

A note on creating mean spectrums;

The rules of logarithms are, to the casual mathematician, a bit strange. We need to be careful when constructing a mean or standard deviation of logarithmic spectrums mainly because log(x)+log(y) does NOT equal log(x+y). So if we create a mean spectrum, then take the log of that, it is not the same as calculating the log of each click fft and then taking the mean. The same applies to standard deviation.

Author:

Jamie Macaulay

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class PamView.PamDialog

PamDialog.PopupListener

Nested classes/interfaces inherited from class java.awt.Dialog

java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.Type

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.BaselineResizeBehavior

Field Summary

Fields inherited from class java.awt.Dialog

DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
ClickSpectrumTemplateEditDialog(java.awt.Window parentFrame, java.awt.Point pt, ClickControl clickControl)

Method Summary

Methods

Modifier and Type	Method and Description
void	addListSelectionListener(javax.swing.event.ListSelectionListener listSelectionListener)
void	addToSpectrum() Save the average event data to a ClickTemplate class and add to list of click templates.
void	cancelButtonPressed() called when the cancel button is pressed before the dialog closes.
javax.swing.JPanel	controls()
static java.util.ArrayList<java.lang.Double>	convertToArrayList(double[] array)
static double[]	convertToDoubleArray(java.util.ArrayList<java.lang.Double> array) Converts and ArrayList to a double[]
ClickTemplate	createTemplate() Creates a click template from the saved instance variables.
void	deleteTemplate(int row) Deletes template from memory; -both the template and corresponding setVisble boolean must be deleted.
double[]	fftMean(java.util.ArrayList<double[]> fftAll) Calculates the average fft for an ArrayList of fft's.
double[]	fftstd(java.util.ArrayList<double[]> fftAll, double[] meanVals) Create standard deviation of all fft's.
java.util.ArrayList<double[]>	getEventFFTs(java.lang.Integer channel, boolean normalise) Get the event ffts for the selected channel.
boolean	getParams() called when the Ok button is pressed.
void	loadTemplate()
java.lang.String	openFileBrowser()
void	restoreDefaultSettings() standard function which should us used to copy default parameters into the dialog controls.
java.lang.String	saveFileBrowser() Opens file save dialog and allows user to select save location.
void	saveTemplate() Saves the current template and standard deviation to a .csv file.
void	saveTemplatePlusSpectrums() Saves a template plus a list of all the spectrums used in creating that template- note the template is from normalised spectrums but the list of spectrums is not normalised- this gives the maximum amount of data to the user.
void	setClickSpectrum(ClickSpectrum clickSpectrum)
boolean	setParams()
static ClickSpectrumTemplateParams	showDialog(java.awt.Window parentFrame, java.awt.Point pt, ClickSpectrum clickSpectrum, ClickSpectrumTemplateParams clickSpectrumTemplateParams, ClickControl clickControl) Creates an instance of the edit template dialog, associated with the Click Spectrum window it was opened from.
void	updateClickSpectrum() Updates the clickSpectrum whenever a template is added or removed.

Methods inherited from class PamView.PamDialog

addComponent, closeLater, enableHelpButton, formatDouble, getButtonPanel, getCancelButton, getCancelObserver, getDefaultButton, getHelpButton, getHelpPoint, getOkButton, getWarningTitle, isSendGeneralSettingsNotification, isWarnDefaultSetting, restoreDefaultSettingsQ, setCancelObserver, setDialogComponent, setDoubleValue, setHelpPoint, setSendGeneralSettingsNotification, setVisible, setWarnDefaultSetting, setWarningTitle, showQuestion, showQuestion, showQuestion, showWarning, showWarning, showWarning

Methods inherited from class javax.swing.JDialog

getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setTransferHandler, update

Methods inherited from class java.awt.Dialog

addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, show, toBack

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, dispatchEvent, enable, enable, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

ClickSpectrumTemplateEditDialog

public ClickSpectrumTemplateEditDialog(java.awt.Window parentFrame,
                               java.awt.Point pt,
                               ClickControl clickControl)

Method Detail

showDialog

public static ClickSpectrumTemplateParams showDialog(java.awt.Window parentFrame,
                                     java.awt.Point pt,
                                     ClickSpectrum clickSpectrum,
                                     ClickSpectrumTemplateParams clickSpectrumTemplateParams,
                                     ClickControl clickControl)

Creates an instance of the edit template dialog, associated with the Click Spectrum window it was opened from.

Parameters:

parentFrame -

pt -

clickSpectrum -

clickSpectrumTemplateParams -

clickControl -

Returns:

new clickSpectrumTemplateParams

setClickSpectrum

public void setClickSpectrum(ClickSpectrum clickSpectrum)

addListSelectionListener

public void addListSelectionListener(javax.swing.event.ListSelectionListener listSelectionListener)

controls

public javax.swing.JPanel controls()

getEventFFTs

public java.util.ArrayList<double[]> getEventFFTs(java.lang.Integer channel,
                                         boolean normalise)

Get the event ffts for the selected channel. If channel is null then then all ffts from every event are selected. Have to be careful here with channel numbers here. If an event does not have any clicks form the selected channel then an empty ArrayList is returned.

Parameters:

channel -

Returns:

openFileBrowser

public java.lang.String openFileBrowser()

loadTemplate

public void loadTemplate()

saveTemplate

public void saveTemplate()

Saves the current template and standard deviation to a .csv file.

saveTemplatePlusSpectrums

public void saveTemplatePlusSpectrums()

Saves a template plus a list of all the spectrums used in creating that template- note the template is from normalised spectrums but the list of spectrums is not normalised- this gives the maximum amount of data to the user.

addToSpectrum

public void addToSpectrum()

Save the average event data to a ClickTemplate class and add to list of click templates. Make visible as a default.

fftMean

public double[] fftMean(java.util.ArrayList<double[]> fftAll)

Calculates the average fft for an ArrayList of fft's. Ignores any NaN values.

Parameters:

fftAll -

Returns:

average fft.

fftstd

public double[] fftstd(java.util.ArrayList<double[]> fftAll,
              double[] meanVals)

Create standard deviation of all fft's.

Parameters:

fftAll- - all the fft's

meanVals- - ArrayList of the means if the fft's ;

Returns:

deleteTemplate

public void deleteTemplate(int row)

Deletes template from memory; -both the template and corresponding setVisble boolean must be deleted.

saveFileBrowser

public java.lang.String saveFileBrowser()

Opens file save dialog and allows user to select save location.

Returns:

Path to save file to

convertToDoubleArray

public static double[] convertToDoubleArray(java.util.ArrayList<java.lang.Double> array)

Converts and ArrayList to a double[]

Parameters:

array -

Returns:

double[] array with same values as inputed ArrayList

convertToArrayList

public static java.util.ArrayList<java.lang.Double> convertToArrayList(double[] array)

createTemplate

public ClickTemplate createTemplate()

Creates a click template from the saved instance variables. Be careful that these variables have been updated when using this function.

Returns:

ClickTemplate

setParams

public boolean setParams()

updateClickSpectrum

public void updateClickSpectrum()

Updates the clickSpectrum whenever a template is added or removed. This function basically changes the clickSpectrum before the dialog box is closed.

getParams

public boolean getParams()

Description copied from class: PamDialog

called when the Ok button is pressed. This must return true in order that the dialog may close. It should also copy all parameters into an object that will be returned by showDialog.

Specified by:

getParams in class PamDialog

cancelButtonPressed

public void cancelButtonPressed()

Description copied from class: PamDialog

called when the cancel button is pressed before the dialog closes. Generally you should set the parameters returned by the dialog to null or some default value, or in some other way indicate that Cancel was pressed.

Specified by:

cancelButtonPressed in class PamDialog

restoreDefaultSettings

public void restoreDefaultSettings()

Description copied from class: PamDialog

standard function which should us used to copy default parameters into the dialog controls.

Specified by:

restoreDefaultSettings in class PamDialog