Package sc.fiji.snt.analysis.sholl.gui

Class ShollOverlay

java.lang.Object

sc.fiji.snt.analysis.sholl.gui.ShollOverlay

All Implemented Interfaces:

ProfileProperties

public class ShollOverlay
extends Object
implements ProfileProperties

Renders Sholl analysis results as graphical overlays on an image, including concentric shells, sampling points, and intersection counts.

Author:

Tiago Ferreira

Field Summary

Fields

Modifier and Type	Field	Description
static final String	COUNT
static final String	POINTS
static final String	PROP
static final String	RADIUS
static final String	SHELL

Fields inherited from interface sc.fiji.snt.analysis.sholl.ProfileProperties

HEMI_EAST, HEMI_NONE, HEMI_NORTH, HEMI_SOUTH, HEMI_WEST, INTG_MEAN, INTG_MEDIAN, INTG_MODE, KEY_2D3D, KEY_CALIBRATION, KEY_CENTER, KEY_CHANNEL_POS, KEY_EFFECTIVE_STEP_SIZE, KEY_EXTRA_MEASUREMENT, KEY_FRAME_POS, KEY_HEMISHELLS, KEY_ID, KEY_NSAMPLES, KEY_NSAMPLES_INTG, KEY_SLICE_POS, KEY_SOURCE, KEY_THRESHOLD_RANGE, SRC_IMG, SRC_TABLE, SRC_TRACES, UNSET

Constructor Summary

Constructors

Constructor	Description
ShollOverlay(Profile profile)
ShollOverlay(Profile profile, ij.ImagePlus imp)
ShollOverlay(Profile profile, ij.ImagePlus imp, boolean clearExistingROIs)

Method Summary

Modifier and Type	Method	Description
void	addCenter()
void	assignProperty(String property)
Set<String>	getLUTs()
ij.gui.Overlay	getOverlay()
static void	remove(ij.gui.Overlay overlay, String property)
void	removePoints()
void	removeShells()
static void	removeShells(ij.gui.Overlay overlay)
static void	removeShollROIs(ij.gui.Overlay overlay)
void	setAlternateShells()
void	setAlternateShells(Color color1, Color color2)
void	setBaseColor(Color baseColor)
void	setGradientShells(Color color1, Color color2)
void	setPointsColor(Color color)
void	setPointsLUT(String lutName)
void	setPointsLUT(String lutName, String property)
void	setPointsLUT(net.imglib2.display.ColorTable colorTable, String property)
void	setPointsOpacity(double percent)
void	setPointsSize(String size)
void	setShellsColor(Color color)
void	setShellsLUT(String lutName)
void	setShellsLUT(String lutName, String property)
void	setShellsLUT(net.imglib2.display.ColorTable colorTable, String property)
void	setShellsOpacity(double percent)
void	setShellsThickness(int strokeWidth)
void	updateDisplay()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

COUNT

public static final String COUNT

See Also:

• Constant Field Values

RADIUS

public static final String RADIUS

See Also:

• Constant Field Values

PROP

public static final String PROP

See Also:

• Constant Field Values

SHELL

public static final String SHELL

See Also:

• Constant Field Values

POINTS

public static final String POINTS

See Also:

• Constant Field Values

Constructor Details

ShollOverlay

public ShollOverlay(Profile profile)

ShollOverlay

public ShollOverlay(Profile profile,
 ij.ImagePlus imp)

ShollOverlay

public ShollOverlay(Profile profile,
 ij.ImagePlus imp,
 boolean clearExistingROIs)

Method Details

updateDisplay

public void updateDisplay()

assignProperty

public void assignProperty(String property)

removeShells

public static void removeShells(ij.gui.Overlay overlay)

removeShollROIs

public static void removeShollROIs(ij.gui.Overlay overlay)

remove

public static void remove(ij.gui.Overlay overlay,
 String property)

getOverlay

public ij.gui.Overlay getOverlay()

removeShells

public void removeShells()

removePoints

public void removePoints()

setBaseColor

public void setBaseColor(Color baseColor)

addCenter

public void addCenter()

setShellsColor

public void setShellsColor(Color color)

setPointsColor

public void setPointsColor(Color color)

getLUTs

public Set<String> getLUTs()

setShellsLUT

public void setShellsLUT(String lutName)

setShellsLUT

public void setShellsLUT(String lutName,
 String property)
                  throws IOException

Throws:

IOException

setPointsLUT

public void setPointsLUT(String lutName,
 String property)
                  throws IOException

Throws:

IOException

setPointsLUT

public void setPointsLUT(String lutName)

setPointsLUT

public void setPointsLUT(net.imglib2.display.ColorTable colorTable,
 String property)

setShellsLUT

public void setShellsLUT(net.imglib2.display.ColorTable colorTable,
 String property)

setShellsThickness

public void setShellsThickness(int strokeWidth)

setShellsOpacity

public void setShellsOpacity(double percent)

setPointsOpacity

public void setPointsOpacity(double percent)

setGradientShells

public void setGradientShells(Color color1,
 Color color2)

setAlternateShells

public void setAlternateShells(Color color1,
 Color color2)

setPointsSize

public void setPointsSize(String size)

setAlternateShells

public void setAlternateShells()