Package sc.fiji.snt.analysis.sholl

Class Profile

java.lang.Object

sc.fiji.snt.analysis.sholl.Profile

All Implemented Interfaces:

ProfileProperties

public class Profile
extends Object
implements ProfileProperties

Defines a Sholl profile

Author:

Tiago Ferreira

Field Summary

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
Profile()	Instantiates a new empty profile.
Profile(double[][] sampledData)	Constructor accepting matrices.
Profile(Number[] radii, Number[] sampledInters)	Legacy constructor accepting arrays.
Profile(List<Number> radii, List<Number> sampledInters)	Default constructor.

Method Summary

Modifier and Type	Method	Description
boolean	add(ProfileEntry entry)
void	assignImage(ij.ImagePlus imp)
ShollPoint	center()
List<Double>	counts()
double[]	countsAsArray()
Profile	duplicate()
double	endRadius()
SortedSet<ProfileEntry>	entries()
boolean	equals(Object o)
List<Double>	extras()
double	getCountAtRadius(double radius)
String	getExtraMeasurement()
Properties	getProperties()
ij.gui.Overlay	getROIs()
ij.gui.Overlay	getROIs(ij.ImagePlus imp)
boolean	hasExtraMeasurement()
int	hashCode()
boolean	hasPoints()
String	identifier()
boolean	is2D()
boolean	isEmpty()
boolean	isIntDensityProfile()
List<Double>	lengths()
double[]	lengthsAsArray()
int	nDimensions()
ShollPlot	plot()
List<Set<ShollPoint>>	points()
List<Double>	radii()
double[]	radiiAsArray()
List<Double>	radiiSquared()
void	scale(double xScale, double yScale, double zScale)
boolean	scaled()
void	setCenter(ShollPoint center)
void	setExtraMeasurement(String measurement, String unit)
void	setIdentifier(String identifier)
void	setIsIntDensityProfile(boolean isIntDensityProfile)
void	setNDimensions(int twoDthreeD)
void	setProperties(Properties properties)
void	setSpatialCalibration(ij.measure.Calibration cal)
int	size()
String	source()
ij.measure.Calibration	spatialCalibration()
double	startRadius()
double	stepSize()
String	toString()
void	trimNaNCounts()
void	trimZeroCounts()
int	zeroCounts()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

Profile

public Profile()

Instantiates a new empty profile.

Profile

public Profile(List<Number> radii,
 List<Number> sampledInters)

Default constructor.

Parameters:

radii - sampled radii

sampledInters - sampled intersection counts

Profile

public Profile(Number[] radii,
 Number[] sampledInters)

Legacy constructor accepting arrays.

Parameters:

radii - sampled radii

sampledInters - sampled intersection counts

Profile

public Profile(double[][] sampledData)

Constructor accepting matrices.

Parameters:

sampledData - sampled data in [n][2] format, where n = number of points (radii: [n][0]; sampledInters: [n][1])

Method Details

identifier

public String identifier()

setIdentifier

public void setIdentifier(String identifier)

radii

public List<Double> radii()

duplicate

public Profile duplicate()

radiiSquared

public List<Double> radiiSquared()

radiiAsArray

public double[] radiiAsArray()

counts

public List<Double> counts()

countsAsArray

public double[] countsAsArray()

lengths

public List<Double> lengths()

extras

public List<Double> extras()

lengthsAsArray

public double[] lengthsAsArray()

points

public List<Set<ShollPoint>> points()

getCountAtRadius

public double getCountAtRadius(double radius)

trimZeroCounts

public void trimZeroCounts()

trimNaNCounts

public void trimNaNCounts()

scale

public void scale(double xScale,
 double yScale,
 double zScale)

entries

public SortedSet<ProfileEntry> entries()

source

public String source()

nDimensions

public int nDimensions()

is2D

public boolean is2D()

setNDimensions

public void setNDimensions(int twoDthreeD)

scaled

public boolean scaled()

hasPoints

public boolean hasPoints()

plot

public ShollPlot plot()

toString

public String toString()

Overrides:

toString in class Object

center

public ShollPoint center()

setCenter

public void setCenter(ShollPoint center)

size

public int size()

startRadius

public double startRadius()

stepSize

public double stepSize()

endRadius

public double endRadius()

spatialCalibration

public ij.measure.Calibration spatialCalibration()

assignImage

public void assignImage(ij.ImagePlus imp)

setSpatialCalibration

public void setSpatialCalibration(ij.measure.Calibration cal)

getProperties

public Properties getProperties()

setProperties

public void setProperties(Properties properties)

getROIs

public ij.gui.Overlay getROIs()

getROIs

public ij.gui.Overlay getROIs(ij.ImagePlus imp)

add

public boolean add(ProfileEntry entry)

zeroCounts

public int zeroCounts()

isEmpty

public boolean isEmpty()

hasExtraMeasurement

public boolean hasExtraMeasurement()

setExtraMeasurement

public void setExtraMeasurement(String measurement,
 String unit)

getExtraMeasurement

public String getExtraMeasurement()

setIsIntDensityProfile

public void setIsIntDensityProfile(boolean isIntDensityProfile)

isIntDensityProfile

public boolean isIntDensityProfile()

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object