Profile (Fiji Javadocs 0-SNAPSHOT API)

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`add(ProfileEntry entry)`
`void`	`assignImage(ij.ImagePlus imp)`
`ShollPoint`	`center()`
`ArrayList<Double>`	`counts()`
`double[]`	`countsAsArray()`
`Profile`	`duplicate()`
`double`	`endRadius()`
`SortedSet<ProfileEntry>`	`entries()`
`boolean`	`equals(Object o)`
`double`	`getCountAtRadius(double radius)`
`Properties`	`getProperties()`
`Overlay`	`getROIs()`
`Overlay`	`getROIs(ij.ImagePlus imp)`
`boolean`	`hasPoints()`
`String`	`identifier()`
`boolean`	`is2D()`
`boolean`	`isEmpty()`
`boolean`	`isIntDensityProfile()`
`int`	`nDimensions()`
`ShollPlot`	`plot()`
`ArrayList<Set<ShollPoint>>`	`points()`
`ArrayList<Double>`	`radii()`
`double[]`	`radiiAsArray()`
`ArrayList<Double>`	`radiiSquared()`
`void`	`scale(double xScale, double yScale, double zScale)`
`boolean`	`scaled()`
`void`	`setCenter(ShollPoint center)`
`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, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail
- 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 Detail

identifier
```
public String identifier()
```

setIdentifier

public void setIdentifier(String identifier)

radii
```
public ArrayList<Double> radii()
```

duplicate
```
public Profile duplicate()
```

radiiSquared

public ArrayList<Double> radiiSquared()

radiiAsArray
```
public double[] radiiAsArray()
```

counts
```
public ArrayList<Double> counts()
```

countsAsArray
```
public double[] countsAsArray()
```

points

public ArrayList<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 Overlay getROIs()
```

getROIs

public Overlay getROIs(ij.ImagePlus imp)

add

public boolean add(ProfileEntry entry)

zeroCounts
```
public int zeroCounts()
```

isEmpty
```
public boolean isEmpty()
```

setIsIntDensityProfile

public void setIsIntDensityProfile(boolean isIntDensityProfile)

isIntDensityProfile
```
public boolean isIntDensityProfile()
```

equals
```
public boolean equals(Object o)
```
Overrides:

equals in class Object

Class Profile

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Profile

Profile

Profile

Profile

Method Detail

identifier

setIdentifier

radii

duplicate

radiiSquared

radiiAsArray

counts

countsAsArray

points

getCountAtRadius

trimZeroCounts

trimNaNCounts

scale

entries

source

nDimensions

is2D

setNDimensions

scaled

hasPoints

plot

toString

center

setCenter

size

startRadius

stepSize

endRadius

spatialCalibration

assignImage

setSpatialCalibration

getProperties

setProperties

getROIs

getROIs

add

zeroCounts

isEmpty

setIsIntDensityProfile

isIntDensityProfile

equals