RATSQuadtree (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- RATSQuadtree

public class RATSQuadtree
extends Object

Field Summary

Fields
Modifier and Type	Field and Description
`boolean`	`bverbose` produce informative messages flag
`int[]`	`dim` the width and height of the images
`int`	`level` the level of this family
`double[]`	`minSzPx` the minimum allowed size in pixels
`float`	`sum` the sum of pixels at this level
`double`	`x0` the coords of this level
`double`	`x1` the coords of this level
`double`	`y0` the coords of this level
`double`	`y1` the coords of this level

Constructor Summary

Constructors
Constructor and Description
`RATSQuadtree(int[] dim, double minSzPx)` This is the entry constructor for the top level leaf
`RATSQuadtree(int[] dim, double[] minSzPx)` This is the entry constructor for the top level leaf
`RATSQuadtree(int[] dim, double[] minSzPx, int level, double x0, double y0, double x1, double y1, RATSQuadtree theParent)` This constructor is used by a Quadtree as it creates its children

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`countLeaflets(int level)` This methods returns the number of leaflets for a given level
`int`	`countLevels()` This method returns the number of subsequent generations plus itself.
`void`	`drawBounds(ij.ImagePlus imp)` This method draws the rectangle
`void`	`drawBounds(int drawLevel, ij.ImagePlus imp)` This method will draw the box for the leaf
`void`	`drawCenter(ij.ImagePlus imp)` This method will draw the center of the box
`void`	`fillWithSums(ij.process.ImageProcessor ip)` Fills the sum values.
`int[]`	`getArrayDim(float[][] arr)` Returns a two element array of [width,height]
`int[]`	`getArrayDim(RATSQuadtree[][] arr)` Returns a two element array of [width,height]
`double[]`	`getCenter()` Returns the center coordinates as [x,y]
`String`	`getChildName(RATSQuadtree qc)` Returns the two letter quadrant code for the provided child as (NW, NE, SW, SE, or NA)
`RATSQuadtree[][]`	`getChildren()` Returns the children of this leaf
`double[]`	`getCoordsDouble()` Returns the coordinates rounded to integer [x0, y0, x1, y1]
`int[]`	`getCoordsInteger()` Returns the coordinates rounded to integer [x0, y0, x1, y1]
`int[]`	`getDim(Object[][] arr)` Returns a two element array of [width,height] for the given input array.
`double[]`	`getDimDouble()` Returns the dimensions of the leaflet as double
`int[]`	`getDimInteger()` Returns the dimensions of the leaflet as integer
`int`	`getLevel()` Returns the level of this quadtree
`RATSQuadtree[][]`	`getLevel(int theLevel)` Returns an array of leaflets in [nw,ne,sw,se] order
`String`	`getName()` Returns the two letter quadrant code for the quadtree
`RATSQuadtree`	`getParent()` Returns the parent of this leaf
`float[]`	`getPixelsFloat(ij.ImagePlus imp)` This method returns the pixels enclosed in this leaflet.
`float[]`	`getPixelsFloat(ij.process.ImageProcessor ip)` This method returns the pixels enclosed in this leaflet.
`RATSQuadtree[][]`	`getSiblings()` Returns the siblings of this leaf
`float[][]`	`getSumArrayFloat(int theLevel, ij.ImagePlus imp)` Returns a 2d array of the sums for the level specified The is really for the top level leaf
`float[][]`	`getSumArrayFloat(int theLevel, ij.process.ImageProcessor ip)` Returns a 2d array of the sums for the level specified The is really for the top level leaf
`float`	`getSumFloat()` Returns the sum (which may not have been assigned, so use this after filling the leaves with the sums.
`float`	`getSumFloat(ij.ImagePlus imp)` Returns the sum of the pixels enclosed in this leaflet
`float`	`getSumFloat(ij.process.ImageProcessor ip)` Returns the sum of the pixels enclosed in this leaflet
`boolean`	`hasChildren()` Returns true if this leaf has children
`float[][]`	`makeArrayFloat(int theLevel)` This method creates a 2d array for the level specified.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - bverbose
```
public boolean bverbose
```
    produce informative messages flag
  - dim
```
public int[] dim
```
    the width and height of the images
  - level
```
public int level
```
    the level of this family
  - minSzPx
```
public double[] minSzPx
```
    the minimum allowed size in pixels
  - x0
```
public double x0
```
    the coords of this level
  - y0
```
public double y0
```
    the coords of this level
  - x1
```
public double x1
```
    the coords of this level
  - y1
```
public double y1
```
    the coords of this level
  - sum
```
public float sum
```
    the sum of pixels at this level
- Constructor Detail
  - RATSQuadtree
```
public RATSQuadtree(int[] dim,
                    double minSzPx)
```
    This is the entry constructor for the top level leaf
    
    Parameters:
    
    dim - the size of the original image
    
    minSzPx - the minimum allowed leaf size in pixels (used for both x and y)
  - RATSQuadtree
```
public RATSQuadtree(int[] dim,
                    double[] minSzPx)
```
    This is the entry constructor for the top level leaf
    
    Parameters:
    
    dim - the size of the original image
    
    minSzPx - the minimum allowed leaf size in pixels [minx, miny]
  - RATSQuadtree
```
public RATSQuadtree(int[] dim,
                    double[] minSzPx,
                    int level,
                    double x0,
                    double y0,
                    double x1,
                    double y1,
                    RATSQuadtree theParent)
```
    This constructor is used by a Quadtree as it creates its children
    
    Parameters:
    
    dim - the size of the original image
    
    minSzPx - the minumum leaf size in pixels
    
    level - the assigned tree level\
    
    x0 - the left coord
    
    y0 - the top coord
    
    x1 - the right coord
    
    y1 - the bottom coord
    
    theParent - reference to the parent quadtree.
- Method Detail
  - fillWithSums
```
public void fillWithSums(ij.process.ImageProcessor ip)
```
    Fills the sum values. This method is for the top level. It manually fills the lowest level. The recursively fills each level above the lowest.
  - getDimInteger
```
public int[] getDimInteger()
```
    Returns the dimensions of the leaflet as integer
    
    Returns:
    
    a vector of [width, height]
  - getDimDouble
```
public double[] getDimDouble()
```
    Returns the dimensions of the leaflet as double
    
    Returns:
    
    a vector of [width, height]
  - getCenter
```
public double[] getCenter()
```
    Returns the center coordinates as [x,y]
  - getCoordsInteger
```
public int[] getCoordsInteger()
```
    Returns the coordinates rounded to integer [x0, y0, x1, y1]
    
    Returns:
    
    a four element array of the coords rounded to the nearest integer
  - getCoordsDouble
```
public double[] getCoordsDouble()
```
    Returns the coordinates rounded to integer [x0, y0, x1, y1]
    
    Returns:
    
    a four element array of the coords rounded to the nearest integer
  - getChildName
```
public String getChildName(RATSQuadtree qc)
```
    Returns the two letter quadrant code for the provided child as (NW, NE, SW, SE, or NA)
    
    Parameters:
    
    qc - the RATSQuadtree child
    
    Returns:
    
    a two letter code indicating the child's quadtrant or NA if this child doesn't belong.
  - getName
```
public String getName()
```
    Returns the two letter quadrant code for the quadtree
    
    Returns:
    
    the two letter code indicating the child's position (NW,NE, SW or SE) if this is the top then "NA" is returned.
  - getLevel
```
public int getLevel()
```
    Returns the level of this quadtree
    
    Returns:
    
    the level of this leaf
  - hasChildren
```
public boolean hasChildren()
```
    Returns true if this leaf has children
  - getChildren
```
public RATSQuadtree[][] getChildren()
```
    Returns the children of this leaf
  - getParent
```
public RATSQuadtree getParent()
```
    Returns the parent of this leaf
  - getSiblings
```
public RATSQuadtree[][] getSiblings()
```
    Returns the siblings of this leaf
    
    Returns:
    
    A 2x2 array of quadtrees or null if no siblings
  - getLevel
```
public RATSQuadtree[][] getLevel(int theLevel)
```
    Returns an array of leaflets in [nw,ne,sw,se] order
    
    Parameters:
    
    theLevel - the zero-based index of the level to retrieve
    
    Returns:
    
    A nxn array of quadtrees at the specified level
  - getSumFloat
```
public float getSumFloat(ij.ImagePlus imp)
```
    Returns the sum of the pixels enclosed in this leaflet
    
    Parameters:
    
    imp - The ImagePlus image of pixels
    
    Returns:
    
    the sum of the pixels
  - getSumFloat
```
public float getSumFloat(ij.process.ImageProcessor ip)
```
    Returns the sum of the pixels enclosed in this leaflet
    
    Parameters:
    
    ip - The imageProcessor of pixels
    
    Returns:
    
    the sum of the pixels
  - getSumFloat
```
public float getSumFloat()
```
    Returns the sum (which may not have been assigned, so use this after filling the leaves with the sums. See fillWithSums()
  - getSumArrayFloat
```
public float[][] getSumArrayFloat(int theLevel,
                                  ij.ImagePlus imp)
```
    Returns a 2d array of the sums for the level specified The is really for the top level leaf
    
    Parameters:
    
    theLevel - the zero-based index level
    
    Returns:
    
    a 2d float array of the float values
  - getSumArrayFloat
```
public float[][] getSumArrayFloat(int theLevel,
                                  ij.process.ImageProcessor ip)
```
    Returns a 2d array of the sums for the level specified The is really for the top level leaf
    
    Parameters:
    
    theLevel - the zero-based index level
    
    Returns:
    
    a 2d float array of the float values
  - getPixelsFloat
```
public float[] getPixelsFloat(ij.ImagePlus imp)
```
    This method returns the pixels enclosed in this leaflet.
    
    Parameters:
    
    imp - the ImagePlus with the pixels
    
    Returns:
    
    an 1d array of single precision values
  - getPixelsFloat
```
public float[] getPixelsFloat(ij.process.ImageProcessor ip)
```
    This method returns the pixels enclosed in this leaflet.
    
    Parameters:
    
    ip - the ImageProcessor with the pixels
    
    Returns:
    
    an 1d array of single precision values
  - countLeaflets
```
public int countLeaflets(int level)
```
    This methods returns the number of leaflets for a given level
    
    Parameters:
    
    level - The zero based level index
    
    Returns:
    
    The number of leaflets at that level
  - countLevels
```
public int countLevels()
```
    This method returns the number of subsequent generations plus itself.
    
    Returns:
    
    the "depth" of the qaudtree which is 1-based
  - drawBounds
```
public void drawBounds(ij.ImagePlus imp)
```
    This method draws the rectangle
    
    Parameters:
    
    imp - the ImagePlus on to which to draw the bounds
  - drawCenter
```
public void drawCenter(ij.ImagePlus imp)
```
    This method will draw the center of the box
    
    Parameters:
    
    imp - the ImagePlus onto which to draw the center
  - drawBounds
```
public void drawBounds(int drawLevel,
                       ij.ImagePlus imp)
```
    This method will draw the box for the leaf
    
    Parameters:
    
    drawLevel - the depth of leaves to draw
    
    imp - the ImagePlus onto which to draw
  - makeArrayFloat
```
public float[][] makeArrayFloat(int theLevel)
```
    This method creates a 2d array for the level specified.
    
    Parameters:
    
    theLevel - the level to create an array for.
  - getArrayDim
```
public int[] getArrayDim(RATSQuadtree[][] arr)
```
    Returns a two element array of [width,height]
    
    Parameters:
    
    arr - The nxn array of quadtrees
    
    Returns:
    
    a two element array of [width,height]
  - getArrayDim
```
public int[] getArrayDim(float[][] arr)
```
    Returns a two element array of [width,height]
    
    Parameters:
    
    arr - the nxm element array of floats
    
    Returns:
    
    a two element array of [width,height]
  - getDim
```
public int[] getDim(Object[][] arr)
```
    Returns a two element array of [width,height] for the given input array.
    
    Parameters:
    
    arr - a nxm array
    
    Returns:
    
    a two element array of [width,height] for the given input array.

Class RATSQuadtree

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

bverbose

dim

level

minSzPx

x0

y0

x1

y1

sum

Constructor Detail

RATSQuadtree

RATSQuadtree

RATSQuadtree

Method Detail

fillWithSums

getDimInteger

getDimDouble

getCenter

getCoordsInteger

getCoordsDouble

getChildName

getName

getLevel

hasChildren

getChildren

getParent

getSiblings

getLevel

getSumFloat

getSumFloat

getSumFloat

getSumArrayFloat

getSumArrayFloat

getPixelsFloat

getPixelsFloat

countLeaflets

countLevels

drawBounds

drawCenter

drawBounds

makeArrayFloat

getArrayDim

getArrayDim

getDim