Counter3D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- Utilities.Counter3D

```
public class Counter3D
extends Object
```
Version:

1.0, 7/11/07

Author:

Fabrice P. Cordelieres, fabrice.cordelieres@gmail.com

Constructor Summary

Constructors
Constructor and Description
`Counter3D(ij.ImagePlus img)` Creates a new instance of Counter3D
`Counter3D(ij.ImagePlus img, int thr)` Creates a new instance of Counter3D.
`Counter3D(ij.ImagePlus img, int thr, int min, int max, boolean exclude, boolean redirect)` Creates a new instance of Counter3D.
`Counter3D(int[] img, String title, int width, int height, int nbSlices)` Creates a new instance of Counter3D.
`Counter3D(int[] img, String title, int width, int height, int nbSlices, ij.measure.Calibration cal)` Creates a new instance of Counter3D.
`Counter3D(int[] img, String title, int width, int height, int nbSlices, int thr)` Creates a new instance of Counter3D.
`Counter3D(int[] img, String title, int width, int height, int nbSlices, int thr, ij.measure.Calibration cal)` Creates a new instance of Counter3D.
`Counter3D(int[] img, String title, int width, int height, int nbSlices, int thr, int min, int max, boolean exclude, boolean redirect, ij.measure.Calibration cal)` Creates a new instance of Counter3D.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addObject(Object3D object)` Add the provided Object3D to the list
`float[][]`	`getCentreOfMassList()` Returns the centres of masses' list.
`ij.ImagePlus`	`getCentreOfMassMap()` Returns the centres of masses' map.
`ij.ImagePlus`	`getCentreOfMassMap(boolean drawNb, boolean whiteNb, int dotSize, int fontSize)` Returns the centres of masses' map.
`float[][]`	`getCentroidList()` Returns the centroïds' list.
`ij.ImagePlus`	`getCentroidMap()` Returns the centroïds' map.
`ij.ImagePlus`	`getCentroidMap(boolean drawNb, boolean whiteNb, int dotSize, int fontSize)` Returns the centroïds' map.
`Object3D`	`getObject(int index)` Returns the object at the provided index, as an Object3D
`void`	`getObjects()` Generates the objects list.
`Vector`	`getObjectsList()` Returns the list of all found objects.
`ij.ImagePlus`	`getObjMap()` Returns the objects map.
`ij.ImagePlus`	`getObjMap(boolean drawNb, int fontSize)` Returns the objects map.
`int[]`	`getObjMapAsArray()` Returns the objects map as a 1D integer array.
`int[][]`	`getSurfPixCoord()` Returns the surface pixels coordinates' list.
`int[]`	`getSurfPixList()` Returns the surface pixels' list.
`ij.ImagePlus`	`getSurfPixMap()` Returns the surface pixels' map.
`ij.ImagePlus`	`getSurfPixMap(boolean drawNb, boolean whiteNb, int fontSize)` Returns the surface pixels' map.
`void`	`removeObject(int index)` Removes the Object3D stored at the provided index.
`void`	`showStatistics(boolean newRT)` Returns an ResultsTable containing statistics on objects: Volume and Surface: number of pixel forming the structures and at its surface respectively. StdDev, Median, IntDen, Min and Max: standard deviation, median, sum, minimum and maximum of all intensities for the current object. X, Y and Z: coordinates of the current object's centroïd. XM, YM and ZM: coordinates of the current object's centre of mass. BX, BY and BZ: coordinates of the top-left corner of the current object's bounding box. B-width, B-height and B-depth: current object's bounding box dimensions.
`void`	`showSummary()` Returns a summary containing the image name and the number of retrieved objects including the set filter size and threshold.
`void`	`showSurfPix()` Returns an ResultsTable containing coordinates of the surface pixels for all objects: Object ID: current object number. X, Y and Z: coordinates of the current object's surface pixel.

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

- Constructor Detail
  - Counter3D
```
public Counter3D(ij.ImagePlus img,
                 int thr,
                 int min,
                 int max,
                 boolean exclude,
                 boolean redirect)
```
    Creates a new instance of Counter3D.
    
    Parameters:
    
    img - specifies the image to convert into an Counter3D.
    
    thr - specifies the threshold value (should be an Integer).
    
    min - specifies the MIN size threshold to be used (should be an Integer).
    
    max - specifies the MAX size threshold to be used (should be an Integer).
    
    exclude - specifies if the objects on the edges should be excluded (should be a boolean).
    
    redirect - specifies if intensities measurements should be redirected to another image defined within the options window (should be a boolean).
  - Counter3D
```
public Counter3D(ij.ImagePlus img,
                 int thr)
```
    Creates a new instance of Counter3D.
    
    Parameters:
    
    img - specifies the image to convert into an Counter3D.
    
    thr - specifies the threshold value (should be an Integer).
  - Counter3D
```
public Counter3D(ij.ImagePlus img)
```
    Creates a new instance of Counter3D
    
    Parameters:
    
    img - specifies the image to convert into an Counter3D.
  - Counter3D
```
public Counter3D(int[] img,
                 String title,
                 int width,
                 int height,
                 int nbSlices,
                 int thr,
                 int min,
                 int max,
                 boolean exclude,
                 boolean redirect,
                 ij.measure.Calibration cal)
```
    Creates a new instance of Counter3D.
    
    Parameters:
    
    img - specifies the array containing the image data.
    
    title - specifies the image title.
    
    width - specifies the image width.
    
    height - specifies the image height.
    
    nbSlices - specifies the image numbre of slices.
    
    thr - specifies the threshold value (should be an Integer).
    
    min - specifies the MIN size threshold to be used (should be an Integer).
    
    max - specifies the MAX size threshold to be used (should be an Integer).
    
    exclude - specifies if the objects on the edges should be excluded (should be a boolean).
    
    redirect - specifies if intensities measurements should be redirected to another image defined within the options window (should be a boolean).
    
    cal - specifies the image calibration to be used.
  - Counter3D
```
public Counter3D(int[] img,
                 String title,
                 int width,
                 int height,
                 int nbSlices,
                 int thr,
                 ij.measure.Calibration cal)
```
    Creates a new instance of Counter3D.
    
    Parameters:
    
    img - specifies the array containing the image data.
    
    title - specifies the image title.
    
    width - specifies the image width.
    
    height - specifies the image height.
    
    nbSlices - specifies the image number of slices.
    
    thr - specifies the threshold value (should be an Integer).
    
    cal - specifies the image calibration to be used.
  - Counter3D
```
public Counter3D(int[] img,
                 String title,
                 int width,
                 int height,
                 int nbSlices,
                 int thr)
```
    Creates a new instance of Counter3D.
    
    Parameters:
    
    img - specifies the array containing the image data.
    
    title - specifies the image title.
    
    width - specifies the image width.
    
    height - specifies the image height.
    
    nbSlices - specifies the image number of slices.
    
    thr - specifies the threshold value (should be an Integer).
  - Counter3D
```
public Counter3D(int[] img,
                 String title,
                 int width,
                 int height,
                 int nbSlices,
                 ij.measure.Calibration cal)
```
    Creates a new instance of Counter3D.
    
    Parameters:
    
    img - specifies the array containing the image data.
    
    title - specifies the image title.
    
    width - specifies the image width.
    
    height - specifies the image height.
    
    nbSlices - specifies the image number of slices.
    
    cal - specifies the image calibration to be used.
  - Counter3D
```
public Counter3D(int[] img,
                 String title,
                 int width,
                 int height,
                 int nbSlices)
```
    Creates a new instance of Counter3D.
    
    Parameters:
    
    img - specifies the array containing the image data.
    
    title - specifies the image title.
    
    width - specifies the image width.
    
    height - specifies the image height.
    
    nbSlices - specifies the image number of slices.
- Method Detail
  - getObjects
```
public void getObjects()
```
    Generates the objects list.
  - getObject
```
public Object3D getObject(int index)
```
    Returns the object at the provided index, as an Object3D
    
    Parameters:
    
    index - the index of the object to return
    
    Returns:
    
    an Object3D or null idf the index is out of bounds
  - addObject
```
public void addObject(Object3D object)
```
    Add the provided Object3D to the list
    
    Parameters:
    
    object - Object3D to add
  - removeObject
```
public void removeObject(int index)
```
    Removes the Object3D stored at the provided index. Does nothing if index is out of bounds.
    
    Parameters:
    
    index - index of the Object3D to be removed
  - getObjectsList
```
public Vector getObjectsList()
```
    Returns the list of all found objects.
    
    Returns:
    
    the list of all found objects as a Object3D array.
  - getObjMap
```
public ij.ImagePlus getObjMap(boolean drawNb,
                              int fontSize)
```
    Returns the objects map.
    
    Parameters:
    
    drawNb - should be true if numbers have to be drawn at each coordinate stored in cenArray (boolean).
    
    fontSize - font size of the numbers to be shown (integer).* @return an ImagePlus containing all found objects, each one carrying pixel value equal to its ID.
  - getObjMap
```
public ij.ImagePlus getObjMap()
```
    Returns the objects map.
    
    Returns:
    
    an ImagePlus containing all found objects, each one carrying pixel value equal to its ID.
  - getObjMapAsArray
```
public int[] getObjMapAsArray()
```
    Returns the objects map as a 1D integer array.
    
    Returns:
    
    an ImagePlus containing all found objects, each one carrying pixel value equal to its ID.
  - getCentreOfMassList
```
public float[][] getCentreOfMassList()
```
    Returns the centres of masses' list.
    
    Returns:
    
    the coordinates of all found centres of masses as a dual float array ([ID][0:x, 1:y, 2:z]).
  - getCentreOfMassMap
```
public ij.ImagePlus getCentreOfMassMap(boolean drawNb,
                                       boolean whiteNb,
                                       int dotSize,
                                       int fontSize)
```
    Returns the centres of masses' map.
    
    Parameters:
    
    drawNb - should be true if numbers have to be drawn at each coordinate stored in cenArray (boolean).
    
    whiteNb - should be true if numbers have to appear white (boolean).
    
    dotSize - size of the dots to be drawn (integer).
    
    fontSize - font size of the numbers to be shown (integer).* @return an ImagePlus containing all centres of masses, each one carrying pixel value equal to its ID.
  - getCentreOfMassMap
```
public ij.ImagePlus getCentreOfMassMap()
```
    Returns the centres of masses' map.
    
    Returns:
    
    an ImagePlus containing all centres of masses, each one carrying pixel value equal to its ID.
  - getCentroidList
```
public float[][] getCentroidList()
```
    Returns the centroïds' list.
    
    Returns:
    
    the coordinates of all found centroïds as a dual float array ([ID][0:x, 1:y, 2:z]).
  - getCentroidMap
```
public ij.ImagePlus getCentroidMap(boolean drawNb,
                                   boolean whiteNb,
                                   int dotSize,
                                   int fontSize)
```
    Returns the centroïds' map.
    
    Parameters:
    
    drawNb - should be true if numbers have to be drawn at each coordinate stored in cenArray (boolean).
    
    whiteNb - should be true if numbers have to appear white (boolean).
    
    dotSize - size of the dots to be drawn (integer).
    
    fontSize - font size of the numbers to be shown (integer).* @return an ImagePlus containing all centroïds, each one carrying pixel value equal to its ID.
  - getCentroidMap
```
public ij.ImagePlus getCentroidMap()
```
    Returns the centroïds' map.
    
    Returns:
    
    an ImagePlus containing all centroïds, each one carrying pixel value equal to its ID.
  - getSurfPixList
```
public int[] getSurfPixList()
```
    Returns the surface pixels' list.
    
    Returns:
    
    the coordinates of all pixels found at the surface of objects as a mono-dimensional integer array.
  - getSurfPixCoord
```
public int[][] getSurfPixCoord()
```
    Returns the surface pixels coordinates' list.
    
    Returns:
    
    the coordinates of all pixels found at the surface of objects as a dual integer array([index][0:x, 1:y, 2:z, 3:ID]).
  - getSurfPixMap
```
public ij.ImagePlus getSurfPixMap(boolean drawNb,
                                  boolean whiteNb,
                                  int fontSize)
```
    Returns the surface pixels' map.
    
    Parameters:
    
    drawNb - should be true if numbers have to be drawn at each coordinate stored in cenArray (boolean).
    
    whiteNb - should be true if numbers have to appear white (boolean).
    
    fontSize - font size of the numbers to be shown (integer).* @return an ImagePlus containing all pixels found at the surface of objects, each one carrying pixel value equal to its ID.
  - getSurfPixMap
```
public ij.ImagePlus getSurfPixMap()
```
    Returns the surface pixels' map.
    
    Returns:
    
    an ImagePlus containing all pixels found at the surface of objects, each one carrying pixel value equal to its ID.
  - showStatistics
```
public void showStatistics(boolean newRT)
```
    Returns an ResultsTable containing statistics on objects:
    - Volume and Surface: number of pixel forming the structures and at its surface respectively.
    - StdDev, Median, IntDen, Min and Max: standard deviation, median, sum, minimum and maximum of all intensities for the current object.
    - X, Y and Z: coordinates of the current object's centroïd.
    - XM, YM and ZM: coordinates of the current object's centre of mass.
    - BX, BY and BZ: coordinates of the top-left corner of the current object's bounding box.
    - B-width, B-height and B-depth: current object's bounding box dimensions.
    Parameters:
    
    newRT - should be false if the result window is to be named "Results", allowing use of "Analyze/Distribution" and "Analyze/Summarize". If true, the window will be named "Statistics for "+image title.
  - showSummary
```
public void showSummary()
```
    Returns a summary containing the image name and the number of retrieved objects including the set filter size and threshold.
  - showSurfPix
```
public void showSurfPix()
```
    Returns an ResultsTable containing coordinates of the surface pixels for all objects:
    - Object ID: current object number.
    - X, Y and Z: coordinates of the current object's surface pixel.

Class Counter3D

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Counter3D

Counter3D

Counter3D

Counter3D

Counter3D

Counter3D

Counter3D

Counter3D

Method Detail

getObjects

getObject

addObject

removeObject

getObjectsList

getObjMap

getObjMap

getObjMapAsArray

getCentreOfMassList

getCentreOfMassMap

getCentreOfMassMap

getCentroidList

getCentroidMap

getCentroidMap

getSurfPixList

getSurfPixCoord

getSurfPixMap

getSurfPixMap

showStatistics

showSummary

showSurfPix