Object3D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- Utilities.Object3D

```
public class Object3D
extends Object
```
Version:

1.0, 7/11/07

Author:

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

Field Summary

Fields
Modifier and Type	Field and Description
`int[]`	`bound_cube_BR` Bounding cube bottom-right corner coordinates (bound_cube_BR[0:x, 1:y, 2:z])
`int`	`bound_cube_depth` Depth of the bounding cube
`int`	`bound_cube_height` Height of the bounding cube
`int[]`	`bound_cube_TL` Bounding cube top-left corner coordinates (bound_cube_TL[0:x, 1:y, 2:z])
`int`	`bound_cube_width` Width of the bounding cube
`float[]`	`c_mass` Coordinates of the centre of mass (c_mass[0:x, 1:y, 2:z]
`ij.measure.Calibration`	`cal` Calibration of the Object3D
`float[]`	`centroid` Coordinates of the centroïd (centroid[0:x, 1:y, 2:z]
`float`	`int_dens` Integrated density / summed intensity
`boolean[]`	`isSurfVoxels` For each obj_voxels[i][j], stores true if current voxel is on surface, false otherwise
`int`	`max` Maximum intensity
`float`	`mean_dist2surf` Mean distance to the surface (distance calibrated measure)
`float`	`mean_gray` Mean intensity
`float`	`median` Median intensity
`float`	`median_dist2surf` Median distance to the surface (distance calibrated measure)
`int`	`min` Minimum intensity
`int[][]`	`obj_voxels` Stores coordinates and intensities of the current Object3D: obj_voxels[index][0:x, 1:y, 2:z, 3:intensity]
`float`	`SD` SD of the intensity
`float`	`SD_dist2surf` SD of the distance to the surface (distance calibrated measure)
`int`	`size` Object3D's size (in pixels or voxels)
`float`	`surf_cal` True calibrated surface measurement
`int`	`surf_size` Number of pixels/voxels on the surface
`Vector<int[]>`	`surf_voxelsCoord` Vector of length 3 array containing the 3D coordinates of all surface pixels

Constructor Summary

Constructors
Constructor and Description
`Object3D(int size)` Creates a new instance of Object3D
`Object3D(int size, ij.measure.Calibration cal)` Creates a new instance of Object3D (distances will be calibrated according to the input calibration)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addVoxel(int x, int y, int z, int val, boolean isSurf, float surf)` Adds a new voxel to the specified Object3D, at the next available slot in the object.
`float`	`median(float[] array)` Calculates the med value of a float array.

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

- Field Detail
  - obj_voxels
```
public int[][] obj_voxels
```
    Stores coordinates and intensities of the current Object3D: obj_voxels[index][0:x, 1:y, 2:z, 3:intensity]
  - isSurfVoxels
```
public boolean[] isSurfVoxels
```
    For each obj_voxels[i][j], stores true if current voxel is on surface, false otherwise
  - surf_voxelsCoord
```
public Vector<int[]> surf_voxelsCoord
```
    Vector of length 3 array containing the 3D coordinates of all surface pixels
  - mean_gray
```
public float mean_gray
```
    Mean intensity
  - median
```
public float median
```
    Median intensity
  - SD
```
public float SD
```
    SD of the intensity
  - min
```
public int min
```
    Minimum intensity
  - max
```
public int max
```
    Maximum intensity
  - int_dens
```
public float int_dens
```
    Integrated density / summed intensity
  - mean_dist2surf
```
public float mean_dist2surf
```
    Mean distance to the surface (distance calibrated measure)
  - median_dist2surf
```
public float median_dist2surf
```
    Median distance to the surface (distance calibrated measure)
  - SD_dist2surf
```
public float SD_dist2surf
```
    SD of the distance to the surface (distance calibrated measure)
  - size
```
public int size
```
    Object3D's size (in pixels or voxels)
  - surf_size
```
public int surf_size
```
    Number of pixels/voxels on the surface
  - surf_cal
```
public float surf_cal
```
    True calibrated surface measurement
  - centroid
```
public float[] centroid
```
    Coordinates of the centroïd (centroid[0:x, 1:y, 2:z]
  - c_mass
```
public float[] c_mass
```
    Coordinates of the centre of mass (c_mass[0:x, 1:y, 2:z]
  - bound_cube_TL
```
public int[] bound_cube_TL
```
    Bounding cube top-left corner coordinates (bound_cube_TL[0:x, 1:y, 2:z])
  - bound_cube_BR
```
public int[] bound_cube_BR
```
    Bounding cube bottom-right corner coordinates (bound_cube_BR[0:x, 1:y, 2:z])
  - bound_cube_width
```
public int bound_cube_width
```
    Width of the bounding cube
  - bound_cube_height
```
public int bound_cube_height
```
    Height of the bounding cube
  - bound_cube_depth
```
public int bound_cube_depth
```
    Depth of the bounding cube
  - cal
```
public ij.measure.Calibration cal
```
    Calibration of the Object3D
- Constructor Detail
  - Object3D
```
public Object3D(int size,
                ij.measure.Calibration cal)
```
    Creates a new instance of Object3D (distances will be calibrated according to the input calibration)
    
    Parameters:
    
    size - specifies the number of voxels for the new 3DObject, distances being calibrated.
    
    cal - calibration to be used for distance/volume measurements
  - Object3D
```
public Object3D(int size)
```
    Creates a new instance of Object3D
    
    Parameters:
    
    size - specifies the number of voxels for the new 3DObject.
- Method Detail
  - addVoxel
```
public void addVoxel(int x,
                     int y,
                     int z,
                     int val,
                     boolean isSurf,
                     float surf)
```
    Adds a new voxel to the specified Object3D, at the next available slot in the object.
    
    Parameters:
    
    x - specifies the x coordinate of the voxel to be added.
    
    y - specifies the y coordinate of the voxel to be added.
    
    z - specifies the z coordinate of the voxel to be added.
    
    val - specifies the intensity of the voxel to be added.
    
    isSurf - specifies if the voxel to be added is on the surface of the object.
  - median
```
public float median(float[] array)
```
    Calculates the med value of a float array.
    
    Parameters:
    
    array - input float array.
    
    Returns:
    
    the med value of the input float array (float).

Class Object3D

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

obj_voxels

isSurfVoxels

surf_voxelsCoord

mean_gray

median

SD

min

max

int_dens

mean_dist2surf

median_dist2surf

SD_dist2surf

size

surf_size

surf_cal

centroid

c_mass

bound_cube_TL

bound_cube_BR

bound_cube_width

bound_cube_height

bound_cube_depth

cal

Constructor Detail

Object3D

Object3D

Method Detail

addVoxel

median