BoundingBox (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.util.BoundingBox

```
public class BoundingBox
extends Object
```
A BoundingBox contains information (including spatial calibration) of a tracing canvas bounding box, i.e., the minimum bounding cuboid containing all nodes (SNTPoints) of a reconstructed structure.

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`String`	`info` Used to store information about this bounding box.
`protected PointInImage`	`origin` The bounding box origin (SE, lower corner)
`protected PointInImage`	`originOpposite` The origin opposite (NW, upper corner)
`protected String`	`spacingUnit`
`double`	`xSpacing` The 'voxel width' of the bounding box
`double`	`ySpacing` The 'voxel height' of the bounding box
`double`	`zSpacing` The 'voxel depth' of the bounding box

Constructor Summary

Constructors
Constructor and Description
`BoundingBox()` Constructs an 'empty' BoundingBox using default values, with the box origin defined as a point with `Double.NaN` coordinates and `Double.NaN` dimensions

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`append(Iterator<? extends SNTPoint> iterator)` Computes the bounding box of the specified point cloud and appends it to this bounding box, resizing it as needed.
`BoundingBox`	`clone()`
`void`	`combine(BoundingBox boundingBox)` Combines Combines this bounding box with another one.
`void`	`compute(Iterator<? extends SNTPoint> iterator)` Computes a new positioning so that this box encloses the specified point cloud.
`boolean`	`contains(BoundingBox boundingBox)` Checks whether the specified BoundingBox is enclosed by this one .
`boolean`	`contains(SNTPoint point)`
`double`	`depth()`
`boolean`	`equals(Object obj)`
`ij.measure.Calibration`	`getCalibration()` Creates a Calibration object using information from this BoundingBox
`SNTPoint`	`getCentroid()`
`double`	`getDiagonal()` Gets the box diagonal
`double[]`	`getDimensions()` Gets this BoundingBox dimensions in real world units.
`double[]`	`getDimensions(boolean scaled)` Gets this BoundingBox dimensions.
`String`	`getUnit()` Gets the length unit of voxel spacing
`boolean`	`hasDimensions()`
`int`	`hashCode()`
`double`	`height()`
`void`	`inferSpacing(Collection<SWCPoint> points)` Infers the voxel spacing of this box from the inter-node distances of a Collection of `SWCPoint`s.
`boolean`	`isScaled()` Checks whether this BoundingBox is spatially calibrated, i.e., if voxel spacing has been specified
`PointInImage`	`origin()` Retrieves the origin of this box.
`PointInImage`	`originOpposite()` Retrieves the origin opposite of this box.
`protected void`	`reset()`
`void`	`setDimensions(long uncalibratedWidth, long uncalibratedHeight, long uncalibratedDepth)` Sets the dimensions of this bounding box using uncalibrated (pixel) lengths.
`void`	`setOrigin(PointInImage origin)` Sets the origin for this box, i.e., its (xMin, yMin, zMin) vertex.
`void`	`setOriginOpposite(PointInImage originOpposite)` Sets the origin opposite for this box, i.e., its (xMax, yMax, zMax) vertex.
`void`	`setSpacing(double xSpacing, double ySpacing, double zSpacing, String spacingUnit)` Sets the voxel spacing.
`void`	`setUnit(String unit)` Sets the default length unit for voxel spacing (typically um, for SWC reconstructions)
`String`	`toString()`
`PointInImage`	`unscaledOrigin()` Retrieves the origin of this box in unscaled ("pixel" units)
`PointInImage`	`unscaledOriginOpposite()` Retrieves the origin opposite of this box in unscaled ("pixel" units)
`double`	`width()`

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - xSpacing
```
public double xSpacing
```
    The 'voxel width' of the bounding box
  - ySpacing
```
public double ySpacing
```
    The 'voxel height' of the bounding box
  - zSpacing
```
public double zSpacing
```
    The 'voxel depth' of the bounding box
  - info
```
public String info
```
    Used to store information about this bounding box. Default is null
  - spacingUnit
```
protected String spacingUnit
```
  - origin
```
protected PointInImage origin
```
    The bounding box origin (SE, lower corner)
  - originOpposite
```
protected PointInImage originOpposite
```
    The origin opposite (NW, upper corner)
- Constructor Detail
  - BoundingBox
```
public BoundingBox()
```
    Constructs an 'empty' BoundingBox using default values, with the box origin defined as a point with Double.NaN coordinates and Double.NaN dimensions
- Method Detail
  - reset
```
protected void reset()
```
  - setSpacing
```
public void setSpacing(double xSpacing,
                       double ySpacing,
                       double zSpacing,
                       String spacingUnit)
```
    Sets the voxel spacing.
    
    Parameters:
    
    xSpacing - the 'voxel width' of the bounding box
    
    ySpacing - the 'voxel height' of the bounding box
    
    zSpacing - the 'voxel depth' of the bounding box
    
    spacingUnit - the length unit
  - compute
```
public void compute(Iterator<? extends SNTPoint> iterator)
```
    Computes a new positioning so that this box encloses the specified point cloud.
    
    Parameters:
    
    iterator - the iterator of the points Collection
  - append
```
public void append(Iterator<? extends SNTPoint> iterator)
```
    Computes the bounding box of the specified point cloud and appends it to this bounding box, resizing it as needed.
    
    Parameters:
    
    iterator - the iterator of the points Collection
  - getCentroid
```
public SNTPoint getCentroid()
```
  - inferSpacing
```
public void inferSpacing(Collection<SWCPoint> points)
```
    Infers the voxel spacing of this box from the inter-node distances of a Collection of SWCPoints.
    
    Parameters:
    
    points - the point collection
  - isScaled
```
public boolean isScaled()
```
    Checks whether this BoundingBox is spatially calibrated, i.e., if voxel spacing has been specified
    
    Returns:
    
    true, if voxel spacing has been specified
  - setUnit
```
public void setUnit(String unit)
```
    Sets the default length unit for voxel spacing (typically um, for SWC reconstructions)
    
    Parameters:
    
    unit - the new unit
  - getUnit
```
public String getUnit()
```
    Gets the length unit of voxel spacing
    
    Returns:
    
    the unit
  - getCalibration
```
public ij.measure.Calibration getCalibration()
```
    Creates a Calibration object using information from this BoundingBox
    
    Returns:
    
    the Calibration object
  - getDimensions
```
public double[] getDimensions()
```
    Gets this BoundingBox dimensions in real world units.
    
    Returns:
    
    the BoundingBox dimensions {width, height, depth}.
  - getDimensions
```
public double[] getDimensions(boolean scaled)
```
    Gets this BoundingBox dimensions.
    
    Parameters:
    
    scaled - If true, dimensions are retrieved in real world units, otherwise in ("pixel") units
    
    Returns:
    
    the BoundingBox dimensions {width, height, depth}.
  - getDiagonal
```
public double getDiagonal()
```
    Gets the box diagonal
    
    Returns:
    
    the diagonal of BoundingBox
  - contains
```
public boolean contains(BoundingBox boundingBox)
```
    Checks whether the specified BoundingBox is enclosed by this one .
    
    Parameters:
    
    boundingBox - the bounding box to be tested
    
    Returns:
    
    true, if successful
  - contains
```
public boolean contains(SNTPoint point)
```
  - combine
```
public void combine(BoundingBox boundingBox)
```
    Combines Combines this bounding box with another one. It is asumed both boxes share the same voxel spacing/Calibration.
    
    Parameters:
    
    boundingBox - the bounding box to be combined.
  - origin
```
public PointInImage origin()
```
    Retrieves the origin of this box.
    
    Returns:
    
    the origin
  - originOpposite
```
public PointInImage originOpposite()
```
    Retrieves the origin opposite of this box.
    
    Returns:
    
    the origin
  - unscaledOrigin
```
public PointInImage unscaledOrigin()
```
    Retrieves the origin of this box in unscaled ("pixel" units)
    
    Returns:
    
    the unscaled origin
  - unscaledOriginOpposite
```
public PointInImage unscaledOriginOpposite()
```
    Retrieves the origin opposite of this box in unscaled ("pixel" units)
    
    Returns:
    
    the unscaled origin opposite
  - width
```
public double width()
```
  - height
```
public double height()
```
  - depth
```
public double depth()
```
  - setDimensions
```
public void setDimensions(long uncalibratedWidth,
                          long uncalibratedHeight,
                          long uncalibratedDepth)
                   throws IllegalArgumentException
```
    Sets the dimensions of this bounding box using uncalibrated (pixel) lengths.
    
    Parameters:
    
    uncalibratedWidth - the uncalibrated width
    
    uncalibratedHeight - the uncalibrated height
    
    uncalibratedDepth - the uncalibrated depth
    
    Throws:
    
    IllegalArgumentException - If origin has not been set or compute(Iterator) has not been called
  - setOrigin
```
public void setOrigin(PointInImage origin)
```
    Sets the origin for this box, i.e., its (xMin, yMin, zMin) vertex.
    
    Parameters:
    
    origin - the new origin
  - setOriginOpposite
```
public void setOriginOpposite(PointInImage originOpposite)
```
    Sets the origin opposite for this box, i.e., its (xMax, yMax, zMax) vertex.
    
    Parameters:
    
    originOpposite - the new origin opposite.
  - hasDimensions
```
public boolean hasDimensions()
```
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - clone
```
public BoundingBox clone()
```
    Overrides:
    
    clone in class Object
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class BoundingBox

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

xSpacing

ySpacing

zSpacing

info

spacingUnit

origin

originOpposite

Constructor Detail

BoundingBox

Method Detail

reset

setSpacing

compute

append

getCentroid

inferSpacing

isScaled

setUnit

getUnit

getCalibration

getDimensions

getDimensions

getDiagonal

contains

contains

combine

origin

originOpposite

unscaledOrigin

unscaledOriginOpposite

width

height

depth

setDimensions

setOrigin

setOriginOpposite

hasDimensions

hashCode

equals

clone

toString