sc.fiji.snt.util

Class BoundingBox

java.lang.Object

sc.fiji.snt.util.BoundingBox

public class BoundingBox
extends java.lang.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
java.lang.String	info Used to store information about this bounding box.
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

Modifier and Type	Method and Description
BoundingBox	clone()
void	compute(java.util.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 .
double	depth()
boolean	equals(BoundingBox box) Compares two BoundingBox objects for equality.
ij.measure.Calibration	getCalibration() Creates a Calibration object using information from this BoundingBox
SNTPoint	getCentroid()
double	getDiagonal() Gets the box diagonal
double[]	getDimensions(boolean scaled) Gets this BoundingBox dimensions.
java.lang.String	getUnit() Gets the length unit of voxel spacing
double	height()
void	inferSpacing(java.util.Collection<SWCPoint> points) Infers the voxel spacing of this box from the inter-node distances of a Collection of SWCPoints.
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.
void	setDimensions(int uncalibratedWidth, int uncalibratedHeight, int uncalibratedDepth) Sets the dimensions of this bounding box using uncalibrated (pixel) lengths.
void	setOrigin(PointInImage origin) Sets the origin for this box, i.e., the Box's SE vertex (lower left corner)
void	setSpacing(double xSpacing, double ySpacing, double zSpacing, java.lang.String spacingUnit) Sets the voxel spacing.
void	setUnit(java.lang.String unit) Sets the default length unit for voxel spacing (typically um, for SWC reconstructions)
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

equals, getClass, hashCode, notify, notifyAll, toString, 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 java.lang.String info

Used to store information about this bounding box. Default is null

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

setSpacing

public void setSpacing(double xSpacing,
                       double ySpacing,
                       double zSpacing,
                       java.lang.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(java.util.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

getCentroid

public SNTPoint getCentroid()

inferSpacing

public void inferSpacing(java.util.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(java.lang.String unit)

Sets the default length unit for voxel spacing (typically um, for SWC reconstructions)

Parameters:

unit - the new unit

getUnit

public java.lang.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(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

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(int uncalibratedWidth,
                          int uncalibratedHeight,
                          int uncalibratedDepth)
                   throws java.lang.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:

java.lang.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., the Box's SE vertex (lower left corner)

Parameters:

origin - the new origin

equals

public boolean equals(BoundingBox box)

Compares two BoundingBox objects for equality.

Parameters:

box - the comparing object

Returns:

true, if successful

clone

public BoundingBox clone()

Overrides:

clone in class java.lang.Object