Package gov.nih.mipav.model.structures

Class ModelStorageBase

java.lang.Object

gov.nih.mipav.model.structures.ModelSerialCloneable

gov.nih.mipav.model.structures.ModelStorageBase

All Implemented Interfaces:

Serializable, Cloneable

Direct Known Subclasses:

ModelHistogram, ModelImage, ModelLUT, ModelRGB

public class ModelStorageBase
extends ModelSerialCloneable

Author:

pandyan

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ModelStorageBase.DataType

Field Summary

Fields

Modifier and Type	Field	Description
static final int	ARGB	Used to indicate that the data buffer is of type ARGB where each channel (A = alpha, R = red, G = green, B = blue) is represented by a unsigned byte value. (4 * UBYTE(8 bits) = 4 bytes)
static final int	ARGB_FLOAT	Used to indicate that the data buffer is of type ARGB where each channel (A = alpha, R = red, G = green, B = blue) is represented by a float value. (4 * FLOAT(32 bits) = 16 bytes)
static final String	ARGB_FLOAT_STRING	Used to indicate, as a String, that the data buffer is of type color (ARGB - floats).
static final String	ARGB_STRING	Used to indicate, as a String, that the data buffer is of type color (ARGB - unsigned bytes).
static final int	ARGB_UINTEGER
static final String	ARGB_UINTEGER_STRING
static final int	ARGB_USHORT	Used to indicate that the data buffer is of type ARGB where each channel (A = alpha, R = red, G = green, B = blue) is represented by a unsigned short value. (4 * USHORT(16 bits) = 8 bytes)
static final String	ARGB_USHORT_STRING	Used to indicate, as a String, that the data buffer is of type color (ARGB - unsigned shorts).
private float	avgInten
private float	avgIntenB
private float	avgIntenG
private float	avgIntenR
static final int	BOOLEAN	Used to indicate that the data buffer is of type Boolean (1 bit per voxel).
static final String	BOOLEAN_STRING	Used to indicate, as a String, that the data buffer is of type boolean.
private ModelStorageBase.DataType	bufferType	Type of image buffer (i.e.
static final String[]	bufferTypeStr	Deprecated. should use enums directly
static final int	BYTE	Used to indicate that the data buffer is of type signed byte (8 bits per voxel).
static final String	BYTE_STRING	Used to indicate, as a String, that the data buffer is of type byte.
static final int	COMPLEX	Used to indicate that the data buffer is of complex type floats (2 x 64 bits per voxel).
static final String	COMPLEX_STRING	Used to indicate, as a String, that the data buffer is of type complex (float).
private BufferBase	data	Storage location of image data.
private int	dataSize	Total buffer length.
static final int	DCOMPLEX	Used to indicate that the data buffer is of complex type of doubles (2 x 128 bits per voxel).
static final String	DCOMPLEX_STRING	Used to indicate, as a String, that the data buffer is of type complex (double).
private int[]	dimExtents	Bounds of the image where.
private int[]	dimOriginalExtents	Bounds of the image where.
static final int	DOUBLE	Used to indicate that the data buffer is of type double (64 bits per voxel).
static final String	DOUBLE_STRING	Used to indicate, as a String, that the data buffer is of type signed double.
protected FileInfoBase[]	fileInfo	Each image slice has a information that describes aspects of each slice of an image.
private int	filterType	DOCUMENT ME!
static final int	FLOAT	Used to indicate that the data buffer is of type float (32 bits per voxel).
static final String	FLOAT_STRING	Used to indicate, as a String, that the data buffer is of type signed float.
private float	freq1	DOCUMENT ME!
private float	freq2	DOCUMENT ME!
private float	freqU	5 variables used in Gabor transform. - should be removed - redesigned
private float	freqV	DOCUMENT ME!
private boolean	haveWindowed	DOCUMENT ME!
private boolean	image25D	Boolean telling if 3D images are processed 1 slice at a time.
static final int	INTEGER	Used to indicate that the data buffer is of type signed integer (32 bits per voxel).
static final String	INTEGER_STRING	Used to indicate, as a String, that the data buffer is of type signed integer.
protected double	lastMax	lastMin and lastMax store the last min and max values for an image. these are used as a trigger for resetting the transfer function.
protected double	lastMin	lastMin and lastMax store the last min and max values for an image. these are used as a trigger for resetting the transfer function.
static final int	LINEAR	Used to indicate linear (ie. bilinear, trilinear) interpolation.
private int	lockStatus	Locking status of the image.
protected boolean	logMagDisp	Boolean telling if log magnitude display is used for the data buffer
static final int	LONG	Used to indicate that the data buffer is of type signed long integer (64 bits per voxel).
static final String	LONG_STRING	Used to indicate, as a String, that the data buffer is of type signed long.
private boolean	m_bConvolve	Set to true when the image is the product of the ffts of two images, so that on an inverse_fft this image will be centered properly.
private boolean	m_bRadiologicalView	When true, display the data in the Radiological View, when false display the Neurological View:.
private final Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA>	m_kColorVector	Surface color vector. - TO BE MOVED - redesigned
private final Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA[]>	m_kMaskColorVector	Surface mask color vector. - TO BE MOVED - redesigned
private final Vector<BitSet>	m_kMaskVector	Surface mask vector.- TO BE MOVED - redesigned.
private double	max	Minimum and maximum image intensity.
private double	maxA	Minimum and maximum for a color image.
private double	maxB	Minimum and maximum for a color image.
private double	maxG	Minimum and maximum for a color image.
private double	maxR	Minimum and maximum for a color image.
private double	min	Minimum and maximum image intensity.
private double	minA	Minimum and maximum for a color image.
private double	minB	Minimum and maximum for a color image.
private double	minG	Minimum and maximum for a color image.
private double	minR	Minimum and maximum for a color image.
private int	nDims	Number of dimensions of the data.
static final int	NEAREST	Used to indicate nearest neighbor interpolation.
private double	noLogMax	Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED
private double	noLogMin	Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED
private double	noLogMinNonZero	Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED
private double	nonZeroMax	Minimum and maximum nonzero intensity. - TO BE MOVED - redesigned
private double	nonZeroMaxB	Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
private double	nonZeroMaxG	Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
private double	nonZeroMaxR	Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
private double	nonZeroMin	Minimum and maximum nonzero intensity. - TO BE MOVED - redesigned
private double	nonZeroMinB	Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
private double	nonZeroMinG	Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
private double	nonZeroMinR	Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
private int	numPixels
private boolean	originalCropCheckbox	DOCUMENT ME!
private boolean	originalDoCrop	DOCUMENT ME!
private int[]	originalEnd	DOCUMENT ME!
private double	originalEpsilon	The maximum filter ripple in Chebyshev I and II The passband ripple in decibels in Elliptic
private int	originalFilterConstruction	DOCUMENT ME!
private int	originalFilterOrder	DOCUMENT ME!
private int	originalKernelDimension	This are variables used by the FFT filter algorithm. - should be removed - redesigned
private double	originalRs	Decibels stopband is down in Elliptic
private int[]	originalStart	DOCUMENT ME!
static final int	RW_LOCKED	Used to indicate that the buffer is locked from reading.
private static final long	serialVersionUID	Use serialVersionUID for interoperability.
static final int	SHORT	Used to indicate that the data buffer is of type signed short (16 bits per voxel).
static final String	SHORT_STRING	Used to indicate, as a String, that the data buffer is of type signed short.
private float	sigmaU	DOCUMENT ME!
private float	sigmaV	DOCUMENT ME!
private double	smallestMagnitudeNegative	smallest magnitude negative and positive.
private double	smallestMagnitudeNegativeB	smallest magnitude negative and positive.
private double	smallestMagnitudeNegativeG	smallest magnitude negative and positive.
private double	smallestMagnitudeNegativeR	smallest magnitude negative and positive.
private double	smallestMagnitudePositive	smallest magnitude negative and positive.
private double	smallestMagnitudePositiveB	smallest magnitude negative and positive.
private double	smallestMagnitudePositiveG	smallest magnitude negative and positive.
private double	smallestMagnitudePositiveR	smallest magnitude negative and positive.
private float	stdDeviation
private float	stdDeviationB
private float	stdDeviationG
private float	stdDeviationR
private double	sumPixelInten
private double	sumPixelIntenB
private double	sumPixelIntenG
private double	sumPixelIntenR
static final int	TAYLOR	Used to indicate Taylor series interpolation.
private float	theta	DOCUMENT ME!
static final int	UBYTE	Used to indicate that the data buffer is of type unsigned byte (8 bits per voxel).
static final String	UBYTE_STRING	Used to indicate, as a String, that the data buffer is of type unsigned byte.
static final int	UINTEGER	Used to indicate that the data buffer is of type unsigned integer (32 bits per voxel).
static final String	UINTEGER_STRING	Used to indicate, as a String, that the data buffer is of type unsigned integer.
private boolean	unequalDim	Boolean telling if unequal dimensions are allowed in the FFT image.
static final int	UNLOCKED	Used to indicate that the buffer is unlocked and can be writen to or read from.
static final int	USHORT	Used to indicate that the data buffer is of type unsigned short (16 bits per voxal).
static final String	USHORT_STRING	Used to indicate, as a String, that the data buffer is of type unsigned short.
static final int	W_LOCKED	Used to indicate that the buffer is locked from writing.
private int	writeLockCount	Locking write count.

Constructor Summary

Constructors

Constructor	Description
ModelStorageBase()	Default constructor.
ModelStorageBase(int type, int[] dimExtents)	Allocates buffer memory of the specified type.
ModelStorageBase(ModelStorageBase.DataType type, int[] dimExtents)	Allocates buffer memory of the specified type.

Method Summary

Modifier and Type	Method	Description
void	addSurfaceMask(int index, BitSet kMask, WildMagic.LibFoundation.Mathematics.ColorRGBA[] kMaskColors, WildMagic.LibFoundation.Mathematics.ColorRGBA kColor)	Adds a surface mask to this image.
protected void	allocateData()	Allocates data based on the data type and dataSize.
void	calcAvgIntenStdDev()	computes the avg intensity got 2d and 3d greyscale and color images
void	calcMinMax()	Calculates the min and max values for the image array.
void	calcMinMax(boolean logMagDisplay)
void	calcMinMaxMag(boolean logMagDisplay)	Calculates the min and max magnitude values for the image array.
void	calcMinMaxNonZero()	Calculates the min and max nonzero values for the image array.
Object	clone()	Copies the object.
protected void	computeDataSize()	Computes the datasize based on the type of buffer.
protected void	construct(ModelStorageBase.DataType type, int[] dimExtents)	Allocates buffer memory of the specified type.
void	convertToFloat()	Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.
void	disposeLocal()	Dispose of memory and call the garbage collector.
final float[]	export(int[] axisOrder, boolean[] axisFlip, int tSlice, int slice, float[] values, boolean bMask)	Exports data based on the mapping from ModelImage space to Patient space.
final float[]	export(int orientation, int tSlice, int slice, float[] values, boolean bMask)	Exports data based on the mapping from ModelImage space to Patient space.
final void	exportComplexData(int start, int length, float[] valuesR, float[] valuesI)	Export data to the real values and the images values arrays.
final void	exportComplexSliceXY(int slice, float[] values, boolean logMagDisplay)	Export XY slice magnitude data into values array.
final Object	exportData(int start, int length)	Export data into values array, in the native type of the model image.
final void	exportData(int start, int length, byte[] values)	Export data into values array.
final void	exportData(int start, int length, double[] values)	Export data in values array.
final void	exportData(int start, int length, float[] values)	Export data to values array.
final void	exportData(int start, int length, int[] values)	Export data into values array.
final void	exportData(int start, int length0, int length1, float[] values)	export data to values array.
final void	exportData(int start, int length, long[] values)	Export data into values array.
final void	exportData(int start, int length, short[] values)	Export data into values array.
final void	exportData(int start, int length, Number[] values)	Export data into values array.
final void	exportData(int start, int length, BitSet values)	Export data into values array.
final void	exportDataNoLock(int start, int length, byte[] values)	Export data into values array WITHOUT locking.
final void	exportDataNoLock(int start, int length, double[] values)	export data into values array WITHOUT locking.
final void	exportDataNoLock(int start, int length, float[] values)	export data in values array WITHOUT using locking.
final void	exportDataNoLock(int start, int length, int[] values)	Export data into values array WITHOUT locking.
final void	exportDataNoLock(int start, int length, long[] values)	export data into values array WITHOUT locking.
final void	exportDataNoLock(int start, int length, short[] values)	Export data into values array WITHOUT locking.
final void	exportDataNoLock(int start, int length, Number[] values)	export data into values array WITHOUT locking.
final void	exportDataNoLock(int start, int length, BitSet values)	export data into values array WITHOUT locking.
final void	exportDComplexData(int start, int length, double[] valuesR, double[] valuesI)	Export data to the real values and the imaginary values arrays.
final void	exportDiagonal(int tSlice, int slice, int[] extents, WildMagic.LibFoundation.Mathematics.Vector3f[] verts, float[] values, boolean bInterpolate)	ShowDiagonal samples the ModelImage data along a non-axis aligned plane.
final void	exportDiagonal(int tSlice, int slice, int[] extents, WildMagic.LibFoundation.Mathematics.Vector3f[] verts, float[] values, boolean bInterpolate, BitSet imageMask, Vector<BitSet> surfaceMask, boolean[] surfaceValues)
final void	exportDiagonal(BitSet duplicateMask, int tSlice, int slice, int[] extents, WildMagic.LibFoundation.Mathematics.Vector3f[] verts, float diameter, boolean bSetZero, float[] values, boolean bInterpolate)	ShowDiagonal samples the ModelImage data along a non-axis aligned plane.
final void	exportDMagData(int start, int length, double[] values)	Export magnitude data to values array.
final void	exportMagData(int start, int length, double[] values)	export magnitude data to values array.
final void	exportMagData(int start, int length, float[] values)	export magnitude data to values array.
final Object	exportRGBData(int offset, int start, int length)	export data in values array.
final void	exportRGBData(int offset, int start, int length, byte[] values)	export data in values array.
final void	exportRGBData(int offset, int start, int length, double[] values)	export data in values array.
final void	exportRGBData(int offset, int start, int length, float[] values)	export data in values array.
final void	exportRGBData(int offset, int start, int length, short[] values)	export data in values array.
final void	exportRGBDataNoLock(int offset, int start, int length, double[] values)	Export data in values array WITHOUT using locking.
final void	exportRGBDataNoLock(int offset, int start, int length, float[] values)	Export data in values array WITHOUT using locking.
final void	exportSliceXY(int slice, byte[] values)	Export XY slice into values array.
final void	exportSliceXY(int slice, double[] values)	export XY slice into values array.
final void	exportSliceXY(int slice, float[] values)	export XY slice into values array.
final void	exportSliceXY(int slice, int[] values)	Export XY slice into values array.
final void	exportSliceXY(int slice, long[] values)	export XY slice into values array.
final void	exportSliceXY(int slice, short[] values)	Export XY slice into values array.
protected void	finalize()	Calls disposeLocal of this class to ensure this class nulls the references to global class variables so that memory will be recovered.
final WildMagic.LibFoundation.Mathematics.Vector3f	findMax(int tSlice, int slice, WildMagic.LibFoundation.Mathematics.Vector3f[] verts, float diameter, boolean bInterpolate)
final Number	get(int position)	function to get data where bounds checking is performed.
final Number	get(int[] position)	nD get data fuction where bounds checking is performed.
final Number	get(int x, int y)	2D get data fuction where bounds checking is performed.
final Number	get(int x, int y, int z)	3D get data fuction where bounds checking is performed.
final Number	get(int x, int y, int z, int b)	4D get data fuction where bounds checking is performed.
float	getAvgInten()
float	getAvgIntenB()
float	getAvgIntenG()
float	getAvgIntenR()
int[]	getAxisOrientation()	Returns the axis orientation of image.
final Number	getBiLinear(float x, float y)	version of get that performs bi-linear interpoloation.
final boolean	getBoolean(int position)	Version of get that does NOT perform bounds checking.
final boolean	getBoolean(int[] position)	n-Dimensional get data fuction where bounds checking is NOT performed.
final boolean	getBoolean(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final boolean	getBoolean(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final boolean	getBoolean(int x, int y, int z, int b)	4D get data fuction where bounds checking is NOT performed.
static String	getBufferTypeStr(int type)	Returns the string for a particular buffer type.
final byte	getByte(int position)	Version of get that does NOT perform bounds checking
final byte	getByte(int[] position)	nD get data fuction where bounds checking is NOT performed.
final byte	getByte(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final byte	getByte(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final byte	getByte(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final byte	getByteBiLinear(float x, float y)	version of get that performs bi-linear interpoloation.
final byte	getByteTriLinear(float x, float y, float z)	version of get that performs tri-linear interpoloation.
final Number	getC(int position, int color)	Color function to get data where bounds checking is performed.
boolean	getConvolve()	Accessor method for the m_bConvolve data memeber.
int	getDataSize()	Get total buffer length.
final ModelStorageBase.DataType	getDataType()	Accessor that returns the image buffer type as an enum.
final double	getDouble(int position)	The interpolated value from the data array.ersion of get that does NOT perform bounds checking.
final double	getDouble(int[] position)	nD get data fuction where bounds checking is NOT performed.
final double	getDouble(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final double	getDouble(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final double	getDouble(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final double	getDoubleBiLinear(float x, float y)	version of get that performs bi-linear interpoloation.
final double	getDoubleTriLinear(float x, float y, float z)	version of get that performs tri-linear interpoloation.
final int[]	getExtents()	Accessor that returns the extents of the image.
final int[]	getExtents(int orientation)	Returns the image extents translated into the Patient-Coordinate systsm:
final int[]	getExtents(int[] aiAxisOrder)	Returns the image extents translated into the Patient-Coordinate system:
final int[]	getExtentsSize(int orientation)
FileInfoBase[]	getFileInfo()	Accessor that returns the fileInfo array (one per slice).
FileInfoBase	getFileInfo(int i)	Accessor that returns the fileInfo of a specific image slice.
final int	getFilterType()	returns type of filter - low, high, bandpass, or bandstop. - TO BE MOVED
final float	getFloat(int position)	Version of get that does NOT perform bounds checking.
final float	getFloat(int[] position)	nD get data function where bounds checking is NOT performed.
final float	getFloat(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final float	getFloat(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final float	getFloat(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final float	getFloatBiLinear(float x, float y)	version of get that performs bi-linear interpoloation.
final float	getFloatC(int x, int y, int c)	2D color get data fuction where bounds checking is NOT performed.
final float	getFloatC(int x, int y, int z, int c)	3D color get data fuction where bounds checking is NOT performed.
final float	getFloatC(int x, int y, int z, int t, int c)	4D get data fuction where bounds checking is NOT performed.
final float	getFloatTriLinear(float x, float y, float z)	version of get that performs tri-linear interpoloation.
final float	getFloatTriLinearBounds(float x, float y, float z)	Get a value using tri-linear interpoloation.
final float	getFloatTriLinearBounds(float x, float y, float z, int c)	Get a value using tri-linear interpoloation.
final float	getFloatTriLinearBoundsTime(float x, float y, float z, int t)	Get a value using tri-linear interpoloation.
final float	getFreq1()	returns frequency 1 of filter.
final float	getFreq2()	returns frequency 2 of filter.
final float	getFreqU()	returns frequency U of filter.
final float	getFreqV()	returns frequency V of filter.
final boolean	getHaveWindowed()	DOCUMENT ME!
int	getHeight(int orientation)	Returns the image height, based on the Patient Coordinates orientation from which the data will be viewed:
boolean	getImage25D()	Accessor that returns the boolean indicating if 3D images are processed one slice at a time.
int	getImageOrientation()	Gets the image orientation (sagittal, axial, ...).
final int	getInt(int position)	Version of get that does NOT perform bounds checking.
final int	getInt(int[] position)	nD get data fuction where bounds checking is NOT performed.
final int	getInt(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final int	getInt(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final int	getInt(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final int	getIntBiLinear(float x, float y)	version of get that performs bi-linear interpoloation.
final int	getIntTriLinear(float x, float y, float z)	Version of get that performs tri-linear interpoloation.
final int	getLockStatus()	Accessor that returns the lock status of the image.
boolean	getLogMagDisplay()	Accessor that returns the boolean indicating if log magnitude displays are used in complex images.
final long	getLong(int position)	Version of get that does NOT perform bounds checking.
final long	getLong(int[] position)	nD get data fuction where bounds checking is NOT performed.
final long	getLong(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final long	getLong(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final long	getLong(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final long	getLongBiLinear(float x, float y)	version of get that performs bi-linear interpoloation.
final long	getLongTriLinear(float x, float y, float z)	Version of get that performs tri-linear interpoloation.
double	getMax()	Accessor that returns the maximum value in the dataArray.
double	getMaxA()	Accessor that returns the maximum alpha value in the dataArray.
double	getMaxB()	Accessor that returns the maximum blue value in the dataArray.
double	getMaxG()	Accessor that returns the maximum green value in the dataArray.
double	getMaxR()	Accessor that returns the maximum red value in the dataArray.
double	getMin()	Accessor that returns the minimum value in the dataArray.
double	getMinA()	Accessor that returns the minimum alpha value in the dataArray.
double	getMinB()	Accessor that returns the minimum blue value in the dataArray.
double	getMinG()	getMinG - Accessor that returns the minimum green value in the dataArray.
double	getMinR()	Accessor that returns the minimum red value in the dataArray.
final int	getNDims()	Accessor that returns the dimensionality of the image.
double	getNoLogMax()	Accessor that returns the maximum value without log processing in the dataArray.
double	getNoLogMin()	Accessor that returns the minimum value without log processing in the dataArray.
double	getNoLogMinNonZero()	Accessor that returns the minimum nonzero value without log processing in the dataArray.
double	getNonZeroMax()	Accessor that returns the smallest magnitude negative value in the dataArray.
double	getNonZeroMaxB()	Accessor that returns the maximum nonzero blue value in the dataArray.
double	getNonZeroMaxG()	Accessor that returns the maximum nonzero green value in the dataArray.
double	getNonZeroMaxR()	Accessor that returns the maximum nonzero red value in the dataArray.
double	getNonZeroMin()	Accessor that returns the minimum nonzero value in the dataArray.
double	getNonZeroMinB()	Accessor that returns the minimum nonzero blue value in the dataArray.
double	getNonZeroMinG()	Accessor that returns the minimum nonzero green value in the dataArray.
double	getNonZeroMinR()	Accessor that returns the minimum nonzero red value in the dataArray.
int	getNumPixels()
float[]	getOrigin()	Returns the origin of the image.
float[]	getOrigin(int index, int orientation)	Returns the image origin for the image translated into the Patient-Coordinate systsm:
final boolean	getOriginalCropCheckbox()	DOCUMENT ME!
final boolean	getOriginalDoCrop()	DOCUMENT ME!
final int[]	getOriginalEnd()	DOCUMENT ME!
final double	getOriginalEpsilon()
final int[]	getOriginalExtents()	Accessor that returns the original extents of the image.
final int	getOriginalFilterConstruction()	returns integer telling filter construction method.
final int	getOriginalFilterOrder()	returns integer telling filter order. - TO BE MOVED
final int	getOriginalKernelDimension()	returns kernel diameter chosen on forward FFT.
final double	getOriginalRs()	Decibels stopband is down in Elliptic
final int[]	getOriginalStart()	DOCUMENT ME!
boolean	getRadiologicalView()	Gets the radiological view flag:
float[]	getResolutions(int index)	Returns the resolutions for the image without regarding resolution difference between slices.
float[]	getResolutions(int index, int orientation)	Returns the resolutions for the image translated into the Patient-Coordinate systsm:
float[]	getResolutions(int index, int[] aiAxisOrder)	Returns the resolutions for the image translated into the Patient-Coordinate systsm:
final short	getShort(int position)	Version of get that does NOT perform bounds checking.
final short	getShort(int[] position)	nD get data fuction where bounds checking is NOT performed.
final short	getShort(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final short	getShort(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final short	getShort(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final short	getShortBiLinear(float x, float y)	version of get that performs bi-linear interpoloation.
final short	getShortTriLinear(float x, float y, float z)	version of get that performs tri-linear interpoloation.
final float	getSigmaU()	returns standard deviation U of filter.
final float	getSigmaV()	returns standard deviation V of filter.
final int	getSize()	Accessor that returns the total size(length) of the data array.
final int	getSliceSize()	Get the nuber of pixels in a slice of the image.
double	getSmallestMagnitudeNegative()	Accessor that returns the smallest magnitude negative value in the dataArray.
double	getSmallestMagnitudeNegativeB()	Accessor that returns the smallest magnitude negative blue value in the dataArray.
double	getSmallestMagnitudeNegativeG()	Accessor that returns the smallest magnitude negative green value in the dataArray.
double	getSmallestMagnitudeNegativeR()	Accessor that returns the smallest magnitude negative red value in the dataArray.
double	getSmallestMagnitudePositive()	Accessor that returns the smallest magnitude positive value in the dataArray.
double	getSmallestMagnitudePositiveB()	Accessor that returns the smallest magnitude positive blue value in the dataArray.
double	getSmallestMagnitudePositiveG()	Accessor that returns the smallest magnitude positive green value in the dataArray.
double	getSmallestMagnitudePositiveR()	Accessor that returns the smallest magnitude positive red value in the dataArray.
float	getStdDeviation()
float	getStdDeviationB()
float	getStdDeviationG()
float	getStdDeviationR()
double	getSumPixelInten()
double	getSumPixelIntenB()
double	getSumPixelIntenG()
double	getSumPixelIntenR()
BitSet	getSurfaceMask(int index)	Returns the surface mask from this image.
WildMagic.LibFoundation.Mathematics.ColorRGBA	getSurfaceMaskColor(int index)	Returns the surface mask from this image.
final float	getTheta()	Returns roation angle theta in radians of filter.
final Number	getTriLinear(float x, float y, float z)	version of get that performs tri-linear interpoloation.
final int	getType()	Accessor that returns the image buffer type.
static double	getTypeMax(int type)	This method return the max value allowed of the type
static double	getTypeMin(int type)	his method return the min value allowed of the type
final String	getTypeString()	Accessor that returns the image type.
final short	getUByte(int position)	version of get that does NOT perform bounds checking.
final short	getUByte(int[] position)	nD get data fuction where bounds checking is NOT performed.
final short	getUByte(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final short	getUByte(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final short	getUByte(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final short	getUByteBiLinear(float x, float y)	Version of get that performs bi-linear interpoloation.
final short	getUByteTriLinear(float x, float y, float z)	Version of get that performs tri-linear interpoloation.
final long	getUInt(int position)	version of get that does NOT perform bounds checking.
final long	getUInt(int[] position)	nD get data fuction where bounds checking is NOT performed.
final long	getUInt(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final long	getUInt(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final long	getUInt(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final long	getUIntBiLinear(float x, float y)	version of get that performs bi-linear interpoloation.
final long	getUIntTriLinear(float x, float y, float z)	version of get that performs tri-linear interpoloation.
boolean	getUnequalDim()	Accessor that returns the boolean indicating if unequal dimensions are allowed in complex images.
int[]	getUnitsOfMeasure()	Returns the units used to measure all dimensions of the image.
int	getUnitsOfMeasure(int index)	Returns the unit used to measure the specific dimension of image.
int[]	getUnitsOfMeasure(int index, int orientation)	Returns the units of measure for the image translated into the Patient-Coordinate systsm:
final int	getUShort(int position)	version of get that does NOT perform bounds checking.
final int	getUShort(int[] position)	nD get data fuction where bounds checking is NOT performed.
final int	getUShort(int x, int y)	2D get data fuction where bounds checking is NOT performed.
final int	getUShort(int x, int y, int z)	3D get data fuction where bounds checking is NOT performed.
final int	getUShort(int x, int y, int z, int t)	4D get data fuction where bounds checking is NOT performed.
final int	getUShortBiLinear(float x, float y)	Version of get that performs bi-linear interpoloation.
final int	getUShortTriLinear(float x, float y, float z)	version of get that performs tri-linear interpoloation.
int[]	getVolumeIterationFactors()	Get the factors needed to iterate through the image volume.
int	getVolumeSize()	Gets the number of pixels in a volume of the image.
int	getWidth(int orientation)	Returns the image width, based on the Patient Coordinates orientation from which the data will be viewed:
final void	importComplexData(int start, float[] valuesR, float[] valuesI, boolean mmFlag, boolean logMagDisplay)	import Complex data (in 2 float units) into data array.
final void	importData(int start, boolean[] values, boolean mmFlag)	Import boolean data into data array.
final void	importData(int start, byte[] values, boolean mmFlag)	Import byte data into data array.
final void	importData(int start, double[] values, boolean mmFlag)	import double data into data array.
final void	importData(int start, float[] values, boolean mmFlag)	import float data into data array.
final void	importData(int start, int[] values, boolean mmFlag)	import integer data into data array.
final void	importData(int start, long[] values, boolean mmFlag)	import long data into data array.
final void	importData(int start, short[] values, boolean mmFlag)	import short data into data array.
final void	importData(int start, Number[] values, boolean mmFlag)	import Number data into data array.
final void	importData(int start, BitSet values, boolean mmFlag)	Import boolean (BitSet) data into data array.
final void	importData(Object value_array)	Import Object.
final void	importDComplexData(int start, double[] valuesR, double[] valuesI, boolean mmFlag, boolean logMagDisplay)	import Complex data (in 2 double units) into data array.
final void	importRGBData(int color, int alphaIndexStart, byte[] values, boolean mmFlag)	Import byte data into data array.
final void	importRGBData(int color, int alphaIndexStart, float[] values, boolean mmFlag)	import float data into data array.
final void	importRGBData(int color, int alphaIndexStart, short[] values, boolean mmFlag)	Import byte data into data array.
final void	importUData(int start, int[] values, boolean mmFlag)	import int data into data array.
final void	importUData(int start, long[] values, boolean mmFlag)	import int data into data array.
final void	importUData(int start, short[] values, boolean mmFlag)	import short data into data array.
void	reallocate(int type)	Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.
void	reallocate(int[] dimExtents)	Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.
void	reallocate(int type, int[] dimExtents)	Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.
void	recomputeDataSize()	Recomputes the datasize based on the type of buffer.
final void	releaseLock()	Releases the lock so that other proceses can read or write the data.
void	removeSurfaceMask(int index)	Removes the surface mask from this image.
BitSet[]	removeSurfaceMasks()	Returns the array of BitSet masks for backup.
void	restoreSurfaceMasks(BitSet[] masks)	Restores the mask list from the array.
final void	set(int[] position, boolean value)	nD set data fuction where bounds checking is NOT performed.
final void	set(int[] position, byte value)	nD set data fuction where bounds checking is NOT performed.
final void	set(int[] position, double value)	nD set data fuction where bounds checking is NOT performed.
final void	set(int[] position, float value)	nD set data fuction where bounds checking is NOT performed.
final void	set(int[] position, int value)	nD set data fuction where bounds checking is NOT performed.
final void	set(int[] position, long value)	nD set data fuction where bounds checking is NOT performed.
final void	set(int[] position, short value)	nD set data fuction where bounds checking is NOT performed.
final boolean	set(int[] position, Number value)	nD set data fuction where bounds checking is performed.
final void	set(int position, boolean value)	version of set that does NOT perform bounds checking
final void	set(int position, byte value)	Version of set that does NOT perform bounds checking.
final void	set(int position, double value)	version of set that does NOT perform bounds checking.
final void	set(int position, float value)	version of set that does NOT perform bounds checking.
final void	set(int position, int value)	Version of set that does NOT perform bounds checking.
final void	set(int x, int y, boolean value)	2D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, byte value)	2D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, double value)	2D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, float value)	2D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int value)	2D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, boolean value)	3D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, byte value)	3D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, double value)	3D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, float value)	3D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, int value)	3D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, int b, boolean value)	4D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, int b, byte value)	4D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, int b, double value)	4D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, int b, float value)	4D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, int b, int value)	4D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, int b, long value)	4D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, int b, short value)	4D fast version of set that does NOT perform bounds checking.
final boolean	set(int x, int y, int z, int b, Number value)	4D get data fuction where bounds checking is performed.
final void	set(int x, int y, int z, long value)	3D fast version of set that does NOT perform bounds checking.
final void	set(int x, int y, int z, short value)	3D fast version of set that does NOT perform bounds checking.
final boolean	set(int x, int y, int z, Number value)	3D set data fuction where bounds checking is performed.
final void	set(int x, int y, long value)	2D fast version of set that does NOT perform bounds checking.
final boolean	set(int x, int y, Number value)	2D get data fuction where bounds checking is performed.
final void	set(int position, long value)	version of set that does NOT perform bounds checking.
final boolean	set(int position, Number value)	Set that does perform bounds checking.
final void	setAll(byte value)	Sets the entire buffer to value passed to this method.
final void	setAll(double value)	Sets the entire buffer to value passed to this method.
final void	setAll(float value)	Sets the entire buffer to value passed to this method.
final void	setAll(int value)	Sets the entire buffer to value passed to this method.
final void	setAll(short value)	Sets the entire buffer to value passed to this method.
final void	setAllUByte(short value)	Sets the entire buffer to value passed to this method.
final void	setAllUShort(int value)	Sets the entire buffer to value passed to this method.
final void	setC(int position, int c, float value)	color version of setC that does NOT perform bounds checking.
final void	setC(int x, int y, int c, float value)	2D fast color version of set that does NOT perform bounds checking.
final void	setC(int x, int y, int z, int c, float value)	3D fast color version of set that does NOT perform bounds checking.
final boolean	setC(int x, int y, int z, int c, Number value)	3D color set data fuction where bounds checking is performed.
final boolean	setC(int position, int color, Number value)	Sets the entire buffer to value passed to this method.
final void	setComplex(int x, int y, int z, int part, float value)
void	setConvolve(boolean bConvolve)	Accessor method for the m_bConvolve data memeber.
void	setExtents(int[] dims)	Sets the dimExtents for this structure.
void	setFileInfo(FileInfoBase[] fInfo)	Accessor that sets the entire fileInfo array of the image.
void	setFileInfo(FileInfoBase fInfo, int idx)	Accessor that sets the fileInfo class for the image.
void	setFilterType(int _filterType)	DOCUMENT ME!
void	setFreq1(float _freq1)	DOCUMENT ME!
void	setFreq2(float _freq2)	DOCUMENT ME!
void	setFreqU(float _freqU)	DOCUMENT ME!
void	setFreqV(float _freqV)	DOCUMENT ME!
void	setHaveWindowed(boolean window)	DOCUMENT ME!
void	setImage25D(boolean _image25D)	Accessor that sets the boolean telling if 3D images are processed one slice at a time.
void	setLock()	Sets the lockFlag to protect data.
final void	setLock(int lockType)	Sets the lockFlag to protect data.
void	setLogMagDisplay(boolean logMagDisplay)	Accessor that sets the boolean telling if log magnitude display is used in a complex image.
void	setMax(double _max)	Accessor that sets the maximum value in the dataArray.
void	setMaxB(double _max)	Accessor that sets the maximum value in the dataArray.
void	setMaxG(double _max)	Accessor that sets the maximum value in the dataArray.
void	setMaxR(double _max)	Accessor that sets the maximum value in the dataArray.
void	setMin(double _min)	Accessor that sets the minimum value in the dataArray.
void	setMinB(double _min)	Accessor that sets the minimum value in the dataArray.
void	setMinG(double _min)	Accessor that sets the minimum value in the dataArray.
void	setMinR(double _min)	Accessor that sets the minimum value in the dataArray.
void	setOriginalCropCheckbox(boolean cropCheckbox)	DOCUMENT ME!
void	setOriginalDoCrop(boolean doCrop)	DOCUMENT ME!
void	setOriginalEnd(int[] end)	DOCUMENT ME!
void	setOriginalEpsilon(double epsilon)
void	setOriginalExtents(int[] dims)	Sets original dimensionality of the images.
void	setOriginalFilterConstruction(int filterConstruction)	DOCUMENT ME!
void	setOriginalFilterOrder(int filterOrder)	DOCUMENT ME!
void	setOriginalKernelDimension(int kDim)	DOCUMENT ME!
void	setOriginalRs(double rs)
void	setOriginalStart(int[] start)	DOCUMENT ME!
void	setRadiologicalView(boolean bEnabled)	Sets the radiological view flag.
void	setResolutions(float[] resolutions)	Sets the resolutions to the specific value for a specific slice indicated by the index parameter.
void	setResolutions(int index, float[] resolutions)	Sets the resolutions to the specific value for a specific slice indicated by the index parameter.
final void	setShort(int x, int y, short value)	2D fast version of set that does NOT perform bounds checking.
final void	setShort(int position, short value)	Sets the image voxel at the specified position to the specified value.
void	setSigmaU(float _sigmaU)	DOCUMENT ME!
void	setSigmaV(float _sigmaV)	DOCUMENT ME!
void	setTheta(float _theta)	DOCUMENT ME!
final void	setType(int type)	Sets the type of data.
final void	setType(ModelStorageBase.DataType type)	Sets the type of data.
final void	setUByte(int[] position, short value)	Sets the image voxel at the specified position to the specified value. nD set data fuction where bounds checking is NOT performed.
final void	setUByte(int x, int y, int z, int b, short value)	Sets the image voxel at the specified position to the specified value. 4D fast version of set that does NOT perform bounds checking.
final void	setUByte(int x, int y, int z, short value)	Sets the image voxel at the specified position to the specified value. 3D fast version of set that does NOT perform bounds checking.
final void	setUByte(int x, int y, short value)	Sets the image voxel at the specified position to the specified value. 2D fast version of set that does NOT perform bounds checking.
final void	setUByte(int position, short value)	Sets the image voxel at the specified position to the specified value.
final void	setUInt(int[] position, long value)	Sets the image voxel at the specified position to the specified value. nD set data fuction where bounds checking is NOT performed.
final void	setUInt(int x, int y, int z, int t, long value)	Sets the image voxel at the specified position to the specified value. 4D fast version of set that does NOT perform bounds checking.
final void	setUInt(int x, int y, int z, long value)	Sets the image voxel at the specified position to the specified value. 3D fast version of set that does NOT perform bounds checking.
final void	setUInt(int x, int y, long value)	Sets the image voxel at the specified position to the specified value. 2D fast version of set that does NOT perform bounds checking.
final void	setUInt(int position, long value)	Sets the image voxel at the specified position to the specified value. version of set that does NOT perform bounds checking.
void	setUnequalDim(boolean unequalDimension)	Accessor that sets the boolean telling if unequal dimesnions are allowed in a complex image.
final void	setUShort(int[] position, int value)	Sets the image voxel at the specified position to the specified value. nD set data fuction where bounds checking is NOT performed.
final void	setUShort(int position, int value)	Sets the image voxel at the specified position to the specified value.
final void	setUShort(int x, int y, int value)	Sets the image voxel at the specified position to the specified value. 2D fast version of set that does NOT perform bounds checking.
final void	setUShort(int x, int y, int z, int value)	Sets the image voxel at the specified position to the specified value. 3D fast version of set that does NOT perform bounds checking.
final void	setUShort(int x, int y, int z, int b, int value)	Sets the image voxel at the specified position to the specified value. 4D fast version of set that does NOT perform bounds checking.

Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneable

nativeClone

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

serialVersionUID

private static final long serialVersionUID

Use serialVersionUID for interoperability.

See Also:

• Constant Field Values

UNLOCKED

public static final int UNLOCKED

Used to indicate that the buffer is unlocked and can be writen to or read from.

See Also:

• Constant Field Values

RW_LOCKED

public static final int RW_LOCKED

Used to indicate that the buffer is locked from reading.

See Also:

• Constant Field Values

W_LOCKED

public static final int W_LOCKED

Used to indicate that the buffer is locked from writing.

See Also:

• Constant Field Values

NEAREST

public static final int NEAREST

Used to indicate nearest neighbor interpolation.

See Also:

• Constant Field Values

LINEAR

public static final int LINEAR

Used to indicate linear (ie. bilinear, trilinear) interpolation.

See Also:

• Constant Field Values

TAYLOR

public static final int TAYLOR

Used to indicate Taylor series interpolation.

See Also:

• Constant Field Values

BOOLEAN

public static final int BOOLEAN

Used to indicate that the data buffer is of type Boolean (1 bit per voxel).

See Also:

• Constant Field Values

BYTE

public static final int BYTE

Used to indicate that the data buffer is of type signed byte (8 bits per voxel).

See Also:

• Constant Field Values

UBYTE

public static final int UBYTE

Used to indicate that the data buffer is of type unsigned byte (8 bits per voxel).

See Also:

• Constant Field Values

SHORT

public static final int SHORT

Used to indicate that the data buffer is of type signed short (16 bits per voxel).

See Also:

• Constant Field Values

USHORT

public static final int USHORT

Used to indicate that the data buffer is of type unsigned short (16 bits per voxal).

See Also:

• Constant Field Values

INTEGER

public static final int INTEGER

Used to indicate that the data buffer is of type signed integer (32 bits per voxel).

See Also:

• Constant Field Values

UINTEGER

public static final int UINTEGER

Used to indicate that the data buffer is of type unsigned integer (32 bits per voxel).

See Also:

• Constant Field Values

LONG

public static final int LONG

Used to indicate that the data buffer is of type signed long integer (64 bits per voxel).

See Also:

• Constant Field Values

FLOAT

public static final int FLOAT

Used to indicate that the data buffer is of type float (32 bits per voxel).

See Also:

• Constant Field Values

DOUBLE

public static final int DOUBLE

Used to indicate that the data buffer is of type double (64 bits per voxel).

See Also:

• Constant Field Values

ARGB

public static final int ARGB

Used to indicate that the data buffer is of type ARGB where each channel (A = alpha, R = red, G = green, B = blue) is represented by a unsigned byte value. (4 * UBYTE(8 bits) = 4 bytes)

See Also:

• Constant Field Values

ARGB_USHORT

public static final int ARGB_USHORT

Used to indicate that the data buffer is of type ARGB where each channel (A = alpha, R = red, G = green, B = blue) is represented by a unsigned short value. (4 * USHORT(16 bits) = 8 bytes)

See Also:

• Constant Field Values

ARGB_FLOAT

public static final int ARGB_FLOAT

Used to indicate that the data buffer is of type ARGB where each channel (A = alpha, R = red, G = green, B = blue) is represented by a float value. (4 * FLOAT(32 bits) = 16 bytes)

See Also:

• Constant Field Values

ARGB_UINTEGER

public static final int ARGB_UINTEGER

See Also:

• Constant Field Values

COMPLEX

public static final int COMPLEX

Used to indicate that the data buffer is of complex type floats (2 x 64 bits per voxel).

See Also:

• Constant Field Values

DCOMPLEX

public static final int DCOMPLEX

Used to indicate that the data buffer is of complex type of doubles (2 x 128 bits per voxel).

See Also:

• Constant Field Values

BOOLEAN_STRING

public static final String BOOLEAN_STRING

Used to indicate, as a String, that the data buffer is of type boolean.

See Also:

• Constant Field Values

BYTE_STRING

public static final String BYTE_STRING

Used to indicate, as a String, that the data buffer is of type byte.

See Also:

• Constant Field Values

UBYTE_STRING

public static final String UBYTE_STRING

Used to indicate, as a String, that the data buffer is of type unsigned byte.

See Also:

• Constant Field Values

SHORT_STRING

public static final String SHORT_STRING

Used to indicate, as a String, that the data buffer is of type signed short.

See Also:

• Constant Field Values

USHORT_STRING

public static final String USHORT_STRING

Used to indicate, as a String, that the data buffer is of type unsigned short.

See Also:

• Constant Field Values

INTEGER_STRING

public static final String INTEGER_STRING

Used to indicate, as a String, that the data buffer is of type signed integer.

See Also:

• Constant Field Values

LONG_STRING

public static final String LONG_STRING

Used to indicate, as a String, that the data buffer is of type signed long.

See Also:

• Constant Field Values

FLOAT_STRING

public static final String FLOAT_STRING

Used to indicate, as a String, that the data buffer is of type signed float.

See Also:

• Constant Field Values

DOUBLE_STRING

public static final String DOUBLE_STRING

Used to indicate, as a String, that the data buffer is of type signed double.

See Also:

• Constant Field Values

ARGB_STRING

public static final String ARGB_STRING

Used to indicate, as a String, that the data buffer is of type color (ARGB - unsigned bytes).

See Also:

• Constant Field Values

ARGB_USHORT_STRING

public static final String ARGB_USHORT_STRING

Used to indicate, as a String, that the data buffer is of type color (ARGB - unsigned shorts).

See Also:

• Constant Field Values

ARGB_UINTEGER_STRING

public static final String ARGB_UINTEGER_STRING

See Also:

• Constant Field Values

ARGB_FLOAT_STRING

public static final String ARGB_FLOAT_STRING

Used to indicate, as a String, that the data buffer is of type color (ARGB - floats).

See Also:

• Constant Field Values

COMPLEX_STRING

public static final String COMPLEX_STRING

Used to indicate, as a String, that the data buffer is of type complex (float).

See Also:

• Constant Field Values

DCOMPLEX_STRING

public static final String DCOMPLEX_STRING

Used to indicate, as a String, that the data buffer is of type complex (double).

See Also:

• Constant Field Values

UINTEGER_STRING

public static final String UINTEGER_STRING

Used to indicate, as a String, that the data buffer is of type unsigned integer.

See Also:

• Constant Field Values

bufferTypeStr

public static final String[] bufferTypeStr

Deprecated.

should use enums directly

String representations of the data types supported by ModelStorageBase.

fileInfo

protected FileInfoBase[] fileInfo

Each image slice has a information that describes aspects of each slice of an image.

lastMin

protected double lastMin

lastMin and lastMax store the last min and max values for an image. these are used as a trigger for resetting the transfer function.

lastMax

protected double lastMax

lastMin and lastMax store the last min and max values for an image. these are used as a trigger for resetting the transfer function.

bufferType

private ModelStorageBase.DataType bufferType

Type of image buffer (i.e. BOOLEAN, BYTE, UBYTE, SHORT ...)

data

private BufferBase data

Storage location of image data.

dataSize

private int dataSize

Total buffer length.

dimExtents

private int[] dimExtents

Bounds of the image where.

• dimExtents[0] = x dimension
• dimExtents[1] = y dimension
• dimExtents[2] = z dimension (typically)
• dimExtents[3] = fourth dimension (ie time)...

dimOriginalExtents

private int[] dimOriginalExtents

Bounds of the image where.

• dimOriginalExtents[0] = x dimension
• dimOriginalExtents[1] = y dimension
• dimOriginalExtents[2] = z dimension (typically)
• dimOriginalExtents[3] = fourth dimension (ie time)...

filterType

private int filterType

DOCUMENT ME! - TO BE MOVED - redesigned

freq1

private float freq1

DOCUMENT ME! - TO BE MOVED - redesigned

freq2

private float freq2

DOCUMENT ME! - TO BE MOVED - redesigned

freqU

private float freqU

5 variables used in Gabor transform. - should be removed - redesigned

freqV

private float freqV

DOCUMENT ME! - TO BE MOVED - redesigned

haveWindowed

private boolean haveWindowed

DOCUMENT ME! - TO BE MOVED - redesigned

image25D

private boolean image25D

Boolean telling if 3D images are processed 1 slice at a time.

lockStatus

private int lockStatus

Locking status of the image. Default = UNLOCKED

logMagDisp

protected boolean logMagDisp

Boolean telling if log magnitude display is used for the data buffer

m_bConvolve

private boolean m_bConvolve

Set to true when the image is the product of the ffts of two images, so that on an inverse_fft this image will be centered properly. Default is false.

m_bRadiologicalView

private boolean m_bRadiologicalView

When true, display the data in the Radiological View, when false display the Neurological View:.

m_kColorVector

private final Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA> m_kColorVector

Surface color vector. - TO BE MOVED - redesigned

m_kMaskColorVector

private final Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA[]> m_kMaskColorVector

Surface mask color vector. - TO BE MOVED - redesigned

m_kMaskVector

private final Vector<BitSet> m_kMaskVector

Surface mask vector.- TO BE MOVED - redesigned.

min

private double min

Minimum and maximum image intensity.

max

private double max

Minimum and maximum image intensity.

minA

private double minA

Minimum and maximum for a color image.

maxA

private double maxA

Minimum and maximum for a color image.

minR

private double minR

Minimum and maximum for a color image.

maxR

private double maxR

Minimum and maximum for a color image.

minG

private double minG

Minimum and maximum for a color image.

maxG

private double maxG

Minimum and maximum for a color image.

minB

private double minB

Minimum and maximum for a color image.

maxB

private double maxB

Minimum and maximum for a color image.

nDims

private int nDims

Number of dimensions of the data.

noLogMin

private double noLogMin

Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED

noLogMax

private double noLogMax

Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED

noLogMinNonZero

private double noLogMinNonZero

Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED

nonZeroMin

private double nonZeroMin

Minimum and maximum nonzero intensity. - TO BE MOVED - redesigned

nonZeroMax

private double nonZeroMax

Minimum and maximum nonzero intensity. - TO BE MOVED - redesigned

nonZeroMinR

private double nonZeroMinR

Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMaxR

private double nonZeroMaxR

Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMinG

private double nonZeroMinG

Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMaxG

private double nonZeroMaxG

Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMinB

private double nonZeroMinB

Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMaxB

private double nonZeroMaxB

Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

originalFilterOrder

private int originalFilterOrder

DOCUMENT ME!- TO BE MOVED - redesigned.

originalEpsilon

private double originalEpsilon

The maximum filter ripple in Chebyshev I and II The passband ripple in decibels in Elliptic

originalRs

private double originalRs

Decibels stopband is down in Elliptic

originalCropCheckbox

private boolean originalCropCheckbox

DOCUMENT ME!- TO BE MOVED - redesigned.

originalDoCrop

private boolean originalDoCrop

DOCUMENT ME! - TO BE MOVED - redesigned

originalEnd

private int[] originalEnd

DOCUMENT ME!- TO BE MOVED - redesigned.

originalFilterConstruction

private int originalFilterConstruction

DOCUMENT ME! - TO BE MOVED- redesigned

originalKernelDimension

private int originalKernelDimension

This are variables used by the FFT filter algorithm. - should be removed - redesigned

originalStart

private int[] originalStart

DOCUMENT ME! - TO BE MOVED - redesigned

sigmaU

private float sigmaU

DOCUMENT ME! - TO BE MOVED - redesigned

sigmaV

private float sigmaV

DOCUMENT ME! - should be removed - redesigned

smallestMagnitudeNegative

private double smallestMagnitudeNegative

smallest magnitude negative and positive.

smallestMagnitudePositive

private double smallestMagnitudePositive

smallest magnitude negative and positive.

smallestMagnitudeNegativeR

private double smallestMagnitudeNegativeR

smallest magnitude negative and positive.

smallestMagnitudePositiveR

private double smallestMagnitudePositiveR

smallest magnitude negative and positive.

smallestMagnitudeNegativeG

private double smallestMagnitudeNegativeG

smallest magnitude negative and positive.

smallestMagnitudePositiveG

private double smallestMagnitudePositiveG

smallest magnitude negative and positive.

smallestMagnitudeNegativeB

private double smallestMagnitudeNegativeB

smallest magnitude negative and positive.

smallestMagnitudePositiveB

private double smallestMagnitudePositiveB

smallest magnitude negative and positive.

theta

private float theta

DOCUMENT ME! - TO BE MOVED - redesigned

unequalDim

private boolean unequalDim

Boolean telling if unequal dimensions are allowed in the FFT image. TO BE MOVED

writeLockCount

private int writeLockCount

Locking write count.

avgInten

private float avgInten

avgIntenR

private float avgIntenR

avgIntenG

private float avgIntenG

avgIntenB

private float avgIntenB

stdDeviation

private float stdDeviation

stdDeviationR

private float stdDeviationR

stdDeviationG

private float stdDeviationG

stdDeviationB

private float stdDeviationB

numPixels

private int numPixels

sumPixelInten

private double sumPixelInten

sumPixelIntenR

private double sumPixelIntenR

sumPixelIntenG

private double sumPixelIntenG

sumPixelIntenB

private double sumPixelIntenB

Constructor Details

ModelStorageBase

public ModelStorageBase()

Default constructor.

ModelStorageBase

public ModelStorageBase(int type,
 int[] dimExtents)

Allocates buffer memory of the specified type.

Parameters:

type - type of buffer to allocate

dimExtents - extents of the buffer in each dimension (multipleid together produces the size of the buffer to be allocated

ModelStorageBase

public ModelStorageBase(ModelStorageBase.DataType type,
 int[] dimExtents)

Allocates buffer memory of the specified type.

Parameters:

type - type of buffer to allocate

dimExtents - extents of the buffer in each dimension (multipleid together produces the size of the buffer to be allocated

Method Details

getBufferTypeStr

public static String getBufferTypeStr(int type)

Returns the string for a particular buffer type.

Parameters:

type - int representing the buffer type (see the static definitions)

Returns:

string representing the buffer type

addSurfaceMask

public void addSurfaceMask(int index,
 BitSet kMask,
 WildMagic.LibFoundation.Mathematics.ColorRGBA[] kMaskColors,
 WildMagic.LibFoundation.Mathematics.ColorRGBA kColor)

Adds a surface mask to this image.

Parameters:

index - the index of the mask.

kMask - the surface mask

kMaskColors - the per-voxel colors for the mask

kColor - the overall mask color if per-voxel mask colors are not defined.

calcMinMax

public void calcMinMax()

Calculates the min and max values for the image array.

calcMinMax

public void calcMinMax(boolean logMagDisplay)

Parameters:

logMagDisplay - if true calculate min and max for log10 of 1 + magnitude Calculates the min and max values for the image array.

calcMinMaxMag

public void calcMinMaxMag(boolean logMagDisplay)

Calculates the min and max magnitude values for the image array.

Parameters:

logMagDisplay - if true calculate min and max for log10 of 1 + magnitude

calcMinMaxNonZero

public void calcMinMaxNonZero()

Calculates the min and max nonzero values for the image array.

clone

public Object clone()

Copies the object.

Overrides:

clone in class ModelSerialCloneable

Returns:

Returns the cloned object.

convertToFloat

public void convertToFloat()
                    throws IOException

Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.

Throws:

IOException - throws an exception if the image model is locked.

disposeLocal

public void disposeLocal()

Dispose of memory and call the garbage collector.

export

public final float[] export(int orientation,
 int tSlice,
 int slice,
 float[] values,
 boolean bMask)
                     throws IOException

Exports data based on the mapping from ModelImage space to Patient space.

Parameters:

orientation - The Patient Orientation of the slice to export

tSlice - Index into the forth dimension

slice - Indicates slice of data to be exported

values - The array in which to write the data

Returns:

A float array of the data mapped to patient space.

Throws:

IOException - Throws an error when there is a locking or bounds error.

export

public final float[] export(int[] axisOrder,
 boolean[] axisFlip,
 int tSlice,
 int slice,
 float[] values,
 boolean bMask)
                     throws IOException

Exports data based on the mapping from ModelImage space to Patient space. The mapping parameters are passed in as the axisOrder and axisFlip arrays.

Parameters:

axisOrder - The mapping of ModelImage space volume axes to Patient space axes

axisFlip - The mapping of ModelImage space volume axes to Patient space axes (invert flags)

tSlice - Index into the forth dimension

slice - Indicates slice of data to be exported

values - The array to write the data into

Returns:

A float array of the data mapped to patient space.

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportComplexData

public final void exportComplexData(int start,
 int length,
 float[] valuesR,
 float[] valuesI)
                             throws IOException

Export data to the real values and the images values arrays.

Parameters:

start - Indicates starting position in data array

length - Length of complex data (in 2 float units) to be copied from data array

valuesR - Array where real data is to be deposited

valuesI - Array where imaginary data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportComplexSliceXY

public final void exportComplexSliceXY(int slice,
 float[] values,
 boolean logMagDisplay)
                                throws IOException

Export XY slice magnitude data into values array.

Parameters:

slice - indicates slice of data to be exported

values - array where data is to be deposited

logMagDisplay - if true display log10 of 1 + data

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final Object exportData(int start,
 int length)
                        throws IOException

Export data into values array, in the native type of the model image.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

Returns:

Object, new array where data has been deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(Object value_array)
                      throws IOException

Import Object. Imports Object array that is exported with the exportData function.

Parameters:

value_array - Object storing data.

Throws:

IOException

exportData

public final void exportData(int start,
 int length,
 Number[] values)
                      throws IOException

Export data into values array.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final void exportData(int start,
 int length,
 BitSet values)
                      throws IOException

Export data into values array.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final void exportData(int start,
 int length,
 byte[] values)
                      throws IOException

Export data into values array.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final void exportData(int start,
 int length,
 short[] values)
                      throws IOException

Export data into values array.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final void exportData(int start,
 int length,
 int[] values)
                      throws IOException

Export data into values array.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final void exportData(int start,
 int length,
 long[] values)
                      throws IOException

Export data into values array.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final void exportData(int start,
 int length,
 float[] values)
                      throws IOException

Export data to values array.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final void exportData(int start,
 int length,
 double[] values)
                      throws IOException

Export data in values array.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportData

public final void exportData(int start,
 int length0,
 int length1,
 float[] values)
                      throws IOException

export data to values array.

Parameters:

start - indicates starting position in data array

length0 - length of first dimension of data to be copied from data array

length1 - length of second dimension of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportDataNoLock

public final void exportDataNoLock(int start,
 int length,
 Number[] values)
                            throws IOException

export data into values array WITHOUT locking.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a bounds error.

exportDataNoLock

public final void exportDataNoLock(int start,
 int length,
 BitSet values)
                            throws IOException

export data into values array WITHOUT locking.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a bounds error.

exportDataNoLock

public final void exportDataNoLock(int start,
 int length,
 byte[] values)
                            throws IOException

Export data into values array WITHOUT locking.

Parameters:

start - Indicates starting position in data array

length - Length of data to be copied from data array

values - Array where data is to be deposited

Throws:

IOException - Throws an error when there is a bounds error.

exportDataNoLock

public final void exportDataNoLock(int start,
 int length,
 short[] values)
                            throws IOException

Export data into values array WITHOUT locking.

Parameters:

start - Indicates starting position in data array

length - Length of data to be copied from data array

values - Array where data is to be deposited

Throws:

IOException - Throws an error when there is a bounds error.

exportDataNoLock

public final void exportDataNoLock(int start,
 int length,
 int[] values)
                            throws IOException

Export data into values array WITHOUT locking.

Parameters:

start - Indicates starting position in data array

length - Length of data to be copied from data array

values - Array where data is to be deposited

Throws:

IOException - Throws an error when there is a bounds error.

exportDataNoLock

public final void exportDataNoLock(int start,
 int length,
 long[] values)
                            throws IOException

export data into values array WITHOUT locking.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a bounds error.

exportDataNoLock

public final void exportDataNoLock(int start,
 int length,
 float[] values)
                            throws IOException

export data in values array WITHOUT using locking.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a bounds error.

exportDataNoLock

public final void exportDataNoLock(int start,
 int length,
 double[] values)
                            throws IOException

export data into values array WITHOUT locking.

Parameters:

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a bounds error.

exportDComplexData

public final void exportDComplexData(int start,
 int length,
 double[] valuesR,
 double[] valuesI)
                              throws IOException

Export data to the real values and the imaginary values arrays.

Parameters:

start - indicates starting position in data array

length - length of complex data (in 2 float units) to be copied from data array

valuesR - array where real data is to be deposited

valuesI - array where imaginary data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportDiagonal

public final void exportDiagonal(int tSlice,
 int slice,
 int[] extents,
 WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
 float[] values,
 boolean bInterpolate)
                          throws IOException

ShowDiagonal samples the ModelImage data along a non-axis aligned plane. The plane may intersect the ModelImage volume, defined in x,y,z space, along a diagonal direction.

This function steps through the image, using the four transformed points to step through the ModelImage along the diagonal directions, read the corresonding point in the ModelImage and write the value into the image array. If bInterpolate is set to true, the ModelImage data for non-interger vertices is interpolated using tri-linear interpolation. Note: there is one loop for steping though he data, no matter which type of plane this object represents (XY, XZ, or ZY).

Parameters:

tSlice - Index into the forth dimension

slice - Indicates slice of data to be exported

extents - Image extents in the local coordinate system.

verts - The rotated non-axis aligned corners of the slice

values - The array in which to write the data.

bInterpolate - If true then use interpolation.

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportDiagonal

public final void exportDiagonal(int tSlice,
 int slice,
 int[] extents,
 WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
 float[] values,
 boolean bInterpolate,
 BitSet imageMask,
 Vector<BitSet> surfaceMask,
 boolean[] surfaceValues)
                          throws IOException

Throws:

IOException

exportDiagonal

public final void exportDiagonal(BitSet duplicateMask,
 int tSlice,
 int slice,
 int[] extents,
 WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
 float diameter,
 boolean bSetZero,
 float[] values,
 boolean bInterpolate)
                          throws IOException

ShowDiagonal samples the ModelImage data along a non-axis aligned plane. The plane may intersect the ModelImage volume, defined in x,y,z space, along a diagonal direction.

This function steps through the image, using the four transformed points to step through the ModelImage along the diagonal directions, read the corresonding point in the ModelImage and write the value into the image array. If bInterpolate is set to true, the ModelImage data for non-interger vertices is interpolated using tri-linear interpolation. Note: there is one loop for steping though he data, no matter which type of plane this object represents (XY, XZ, or ZY).

Parameters:

tSlice - Index into the forth dimension

slice - Indicates slice of data to be exported

extents - Image extents in the local coordinate system.

verts - The rotated non-axis aligned corners of the slice

values - The array in which to write the data.

bInterpolate - If true then use interpolation.

Throws:

IOException - Throws an error when there is a locking or bounds error.

findMax

public final WildMagic.LibFoundation.Mathematics.Vector3f findMax(int tSlice,
 int slice,
 WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
 float diameter,
 boolean bInterpolate)
                                                           throws IOException

Throws:

IOException

exportDMagData

public final void exportDMagData(int start,
 int length,
 double[] values)
                          throws IOException

Export magnitude data to values array.

Parameters:

start - indicates starting position in data array

length - length of magnitude data to be copied from data array

values - array where magnitude data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportMagData

public final void exportMagData(int start,
 int length,
 float[] values)
                         throws IOException

export magnitude data to values array.

Parameters:

start - indicates starting position in data array

length - length of magnitude data to be copied from data array

values - array where magnitude data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportMagData

public final void exportMagData(int start,
 int length,
 double[] values)
                         throws IOException

export magnitude data to values array.

Parameters:

start - indicates starting position in data array

length - length of magnitude data to be copied from data array

values - array where magnitude data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportRGBData

public final Object exportRGBData(int offset,
 int start,
 int length)
                           throws IOException

export data in values array.

Parameters:

offset - correct offset for RED, GREEN, or BLUE component to be exported

start - indicates starting position in data array

length - length of data to be copied from data array

Returns:

Object, new array where data has been deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportRGBData

public final void exportRGBData(int offset,
 int start,
 int length,
 byte[] values)
                         throws IOException

export data in values array.

Parameters:

offset - correct offset for RED, GREEN, or BLUE component to be exported

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportRGBData

public final void exportRGBData(int offset,
 int start,
 int length,
 short[] values)
                         throws IOException

export data in values array.

Parameters:

offset - correct offset for RED, GREEN, or BLUE component to be exported

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportRGBData

public final void exportRGBData(int offset,
 int start,
 int length,
 float[] values)
                         throws IOException

export data in values array.

Parameters:

offset - correct offset for RED, GREEN, or BLUE component to be exported

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportRGBData

public final void exportRGBData(int offset,
 int start,
 int length,
 double[] values)
                         throws IOException

export data in values array.

Parameters:

offset - correct offset for RED, GREEN, or BLUE component to be exported

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportRGBDataNoLock

public final void exportRGBDataNoLock(int offset,
 int start,
 int length,
 float[] values)
                               throws IOException

Export data in values array WITHOUT using locking.

Parameters:

offset - offset into the data array

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportRGBDataNoLock

public final void exportRGBDataNoLock(int offset,
 int start,
 int length,
 double[] values)
                               throws IOException

Export data in values array WITHOUT using locking.

Parameters:

offset - offset into the data array

start - indicates starting position in data array

length - length of data to be copied from data array

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportSliceXY

public final void exportSliceXY(int slice,
 byte[] values)
                         throws IOException

Export XY slice into values array.

Parameters:

slice - Indicates slice of data to be exported

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportSliceXY

public final void exportSliceXY(int slice,
 short[] values)
                         throws IOException

Export XY slice into values array.

Parameters:

slice - Indicates slice of data to be exported.

values - Array where data is to be deposited.

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportSliceXY

public final void exportSliceXY(int slice,
 int[] values)
                         throws IOException

Export XY slice into values array.

Parameters:

slice - Indicates slice of data to be exported.

values - Array where data is to be deposited.

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportSliceXY

public final void exportSliceXY(int slice,
 long[] values)
                         throws IOException

export XY slice into values array.

Parameters:

slice - indicates slice of data to be exported

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportSliceXY

public final void exportSliceXY(int slice,
 float[] values)
                         throws IOException

export XY slice into values array.

Parameters:

slice - indicates slice of data to be exported

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

exportSliceXY

public final void exportSliceXY(int slice,
 double[] values)
                         throws IOException

export XY slice into values array.

Parameters:

slice - indicates slice of data to be exported

values - array where data is to be deposited

Throws:

IOException - Throws an error when there is a locking or bounds error.

get

public final Number get(int position)

function to get data where bounds checking is performed.

Parameters:

position - position in one dimensional array

Returns:

returns value if position in data array range

get

public final Number get(int[] position)

nD get data fuction where bounds checking is performed.

Parameters:

position - array of coordinate values

Returns:

returns true if position in data array range

get

public final Number get(int x,
 int y)

2D get data fuction where bounds checking is performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

returns value if position in data array range

get

public final Number get(int x,
 int y,
 int z)

3D get data fuction where bounds checking is performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

returns value if position in data array range

get

public final Number get(int x,
 int y,
 int z,
 int b)

4D get data fuction where bounds checking is performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate (ie. multi-modality images or time)

Returns:

returns true if position in data array range

getAxisOrientation

public int[] getAxisOrientation()

Returns the axis orientation of image.

Returns:

the axis orientation of image

getBiLinear

public final Number getBiLinear(float x,
 float y)

version of get that performs bi-linear interpoloation. Note - does perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The Number of the bilinearly interpolated data.

getBoolean

public final boolean getBoolean(int position)

Version of get that does NOT perform bounds checking.

Parameters:

position - index into the data.

Returns:

The boolean value from the data array.

getBoolean

public final boolean getBoolean(int[] position)

n-Dimensional get data fuction where bounds checking is NOT performed.

Parameters:

position - index into the data

Returns:

returns true if position in data array range

getBoolean

public final boolean getBoolean(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

value

getBoolean

public final boolean getBoolean(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate*

Returns:

The value at that position in the data array.

getBoolean

public final boolean getBoolean(int x,
 int y,
 int z,
 int b)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - 4th dimension coordinate.*

Returns:

The value at that position in the data array.

getByte

public final byte getByte(int position)

Version of get that does NOT perform bounds checking

Parameters:

position - position in one dimensional array.

position - Indexe into the data array.

Returns:

The value at that position in the data array.

getByte

public final byte getByte(int[] position)

nD get data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

Returns:

returns true if position in data array range

getByte

public final byte getByte(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

value at that position in the data array

getByte

public final byte getByte(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

value at that position in the data array

getByte

public final byte getByte(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate (usually the slice plane index)

t - t coordinate (usually the volume index)

Returns:

value at that position in the data array

getByteBiLinear

public final byte getByteBiLinear(float x,
 float y)

version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The interpolated value from the data array.

getByteTriLinear

public final byte getByteTriLinear(float x,
 float y,
 float z)

version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The interpolated value from the data array.

getC

public final Number getC(int position,
 int color)

Color function to get data where bounds checking is performed.

Parameters:

position - position in one dimensional array

color - DOCUMENT ME!

Returns:

returns value if position in data array range

getConvolve

public boolean getConvolve()

Accessor method for the m_bConvolve data memeber.

Returns:

m_bConvolve, true when this images is the product of fft( imageA ) fft( imageB )

getDouble

public final double getDouble(int position)

The interpolated value from the data array.ersion of get that does NOT perform bounds checking.

Parameters:

position - index into one dimensional array

Returns:

The value from the data array.

getDouble

public final double getDouble(int[] position)

nD get data fuction where bounds checking is NOT performed.

Parameters:

position - Index into one dimensional array

Returns:

The value from the data array.

getDouble

public final double getDouble(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

Value at that position in the data array

getDouble

public final double getDouble(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

Value at that position in the data array

getDouble

public final double getDouble(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate (usually the volume index)*

Returns:

The value at that position in the data array.

getDoubleBiLinear

public final double getDoubleBiLinear(float x,
 float y)

version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The interpolated value at that position in the data array.

getDoubleTriLinear

public final double getDoubleTriLinear(float x,
 float y,
 float z)

version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The value at that position in the data array.

getExtents

public final int[] getExtents()

Accessor that returns the extents of the image.

Returns:

array of ints indicating the extents in each dimension

getExtents

public final int[] getExtents(int orientation)

Returns the image extents translated into the Patient-Coordinate systsm:

Parameters:

orientation - the Patient-Coordinate view for which the extents are needed:

Returns:

Extents for the image in Patient Coordinates

getExtents

public final int[] getExtents(int[] aiAxisOrder)

Returns the image extents translated into the Patient-Coordinate system:

Parameters:

aiAxisOrder - the Patient-Coordinate order of the original data for which the extents are needed:

Returns:

Extents for the image in Patient Coordinates

getExtentsSize

public final int[] getExtentsSize(int orientation)

getFileInfo

public FileInfoBase[] getFileInfo()

Accessor that returns the fileInfo array (one per slice).

Returns:

fileInfo array structure

getFileInfo

public FileInfoBase getFileInfo(int i)

Accessor that returns the fileInfo of a specific image slice.

Parameters:

i - index that indicates image slice

Returns:

fileInfo array structure for a specific image slice

getFilterType

public final int getFilterType()

returns type of filter - low, high, bandpass, or bandstop. - TO BE MOVED

Returns:

filterType

getFloat

public final float getFloat(int position)

Version of get that does NOT perform bounds checking.

Parameters:

position - index into the one dimensional data array

Returns:

The value at that position in the data array.

getFloat

public final float getFloat(int[] position)

nD get data function where bounds checking is NOT performed.

Parameters:

position - index into the one dimensional data array

Returns:

The value at that position in the data array.

getFloat

public final float getFloat(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

The value at that position in the data array.

getFloat

public final float getFloat(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The value at that position in the data array.

getFloat

public final float getFloat(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

Returns:

The value at that position in the data array.

getFloatBiLinear

public final float getFloatBiLinear(float x,
 float y)

version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The interpolated value at that position in the data array.

getFloatC

public final float getFloatC(int x,
 int y,
 int c)

2D color get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

c - color channel index

Returns:

value at that position in the data array

getFloatC

public final float getFloatC(int x,
 int y,
 int z,
 int c)

3D color get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

c - color channel index

Returns:

value at that position in the data array

getFloatC

public final float getFloatC(int x,
 int y,
 int z,
 int t,
 int c)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

c - color channel index

Returns:

The value at that position in the data array.

getFloatTriLinear

public final float getFloatTriLinear(float x,
 float y,
 float z)

version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The value at that position in the data array.

getFloatTriLinearBounds

public final float getFloatTriLinearBounds(float x,
 float y,
 float z)

Get a value using tri-linear interpoloation. Note - DOES perform bounds checking (both that x,y,z are valid and that the interp indicies don't cause exceptions).

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

interpolated value if in bounds, 0 if not.

getFloatTriLinearBoundsTime

public final float getFloatTriLinearBoundsTime(float x,
 float y,
 float z,
 int t)

Get a value using tri-linear interpoloation. Note - DOES perform bounds checking (both that x,y,z are valid and that the interp indicies don't cause exceptions).

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

Returns:

interpolated value if in bounds, 0 if not.

getFloatTriLinearBounds

public final float getFloatTriLinearBounds(float x,
 float y,
 float z,
 int c)

Get a value using tri-linear interpoloation. Note - DOES perform bounds checking (both that x,y,z are valid and that the interp indicies don't cause exceptions).

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

c - color-coordinate

Returns:

interpolated value if in bounds, 0 if not.

getFreq1

public final float getFreq1()

returns frequency 1 of filter.

Returns:

freq1

getFreq2

public final float getFreq2()

returns frequency 2 of filter.

Returns:

freq2

getFreqU

public final float getFreqU()

returns frequency U of filter.

Returns:

freqU

getFreqV

public final float getFreqV()

returns frequency V of filter.

Returns:

freqV

getHaveWindowed

public final boolean getHaveWindowed()

DOCUMENT ME! - TO BE MOVED

Returns:

DOCUMENT ME!

getHeight

public int getHeight(int orientation)

Returns the image height, based on the Patient Coordinates orientation from which the data will be viewed:

Parameters:

orientation - the Patient-Viewing orientation

Returns:

The image height for the viewing orientation

getImage25D

public boolean getImage25D()

Accessor that returns the boolean indicating if 3D images are processed one slice at a time.

Returns:

boolean telling if slice by slice processing occurs in 3D

getImageOrientation

public int getImageOrientation()

Gets the image orientation (sagittal, axial, ...).

Returns:

integer representing the orientation

getInt

public final int getInt(int position)

Version of get that does NOT perform bounds checking.

Parameters:

position - position in one dimensional array

Returns:

value at that position in the data array

getInt

public final int getInt(int[] position)

nD get data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

Returns:

returns true if position in data array range

getInt

public final int getInt(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

value at that position in the data array

getInt

public final int getInt(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

value at that position in the data array

getInt

public final int getInt(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

Returns:

The value at that position in the data array

getIntBiLinear

public final int getIntBiLinear(float x,
 float y)

version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The interpolated value at that position in the data array

getIntTriLinear

public final int getIntTriLinear(float x,
 float y,
 float z)

Version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The value at that position in the data array

getLockStatus

public final int getLockStatus()

Accessor that returns the lock status of the image.

Returns:

lock status

getLogMagDisplay

public boolean getLogMagDisplay()

Accessor that returns the boolean indicating if log magnitude displays are used in complex images.

Returns:

boolean telling if log display is used

getLong

public final long getLong(int position)

Version of get that does NOT perform bounds checking.

Parameters:

position - The index in one dimensional array

Returns:

The value at that position in the data array

getLong

public final long getLong(int[] position)

nD get data fuction where bounds checking is NOT performed.

Parameters:

position - The index in one dimensional array

Returns:

The value at that position in the data array

getLong

public final long getLong(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

value at that position in the data array

getLong

public final long getLong(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

value at that position in the data array

getLong

public final long getLong(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

Returns:

value at that position in the data array

getLongBiLinear

public final long getLongBiLinear(float x,
 float y)

version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The interpolated value at that position in the data array

getLongTriLinear

public final long getLongTriLinear(float x,
 float y,
 float z)

Version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The interpolated value at that position in the data array

getMax

public double getMax()

Accessor that returns the maximum value in the dataArray.

Returns:

double indicating maximum value in the dataArray

getMaxA

public double getMaxA()

Accessor that returns the maximum alpha value in the dataArray.

Returns:

double indicating maximum alpha value in the dataArray

getMaxB

public double getMaxB()

Accessor that returns the maximum blue value in the dataArray.

Returns:

double indicating maximum blue value in the dataArray

getMaxG

public double getMaxG()

Accessor that returns the maximum green value in the dataArray.

Returns:

double indicating maximum green value in the dataArray

getMaxR

public double getMaxR()

Accessor that returns the maximum red value in the dataArray.

Returns:

double indicating maximum red value in the dataArray

getMin

public double getMin()

Accessor that returns the minimum value in the dataArray.

Returns:

double indicating minimum value in the dataArray

getMinA

public double getMinA()

Accessor that returns the minimum alpha value in the dataArray.

Returns:

double indicating minimum alpha value in the dataArray

getMinB

public double getMinB()

Accessor that returns the minimum blue value in the dataArray.

Returns:

double indicating minimum blue value in the dataArray

getMinG

public double getMinG()

getMinG - Accessor that returns the minimum green value in the dataArray.

Returns:

double indicating minimum green value in the dataArray

getMinR

public double getMinR()

Accessor that returns the minimum red value in the dataArray.

Returns:

double indicating minimum red value in the dataArray

getNDims

public final int getNDims()

Accessor that returns the dimensionality of the image.

Returns:

int indicating the number of dimensions

getNoLogMax

public double getNoLogMax()

Accessor that returns the maximum value without log processing in the dataArray.

Returns:

double indicating maximum value in the dataArray

getNoLogMin

public double getNoLogMin()

Accessor that returns the minimum value without log processing in the dataArray.

Returns:

double indicating minimum value in the dataArray

getNoLogMinNonZero

public double getNoLogMinNonZero()

Accessor that returns the minimum nonzero value without log processing in the dataArray.

Returns:

double indicating minimum value in the dataArray

getNonZeroMax

public double getNonZeroMax()

Accessor that returns the smallest magnitude negative value in the dataArray.

Returns:

double indicating maximum nonzero value in the dataArray NaN if no nonzero value present

getNonZeroMaxB

public double getNonZeroMaxB()

Accessor that returns the maximum nonzero blue value in the dataArray.

Returns:

double indicating maximum nonzero blue value in the dataArray NaN if no nonzero blue value present

getNonZeroMaxG

public double getNonZeroMaxG()

Accessor that returns the maximum nonzero green value in the dataArray.

Returns:

double indicating maximum nonzero green value in the dataArray NaN if no nonzero green value present

getNonZeroMaxR

public double getNonZeroMaxR()

Accessor that returns the maximum nonzero red value in the dataArray.

Returns:

double indicating maximum nonzero red value in the dataArray NaN if no nonzero red value present

getNonZeroMin

public double getNonZeroMin()

Accessor that returns the minimum nonzero value in the dataArray.

Returns:

double indicating minimum nonzero value in the dataArray NaN if no nonzero value present

getNonZeroMinB

public double getNonZeroMinB()

Accessor that returns the minimum nonzero blue value in the dataArray.

Returns:

double indicating minimum nonzero blue value in the dataArray NaN if no nonzero blue value present

getNonZeroMinG

public double getNonZeroMinG()

Accessor that returns the minimum nonzero green value in the dataArray.

Returns:

double indicating minimum nonzero green value in the dataArray NaN if no nonzero green value present

getNonZeroMinR

public double getNonZeroMinR()

Accessor that returns the minimum nonzero red value in the dataArray.

Returns:

double indicating minimum nonzero red value in the dataArray NaN if no nonzero red value present

getOrigin

public float[] getOrigin()

Returns the origin of the image.

Returns:

the origin of the image

getOrigin

public float[] getOrigin(int index,
 int orientation)

Returns the image origin for the image translated into the Patient-Coordinate systsm:

Parameters:

index - the fileInfo index

orientation - the Patient-Coordinate view for which the origin are needed:

Returns:

the origin of the image in Patient Coordinates

getOriginalFilterOrder

public final int getOriginalFilterOrder()

returns integer telling filter order. - TO BE MOVED

Returns:

value indicating the filter order;

getOriginalEpsilon

public final double getOriginalEpsilon()

Returns:

value indicating the maximum filter ripple in Chdebyshev Type I and II or passband ripple in decibels in Elliptic

getOriginalRs

public final double getOriginalRs()

Decibels stopband is down in Elliptic

getOriginalCropCheckbox

public final boolean getOriginalCropCheckbox()

DOCUMENT ME! - TO BE MOVED

Returns:

DOCUMENT ME!

getOriginalDoCrop

public final boolean getOriginalDoCrop()

DOCUMENT ME! - TO BE MOVED

Returns:

DOCUMENT ME!

getOriginalEnd

public final int[] getOriginalEnd()

DOCUMENT ME! -TO BE MOVED

Returns:

DOCUMENT ME!

getOriginalExtents

public final int[] getOriginalExtents()

Accessor that returns the original extents of the image.

Returns:

array of ints indicating the original extents in each dimension

getOriginalFilterConstruction

public final int getOriginalFilterConstruction()

returns integer telling filter construction method.

Returns:

int showing original filter construction method

getOriginalKernelDimension

public final int getOriginalKernelDimension()

returns kernel diameter chosen on forward FFT.

Returns:

int showing original kernel diameter chosen on forward FFT

getOriginalStart

public final int[] getOriginalStart()

DOCUMENT ME! - TO BE MOVED

Returns:

DOCUMENT ME!

getRadiologicalView

public boolean getRadiologicalView()

Gets the radiological view flag:

Returns:

the RadiologicalView on/off

getResolutions

public float[] getResolutions(int index)

Returns the resolutions for the image without regarding resolution difference between slices.

Parameters:

index - The index indicating which data slice to exact the resolutions

Returns:

the resolutions for the data slice

getResolutions

public float[] getResolutions(int index,
 int orientation)

Returns the resolutions for the image translated into the Patient-Coordinate systsm:

Parameters:

index - the fileInfo index

orientation - the Patient-Coordinate view for which the resolutions are needed:

Returns:

the resolutions for the image in Patient Coordinates

getResolutions

public float[] getResolutions(int index,
 int[] aiAxisOrder)

Returns the resolutions for the image translated into the Patient-Coordinate systsm:

Parameters:

index - the fileInfo index

aiAxisOrder - the Patient-Coordinate order of the original data for which the resolutions are needed:

Returns:

the resolutions for the image in Patient Coordinates

getShort

public final short getShort(int position)

Version of get that does NOT perform bounds checking.

Parameters:

position - The index into the one dimensional array

Returns:

The value at that position in the data array

getShort

public final short getShort(int[] position)

nD get data fuction where bounds checking is NOT performed.

Parameters:

position - The index into the one dimensional array

Returns:

The value at that position in the data array

getShort

public final short getShort(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

value at that position in the data array

getShort

public final short getShort(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

value at that position in the data array

getShort

public final short getShort(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

Returns:

value at that position in the data array

getShortBiLinear

public final short getShortBiLinear(float x,
 float y)

version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The value at that position in the data array

getShortTriLinear

public final short getShortTriLinear(float x,
 float y,
 float z)

version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The intoplated value at that position in the data array

getSigmaU

public final float getSigmaU()

returns standard deviation U of filter. TO BE MOVED

Returns:

sigmaU

getSigmaV

public final float getSigmaV()

returns standard deviation V of filter. TO BE MOVED

Returns:

sigmaV

getSize

public final int getSize()

Accessor that returns the total size(length) of the data array.

Returns:

Value indicating the number of data points in the data array

getSliceSize

public final int getSliceSize()

Get the nuber of pixels in a slice of the image.

Returns:

the number of pixels in a slice

getSmallestMagnitudeNegative

public double getSmallestMagnitudeNegative()

Accessor that returns the smallest magnitude negative value in the dataArray.

Returns:

value indicating smallest magnitude negative value in the dataArray NaN if no negative value is present

getSmallestMagnitudeNegativeB

public double getSmallestMagnitudeNegativeB()

Accessor that returns the smallest magnitude negative blue value in the dataArray.

Returns:

value indicating smallest magnitude negative blue value in the dataArray NaN if no negative blue value is present

getSmallestMagnitudeNegativeG

public double getSmallestMagnitudeNegativeG()

Accessor that returns the smallest magnitude negative green value in the dataArray.

Returns:

value indicating smallest magnitude negative green value in the dataArray NaN if no negative green value is present

getSmallestMagnitudeNegativeR

public double getSmallestMagnitudeNegativeR()

Accessor that returns the smallest magnitude negative red value in the dataArray.

Returns:

value indicating smallest magnitude negative red value in the dataArray NaN if no negative red value is present

getSmallestMagnitudePositive

public double getSmallestMagnitudePositive()

Accessor that returns the smallest magnitude positive value in the dataArray.

Returns:

value indicating smallest magnitude positive value in the dataArray NaN if no positive value is present

getSmallestMagnitudePositiveB

public double getSmallestMagnitudePositiveB()

Accessor that returns the smallest magnitude positive blue value in the dataArray.

Returns:

value indicating smallest magnitude positive blue value in the dataArray NaN if no positive blue value is present

getSmallestMagnitudePositiveG

public double getSmallestMagnitudePositiveG()

Accessor that returns the smallest magnitude positive green value in the dataArray.

Returns:

value indicating smallest magnitude positive green value in the dataArray NaN if no positive green value is present

getSmallestMagnitudePositiveR

public double getSmallestMagnitudePositiveR()

Accessor that returns the smallest magnitude positive red value in the dataArray.

Returns:

value indicating smallest magnitude positive red value in the dataArray NaN if no positive red value is present

getSurfaceMask

public BitSet getSurfaceMask(int index)

Returns the surface mask from this image.

Parameters:

index - the index of the mask to remove.

Returns:

the BitSet mask

getSurfaceMaskColor

public WildMagic.LibFoundation.Mathematics.ColorRGBA getSurfaceMaskColor(int index)

Returns the surface mask from this image.

Parameters:

index - the index of the mask to remove.

Returns:

the BitSet mask

getTheta

public final float getTheta()

Returns roation angle theta in radians of filter. TO BE MOVED

Returns:

theta

getTriLinear

public final Number getTriLinear(float x,
 float y,
 float z)

version of get that performs tri-linear interpoloation. Note - does perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The introplated value at that position in the data array

getType

public final int getType()

Accessor that returns the image buffer type.

Returns:

Indicates the data buffer type

getDataType

public final ModelStorageBase.DataType getDataType()

Accessor that returns the image buffer type as an enum.

Returns:

The data buffer type

getTypeString

public final String getTypeString()

Accessor that returns the image type.

Returns:

The data buffer type as a String.

getUByte

public final short getUByte(int position)

version of get that does NOT perform bounds checking.

Parameters:

position - The index into the one dimensional array

Returns:

DOCUMENT ME!

getUByte

public final short getUByte(int[] position)

nD get data fuction where bounds checking is NOT performed.

Parameters:

position - The index into the one dimensional array

Returns:

The value at that position in the data array

getUByte

public final short getUByte(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

The interpolated value at that position in the data array.

getUByte

public final short getUByte(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The value at that position in the data array.

getUByte

public final short getUByte(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

Returns:

The value at that position in the data array

getUByteBiLinear

public final short getUByteBiLinear(float x,
 float y)

Version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The interpolated value at that position in the data array.

getUByteTriLinear

public final short getUByteTriLinear(float x,
 float y,
 float z)

Version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The interpolated value at that position in the data array.

getUInt

public final long getUInt(int position)

version of get that does NOT perform bounds checking.

Parameters:

position - position in one dimensional array

Returns:

The value at that position in the data array.

getUInt

public final long getUInt(int[] position)

nD get data fuction where bounds checking is NOT performed.

Parameters:

position - The index into the array of data.

Returns:

The value at that position in the data array.

getUInt

public final long getUInt(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

value at that position in the data array

getUInt

public final long getUInt(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

value at that position in the data array

getUInt

public final long getUInt(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

Returns:

The value at that position in the data array.

getUIntBiLinear

public final long getUIntBiLinear(float x,
 float y)

version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The value at that position in the data array.

getUIntTriLinear

public final long getUIntTriLinear(float x,
 float y,
 float z)

version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The interpolated value at that position in the data array.

getUnequalDim

public boolean getUnequalDim()

Accessor that returns the boolean indicating if unequal dimensions are allowed in complex images. TO BE MOVED

Returns:

Indicated if unequal dimensions are allowed

getUnitsOfMeasure

public int[] getUnitsOfMeasure()

Returns the units used to measure all dimensions of the image.

Returns:

The units used to measure all dimensions of the image.

getUnitsOfMeasure

public int getUnitsOfMeasure(int index)

Returns the unit used to measure the specific dimension of image.

Parameters:

index - The index of specific dimension

Returns:

The unit used to measure the specific dimension

getUnitsOfMeasure

public int[] getUnitsOfMeasure(int index,
 int orientation)

Returns the units of measure for the image translated into the Patient-Coordinate systsm:

Parameters:

index - the fileInfo index

orientation - the Patient-Coordinate view for which the units of measure are needed:

Returns:

the units of measure for the image in Patient Coordinates

getUShort

public final int getUShort(int position)

version of get that does NOT perform bounds checking.

Parameters:

position - The index into the one dimensional array

Returns:

The value at that position in the data array

getUShort

public final int getUShort(int[] position)

nD get data fuction where bounds checking is NOT performed.

Parameters:

position - The index into the one dimensional array

Returns:

The value at that position in the data array

getUShort

public final int getUShort(int x,
 int y)

2D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

Returns:

The value at that position in the data array

getUShort

public final int getUShort(int x,
 int y,
 int z)

3D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The value at that position in the data array

getUShort

public final int getUShort(int x,
 int y,
 int z,
 int t)

4D get data fuction where bounds checking is NOT performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

Returns:

The value at that position in the data array

getUShortBiLinear

public final int getUShortBiLinear(float x,
 float y)

Version of get that performs bi-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

Returns:

The interpolated value at that position in the data array.

getUShortTriLinear

public final int getUShortTriLinear(float x,
 float y,
 float z)

version of get that performs tri-linear interpoloation. Note - does NOT perform bounds checking

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

Returns:

The interpolated value at that position in the data array.

getVolumeIterationFactors

public int[] getVolumeIterationFactors()

Get the factors needed to iterate through the image volume. Can be multiplied against iterators to retreive the index into the image volume data.

Returns:

multiples of dimExtents[] for the image

getVolumeSize

public int getVolumeSize()

Gets the number of pixels in a volume of the image.

getWidth

public int getWidth(int orientation)

Returns the image width, based on the Patient Coordinates orientation from which the data will be viewed:

Parameters:

orientation - the Patient-Viewing orientation

Returns:

dimExtents representing the image width for the viewing orientation

importComplexData

public final void importComplexData(int start,
 float[] valuesR,
 float[] valuesI,
 boolean mmFlag,
 boolean logMagDisplay)
                             throws IOException

import Complex data (in 2 float units) into data array.

Parameters:

start - indicates starting position in data array

valuesR - array where real data is to be acquired

valuesI - array where imaginary data is to be acquired

mmFlag - whether or not to calculate min and max magnitude values for the image

logMagDisplay - whether or not min and max are calculated for log10 of 1 + magnitude array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 Number[] values,
 boolean mmFlag)
                      throws IOException

import Number data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 BitSet values,
 boolean mmFlag)
                      throws IOException

Import boolean (BitSet) data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 boolean[] values,
 boolean mmFlag)
                      throws IOException

Import boolean data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 byte[] values,
 boolean mmFlag)
                      throws IOException

Import byte data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 short[] values,
 boolean mmFlag)
                      throws IOException

import short data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 int[] values,
 boolean mmFlag)
                      throws IOException

import integer data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 long[] values,
 boolean mmFlag)
                      throws IOException

import long data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 float[] values,
 boolean mmFlag)
                      throws IOException

import float data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importData

public final void importData(int start,
 double[] values,
 boolean mmFlag)
                      throws IOException

import double data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importDComplexData

public final void importDComplexData(int start,
 double[] valuesR,
 double[] valuesI,
 boolean mmFlag,
 boolean logMagDisplay)
                              throws IOException

import Complex data (in 2 double units) into data array.

Parameters:

start - indicates starting position in data array

valuesR - array where real data is to be acquired

valuesI - array where imaginary data is to be acquired

mmFlag - whether or not to calculate min and max magnitude values for the image

logMagDisplay - whether or not min and max are calculated for log10 of 1 + magnitude array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importRGBData

public final void importRGBData(int color,
 int alphaIndexStart,
 byte[] values,
 boolean mmFlag)
                         throws IOException

Import byte data into data array.

Parameters:

color - color planes are interleaved, so color offsets the appropriate interleave interval

alphaIndexStart - indicates starting position in data array which points to the alpha value

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importRGBData

public final void importRGBData(int color,
 int alphaIndexStart,
 short[] values,
 boolean mmFlag)
                         throws IOException

Import byte data into data array.

Parameters:

color - color planes are interleaved, so color offsets the appropriate interleave interval

alphaIndexStart - indicates starting position in data array which points to the alpha value

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importRGBData

public final void importRGBData(int color,
 int alphaIndexStart,
 float[] values,
 boolean mmFlag)
                         throws IOException

import float data into data array.

Parameters:

color - color planes are interleaved, so color offsets the appropriate interleave interval

alphaIndexStart - indicates starting position in data array which points to the alpha value

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importUData

public final void importUData(int start,
 short[] values,
 boolean mmFlag)
                       throws IOException

import short data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importUData

public final void importUData(int start,
 int[] values,
 boolean mmFlag)
                       throws IOException

import int data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

importUData

public final void importUData(int start,
 long[] values,
 boolean mmFlag)
                       throws IOException

import int data into data array.

Parameters:

start - indicates starting position in data array

values - array where data is to be acquired

mmFlag - whether or not to calculate min and max values for the image array

Throws:

IOException - Throws an error when there is a locking or bounds error.

reallocate

public void reallocate(int type)
                throws IOException

Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.

Parameters:

type - type of new buffer

Throws:

IOException - throws an exception if the image model is locked.

reallocate

public void reallocate(int[] dimExtents)
                throws IOException

Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.

Parameters:

dimExtents - extents of the buffer in each dimension (multipleid together produces the size of the buffer to be allocated

Throws:

IOException - throws an exception if the image model is locked.

reallocate

public void reallocate(int type,
 int[] dimExtents)
                throws IOException

Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.

Parameters:

type - type of new buffer

dimExtents - extents of the buffer in each dimension (multiplied together produces the size of the buffer to be allocated

Throws:

IOException - throws an exception if the image model is locked.

recomputeDataSize

public void recomputeDataSize()

Recomputes the datasize based on the type of buffer. If the datasize has changed, then the data array needs to be reallocated. So this method will also reconstruct the data array in this case. This method must be called if the extents of an buffer have been changed.

WARNING: This will clear any existing data if the dataSize is changed.

releaseLock

public final void releaseLock()

Releases the lock so that other proceses can read or write the data.

removeSurfaceMask

public void removeSurfaceMask(int index)

Removes the surface mask from this image.

Parameters:

index - The index of the mask to remove.

removeSurfaceMasks

public BitSet[] removeSurfaceMasks()

Returns the array of BitSet masks for backup.

Returns:

the BitSet mask array.

restoreSurfaceMasks

public void restoreSurfaceMasks(BitSet[] masks)

Restores the mask list from the array.

Parameters:

masks - array of BitSet masks

set

public final boolean set(int position,
 Number value)

Set that does perform bounds checking.

Parameters:

position - position in one dimensional array

value - The value to stored in the data array.

Returns:

returns value if position in data array range

set

public final boolean set(int[] position,
 Number value)

nD set data fuction where bounds checking is performed.

Parameters:

position - The coordinate into the 1D data array

value - The value to stored in the data array.

Returns:

returns true if position in data array range

set

public final void set(int position,
 boolean value)

version of set that does NOT perform bounds checking

Parameters:

position - position in one dimensional array.

value - The value to stored in the data array.

position - The index into the data array.

set

public final void set(int[] position,
 boolean value)

nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - The value to stored in the data array.

set

public final void set(int position,
 byte value)

Version of set that does NOT perform bounds checking.

Parameters:

position - The position in one dimensional array

value - The value to stored in the data array.

set

public final void set(int[] position,
 byte value)

nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

set

public final void set(int[] position,
 short value)

nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

set

public final void set(int position,
 int value)

Version of set that does NOT perform bounds checking.

Parameters:

position - position in one dimensional array

value - The value to stored in the data array.

set

public final void set(int[] position,
 int value)

nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

set

public final void set(int position,
 long value)

version of set that does NOT perform bounds checking.

Parameters:

position - position in one dimensional array

value - The value to stored in the data array.

set

public final void set(int[] position,
 long value)

nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

set

public final void set(int position,
 float value)

version of set that does NOT perform bounds checking.

Parameters:

position - position in one dimensional array

value - data that will be stored in the data array

set

public final void set(int[] position,
 float value)

nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

set

public final void set(int position,
 double value)

version of set that does NOT perform bounds checking.

Parameters:

position - position in one dimensional array

value - The value to stored in the data array.

set

public final void set(int[] position,
 double value)

nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

set

public final boolean set(int x,
 int y,
 Number value)

2D get data fuction where bounds checking is performed.

Parameters:

x - x coordinate

y - y coordinate

value - set data array to this value

Returns:

returns true if position in data array range

set

public final void set(int x,
 int y,
 boolean value)

2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 byte value)

2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 int value)

2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 long value)

2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 float value)

2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 double value)

2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - The value to stored in the data array.

set

public final boolean set(int x,
 int y,
 int z,
 Number value)

3D set data fuction where bounds checking is performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - set data array to this value

Returns:

returns true if position in data array range

set

public final void set(int x,
 int y,
 int z,
 boolean value)

3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 int z,
 byte value)

3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 int z,
 short value)

3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 int z,
 int value)

3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 int z,
 long value)

3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 int z,
 float value)

3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - The value to stored in the data array.

set

public final void set(int x,
 int y,
 int z,
 double value)

3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - The value to stored in the data array.

set

public final boolean set(int x,
 int y,
 int z,
 int b,
 Number value)

4D get data fuction where bounds checking is performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate (ie. multi modality images or time)

value - The value to stored in the data array.

Returns:

returns true if position in data array range

set

public final void set(int x,
 int y,
 int z,
 int b,
 boolean value)

4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - set data array to this value

set

public final void set(int x,
 int y,
 int z,
 int b,
 byte value)

4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - set data array to this value

set

public final void set(int x,
 int y,
 int z,
 int b,
 short value)

4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - set data array to this value

set

public final void set(int x,
 int y,
 int z,
 int b,
 int value)

4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - set data array to this value

set

public final void set(int x,
 int y,
 int z,
 int b,
 long value)

4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - set data array to this value

set

public final void set(int x,
 int y,
 int z,
 int b,
 float value)

4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - set data array to this value

set

public final void set(int x,
 int y,
 int z,
 int b,
 double value)

4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - set data array to this value

setAll

public final void setAll(float value)

Sets the entire buffer to value passed to this method.

Parameters:

value - float data that will be stored in the data array

setAll

public final void setAll(byte value)

Sets the entire buffer to value passed to this method.

Parameters:

value - byte data that will be stored in the data array

setAll

public final void setAll(short value)

Sets the entire buffer to value passed to this method.

Parameters:

value - short data that will be stored in the data array

setAll

public final void setAll(int value)

Sets the entire buffer to value passed to this method.

Parameters:

value - int data that will be stored in the data array

setAll

public final void setAll(double value)

Sets the entire buffer to value passed to this method.

Parameters:

value - double data that will be stored in the data array

setAllUByte

public final void setAllUByte(short value)

Sets the entire buffer to value passed to this method.

Parameters:

value - UByte data that will be stored in the data array

setAllUShort

public final void setAllUShort(int value)

Sets the entire buffer to value passed to this method.

Parameters:

value - UShort data that will be stored in the data array

setC

public final boolean setC(int position,
 int color,
 Number value)

Sets the entire buffer to value passed to this method.

Parameters:

position - position in one dimensional array

color - The color channel to be modified

value - set data array to this value

Returns:

returns value if position in data array range

setC

public final void setC(int position,
 int c,
 float value)

color version of setC that does NOT perform bounds checking.

Parameters:

position - position in one dimensional array

c - The color channel to be modified

value - set data array to this value

setC

public final void setC(int x,
 int y,
 int c,
 float value)

2D fast color version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

c - The color channel to be modified

value - set data array to this value

setC

public final boolean setC(int x,
 int y,
 int z,
 int c,
 Number value)

3D color set data fuction where bounds checking is performed.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

c - A,R,G, or B

value - set data array to this value

Returns:

returns true if position in data array range

setC

public final void setC(int x,
 int y,
 int z,
 int c,
 float value)

3D fast color version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

c - The color channel to be modified

value - set data array to this value

setComplex

public final void setComplex(int x,
 int y,
 int z,
 int part,
 float value)

Parameters:

x -

y -

z -

part - 0 for real 1 for imaginary

value -

setConvolve

public void setConvolve(boolean bConvolve)

Accessor method for the m_bConvolve data memeber.

Parameters:

bConvolve - true when this images is the product of fft( imageA ) fft( imageB )

setExtents

public void setExtents(int[] dims)

Sets the dimExtents for this structure.

Parameters:

dims - The data's dimensionality.

setFileInfo

public void setFileInfo(FileInfoBase[] fInfo)

Accessor that sets the entire fileInfo array of the image.

Parameters:

fInfo - structure

setFileInfo

public void setFileInfo(FileInfoBase fInfo,
 int idx)

Accessor that sets the fileInfo class for the image.

Parameters:

fInfo - fileInfo structure.

idx - index that typically indicates image slice.

setFilterType

public void setFilterType(int _filterType)

DOCUMENT ME! TO BE MOVED

Parameters:

_filterType - int

setFreq1

public void setFreq1(float _freq1)

DOCUMENT ME! TO BE MOVED

Parameters:

_freq1 - float

setFreq2

public void setFreq2(float _freq2)

DOCUMENT ME! TO BE MOVED

Parameters:

_freq2 - float

setFreqU

public void setFreqU(float _freqU)

DOCUMENT ME! TO BE MOVED

Parameters:

_freqU - float

setFreqV

public void setFreqV(float _freqV)

DOCUMENT ME! TO BE MOVED

Parameters:

_freqV - float

setHaveWindowed

public void setHaveWindowed(boolean window)

DOCUMENT ME! TO BE MOVED

Parameters:

window - boolean

setImage25D

public void setImage25D(boolean _image25D)

Accessor that sets the boolean telling if 3D images are processed one slice at a time.

Parameters:

_image25D - Set true if images are processed one slice at a time.

setLock

public void setLock()
             throws IOException

Sets the lockFlag to protect data. When the flag is set no other processes can read or write the data

Throws:

IOException - Throws an error if image is already locked.

setLock

public final void setLock(int lockType)
                   throws IOException

Sets the lockFlag to protect data. When the flag is set no other processes can read or write the data

Parameters:

lockType - The type of read/write lock that is to be set.

Throws:

IOException - Throws an error if image is already locked.

setLogMagDisplay

public void setLogMagDisplay(boolean logMagDisplay)

Accessor that sets the boolean telling if log magnitude display is used in a complex image. TO BE MOVED

Parameters:

logMagDisplay - DOCUMENT ME!

setMax

public void setMax(double _max)

Accessor that sets the maximum value in the dataArray.

Parameters:

_max - Indicates the maximum value in the data array

setMin

public void setMin(double _min)

Accessor that sets the minimum value in the dataArray.

Parameters:

_min - Indicates the minimum value in the data array

setMaxR

public void setMaxR(double _max)

Accessor that sets the maximum value in the dataArray.

Parameters:

_max - Indicates the maximum value in the data array

setMinR

public void setMinR(double _min)

Accessor that sets the minimum value in the dataArray.

Parameters:

_min - Indicates the minimum value in the data array

setMaxG

public void setMaxG(double _max)

Accessor that sets the maximum value in the dataArray.

Parameters:

_max - Indicates the maximum value in the data array

setMinG

public void setMinG(double _min)

Accessor that sets the minimum value in the dataArray.

Parameters:

_min - Indicates the minimum value in the data array

setMaxB

public void setMaxB(double _max)

Accessor that sets the maximum value in the dataArray.

Parameters:

_max - Indicates the maximum value in the data array

setMinB

public void setMinB(double _min)

Accessor that sets the minimum value in the dataArray.

Parameters:

_min - Indicates the minimum value in the data array

setOriginalFilterOrder

public void setOriginalFilterOrder(int filterOrder)

DOCUMENT ME! TO BE MOVED

Parameters:

filterOrder - DOCUMENT ME!

setOriginalEpsilon

public void setOriginalEpsilon(double epsilon)

Parameters:

epsilon - maximum filter ripple in Chebyshev I and II or maximum passband ripple in decibels in Elliptic

setOriginalRs

public void setOriginalRs(double rs)

setOriginalCropCheckbox

public void setOriginalCropCheckbox(boolean cropCheckbox)

DOCUMENT ME! TO BE MOVED

Parameters:

cropCheckbox - boolean

setOriginalDoCrop

public void setOriginalDoCrop(boolean doCrop)

DOCUMENT ME! TO BE MOVED

Parameters:

doCrop - boolean

setOriginalEnd

public void setOriginalEnd(int[] end)

DOCUMENT ME! TO BE MOVED

Parameters:

end - int[]

setOriginalExtents

public void setOriginalExtents(int[] dims)

Sets original dimensionality of the images. TO BE MOVED

Parameters:

dims - int[] dimensionality for x,y, and z ... dimensions

setOriginalFilterConstruction

public void setOriginalFilterConstruction(int filterConstruction)

DOCUMENT ME! TO BE MOVED

Parameters:

filterConstruction - DOCUMENT ME!

setOriginalKernelDimension

public void setOriginalKernelDimension(int kDim)

DOCUMENT ME! TO BE MOVED

Parameters:

kDim - DOCUMENT ME!

setOriginalStart

public void setOriginalStart(int[] start)

DOCUMENT ME! TO BE MOVED

Parameters:

start - int[]

setRadiologicalView

public void setRadiologicalView(boolean bEnabled)

Sets the radiological view flag.

Parameters:

bEnabled - when true the radiological view is displayed, when false the neurological view is displayed.

setResolutions

public void setResolutions(int index,
 float[] resolutions)

Sets the resolutions to the specific value for a specific slice indicated by the index parameter.

Parameters:

index - index that typically indicates image slice.

resolutions - the image's voxel resolutions

setResolutions

public void setResolutions(float[] resolutions)

Sets the resolutions to the specific value for a specific slice indicated by the index parameter.

Parameters:

resolutions - the image's voxel resolutions

setShort

public final void setShort(int position,
 short value)

Sets the image voxel at the specified position to the specified value.

Parameters:

position - position in one dimensional array.

value - the new voxel value.

setShort

public final void setShort(int x,
 int y,
 short value)

2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - the new voxel value.

setSigmaU

public void setSigmaU(float _sigmaU)

DOCUMENT ME! TO BE MOVED

Parameters:

_sigmaU - float

setSigmaV

public void setSigmaV(float _sigmaV)

DOCUMENT ME! TO BE MOVED

Parameters:

_sigmaV - float

setTheta

public void setTheta(float _theta)

DOCUMENT ME! TO BE MOVED

Parameters:

_theta - float

setType

public final void setType(int type)

Sets the type of data.

Parameters:

type - the type of data

setType

public final void setType(ModelStorageBase.DataType type)

Sets the type of data.

Parameters:

type - the type of data

setUByte

public final void setUByte(int position,
 short value)

Sets the image voxel at the specified position to the specified value.

Parameters:

position - position in one dimensional array

value - the new voxel value.

setUByte

public final void setUByte(int[] position,
 short value)

Sets the image voxel at the specified position to the specified value. nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

setUByte

public final void setUByte(int x,
 int y,
 short value)

Sets the image voxel at the specified position to the specified value. 2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - the new voxel value.

setUByte

public final void setUByte(int x,
 int y,
 int z,
 short value)

Sets the image voxel at the specified position to the specified value. 3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - the new voxel value.

setUByte

public final void setUByte(int x,
 int y,
 int z,
 int b,
 short value)

Sets the image voxel at the specified position to the specified value. 4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - the new voxel value.

setUInt

public final void setUInt(int position,
 long value)

Sets the image voxel at the specified position to the specified value. version of set that does NOT perform bounds checking.

Parameters:

position - position in one dimensional array

value - the new voxel value.

setUInt

public final void setUInt(int[] position,
 long value)

Sets the image voxel at the specified position to the specified value. nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

setUInt

public final void setUInt(int x,
 int y,
 long value)

Sets the image voxel at the specified position to the specified value. 2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - the new voxel value.

setUInt

public final void setUInt(int x,
 int y,
 int z,
 long value)

Sets the image voxel at the specified position to the specified value. 3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - the new voxel value.

setUInt

public final void setUInt(int x,
 int y,
 int z,
 int t,
 long value)

Sets the image voxel at the specified position to the specified value. 4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

t - t coordinate

value - the new voxel value.

setUnequalDim

public void setUnequalDim(boolean unequalDimension)

Accessor that sets the boolean telling if unequal dimesnions are allowed in a complex image. TO BE MOVED

Parameters:

unequalDimension - DOCUMENT ME!

setUShort

public final void setUShort(int position,
 int value)

Sets the image voxel at the specified position to the specified value.

Parameters:

position - position in one dimensional array

value - The value to stored in the data array.

setUShort

public final void setUShort(int[] position,
 int value)

Sets the image voxel at the specified position to the specified value. nD set data fuction where bounds checking is NOT performed.

Parameters:

position - array of coordinate values

value - data that will be stored in the data array

setUShort

public final void setUShort(int x,
 int y,
 int value)

Sets the image voxel at the specified position to the specified value. 2D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

value - the new voxel value.

setUShort

public final void setUShort(int x,
 int y,
 int z,
 int value)

Sets the image voxel at the specified position to the specified value. 3D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

value - the new voxel value.

setUShort

public final void setUShort(int x,
 int y,
 int z,
 int b,
 int value)

Sets the image voxel at the specified position to the specified value. 4D fast version of set that does NOT perform bounds checking.

Parameters:

x - x coordinate

y - y coordinate

z - z coordinate

b - b coordinate

value - the new voxel value.

allocateData

protected void allocateData()

Allocates data based on the data type and dataSize. Since this can be used to reallocate data, first set the data to null and do some garbage collecting.

getTypeMin

public static double getTypeMin(int type)

his method return the min value allowed of the type

Parameters:

type -

Returns:

getTypeMax

public static double getTypeMax(int type)

This method return the max value allowed of the type

Parameters:

type -

Returns:

calcAvgIntenStdDev

public void calcAvgIntenStdDev()

computes the avg intensity got 2d and 3d greyscale and color images

getStdDeviation

public float getStdDeviation()

getAvgInten

public float getAvgInten()

getNumPixels

public int getNumPixels()

getSumPixelInten

public double getSumPixelInten()

getAvgIntenB

public float getAvgIntenB()

getAvgIntenG

public float getAvgIntenG()

getAvgIntenR

public float getAvgIntenR()

getStdDeviationB

public float getStdDeviationB()

getStdDeviationG

public float getStdDeviationG()

getStdDeviationR

public float getStdDeviationR()

getSumPixelIntenB

public double getSumPixelIntenB()

getSumPixelIntenG

public double getSumPixelIntenG()

getSumPixelIntenR

public double getSumPixelIntenR()

computeDataSize

protected void computeDataSize()

Computes the datasize based on the type of buffer.

construct

protected void construct(ModelStorageBase.DataType type,
 int[] dimExtents)

Allocates buffer memory of the specified type.

Parameters:

type - type of buffer to allocate

dimExtents - extents of the buffer in each dimension (multiplied together produces the size of the buffer to be allocated

finalize

protected void finalize()
                 throws Throwable

Calls disposeLocal of this class to ensure this class nulls the references to global class variables so that memory will be recovered.

Overrides:

finalize in class Object

Throws:

Throwable - Throws an error if the finalization failed.

getDataSize

public int getDataSize()

Get total buffer length.