java.lang.Object
- gov.nih.mipav.model.structures.ModelSerialCloneable
- - gov.nih.mipav.model.structures.ModelStorageBase

All Implemented Interfaces:

java.io.Serializable, java.lang.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 class ModelStorageBase.DataType

Field Summary

Fields
Modifier and Type	Field	Description
`static 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 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 java.lang.String`	`ARGB_FLOAT_STRING`	Used to indicate, as a String, that the data buffer is of type color (ARGB - floats).
`static java.lang.String`	`ARGB_STRING`	Used to indicate, as a String, that the data buffer is of type color (ARGB - unsigned bytes).
`static int`	`ARGB_UINTEGER`
`static java.lang.String`	`ARGB_UINTEGER_STRING`
`static 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 java.lang.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 int`	`BOOLEAN`	Used to indicate that the data buffer is of type Boolean (1 bit per voxel).
`static java.lang.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 java.lang.String[]`	`bufferTypeStr`	Deprecated. should use enums directly
`static int`	`BYTE`	Used to indicate that the data buffer is of type signed byte (8 bits per voxel).
`static java.lang.String`	`BYTE_STRING`	Used to indicate, as a String, that the data buffer is of type byte.
`static int`	`COMPLEX`	Used to indicate that the data buffer is of complex type floats (2 x 64 bits per voxel).
`static java.lang.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 int`	`DCOMPLEX`	Used to indicate that the data buffer is of complex type of doubles (2 x 128 bits per voxel).
`static java.lang.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 int`	`DOUBLE`	Used to indicate that the data buffer is of type double (64 bits per voxel).
`static java.lang.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 int`	`FLOAT`	Used to indicate that the data buffer is of type float (32 bits per voxel).
`static java.lang.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 int`	`INTEGER`	Used to indicate that the data buffer is of type signed integer (32 bits per voxel).
`static java.lang.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 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 int`	`LONG`	Used to indicate that the data buffer is of type signed long integer (64 bits per voxel).
`static java.lang.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 java.util.Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA>`	`m_kColorVector`	Surface color vector. - TO BE MOVED - redesigned
`private java.util.Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA[]>`	`m_kMaskColorVector`	Surface mask color vector. - TO BE MOVED - redesigned
`private java.util.Vector<java.util.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 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 int`	`RW_LOCKED`	Used to indicate that the buffer is locked from reading.
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`static int`	`SHORT`	Used to indicate that the data buffer is of type signed short (16 bits per voxel).
`static java.lang.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 int`	`TAYLOR`	Used to indicate Taylor series interpolation.
`private float`	`theta`	DOCUMENT ME!
`static int`	`UBYTE`	Used to indicate that the data buffer is of type unsigned byte (8 bits per voxel).
`static java.lang.String`	`UBYTE_STRING`	Used to indicate, as a String, that the data buffer is of type unsigned byte.
`static int`	`UINTEGER`	Used to indicate that the data buffer is of type unsigned integer (32 bits per voxel).
`static java.lang.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 int`	`UNLOCKED`	Used to indicate that the buffer is unlocked and can be writen to or read from.
`static int`	`USHORT`	Used to indicate that the data buffer is of type unsigned short (16 bits per voxal).
`static java.lang.String`	`USHORT_STRING`	Used to indicate, as a String, that the data buffer is of type unsigned short.
`static 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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addSurfaceMask(int index, java.util.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.
`java.lang.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.
`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.
`float[]`	`export(int orientation, int tSlice, int slice, float[] values, boolean bMask)`	Exports data based on the mapping from ModelImage space to Patient space.
`void`	`exportComplexData(int start, int length, float[] valuesR, float[] valuesI)`	Export data to the real values and the images values arrays.
`void`	`exportComplexSliceXY(int slice, float[] values, boolean logMagDisplay)`	Export XY slice magnitude data into values array.
`java.lang.Object`	`exportData(int start, int length)`	Export data into values array, in the native type of the model image.
`void`	`exportData(int start, int length, byte[] values)`	Export data into values array.
`void`	`exportData(int start, int length, double[] values)`	Export data in values array.
`void`	`exportData(int start, int length, float[] values)`	Export data to values array.
`void`	`exportData(int start, int length, int[] values)`	Export data into values array.
`void`	`exportData(int start, int length0, int length1, float[] values)`	export data to values array.
`void`	`exportData(int start, int length, long[] values)`	Export data into values array.
`void`	`exportData(int start, int length, short[] values)`	Export data into values array.
`void`	`exportData(int start, int length, java.lang.Number[] values)`	Export data into values array.
`void`	`exportData(int start, int length, java.util.BitSet values)`	Export data into values array.
`void`	`exportDataNoLock(int start, int length, byte[] values)`	Export data into values array WITHOUT locking.
`void`	`exportDataNoLock(int start, int length, double[] values)`	export data into values array WITHOUT locking.
`void`	`exportDataNoLock(int start, int length, float[] values)`	export data in values array WITHOUT using locking.
`void`	`exportDataNoLock(int start, int length, int[] values)`	Export data into values array WITHOUT locking.
`void`	`exportDataNoLock(int start, int length, long[] values)`	export data into values array WITHOUT locking.
`void`	`exportDataNoLock(int start, int length, short[] values)`	Export data into values array WITHOUT locking.
`void`	`exportDataNoLock(int start, int length, java.lang.Number[] values)`	export data into values array WITHOUT locking.
`void`	`exportDataNoLock(int start, int length, java.util.BitSet values)`	export data into values array WITHOUT locking.
`void`	`exportDComplexData(int start, int length, double[] valuesR, double[] valuesI)`	Export data to the real values and the imaginary values arrays.
`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.
`void`	`exportDiagonal(int tSlice, int slice, int[] extents, WildMagic.LibFoundation.Mathematics.Vector3f[] verts, float[] values, boolean bInterpolate, java.util.BitSet imageMask, java.util.Vector<java.util.BitSet> surfaceMask, boolean[] surfaceValues)`
`void`	`exportDiagonal(java.util.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.
`void`	`exportDMagData(int start, int length, double[] values)`	Export magnitude data to values array.
`void`	`exportMagData(int start, int length, double[] values)`	export magnitude data to values array.
`void`	`exportMagData(int start, int length, float[] values)`	export magnitude data to values array.
`java.lang.Object`	`exportRGBData(int offset, int start, int length)`	export data in values array.
`void`	`exportRGBData(int offset, int start, int length, byte[] values)`	export data in values array.
`void`	`exportRGBData(int offset, int start, int length, double[] values)`	export data in values array.
`void`	`exportRGBData(int offset, int start, int length, float[] values)`	export data in values array.
`void`	`exportRGBData(int offset, int start, int length, short[] values)`	export data in values array.
`void`	`exportRGBDataNoLock(int offset, int start, int length, double[] values)`	Export data in values array WITHOUT using locking.
`void`	`exportRGBDataNoLock(int offset, int start, int length, float[] values)`	Export data in values array WITHOUT using locking.
`void`	`exportSliceXY(int slice, byte[] values)`	Export XY slice into values array.
`void`	`exportSliceXY(int slice, double[] values)`	export XY slice into values array.
`void`	`exportSliceXY(int slice, float[] values)`	export XY slice into values array.
`void`	`exportSliceXY(int slice, int[] values)`	Export XY slice into values array.
`void`	`exportSliceXY(int slice, long[] values)`	export XY slice into values array.
`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.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`findMax(int tSlice, int slice, WildMagic.LibFoundation.Mathematics.Vector3f[] verts, float diameter, boolean bInterpolate)`
`java.lang.Number`	`get(int position)`	function to get data where bounds checking is performed.
`java.lang.Number`	`get(int[] position)`	nD get data fuction where bounds checking is performed.
`java.lang.Number`	`get(int x, int y)`	2D get data fuction where bounds checking is performed.
`java.lang.Number`	`get(int x, int y, int z)`	3D get data fuction where bounds checking is performed.
`java.lang.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.
`java.lang.Number`	`getBiLinear(float x, float y)`	version of get that performs bi-linear interpoloation.
`boolean`	`getBoolean(int position)`	Version of get that does NOT perform bounds checking.
`boolean`	`getBoolean(int[] position)`	n-Dimensional get data fuction where bounds checking is NOT performed.
`boolean`	`getBoolean(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`boolean`	`getBoolean(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`boolean`	`getBoolean(int x, int y, int z, int b)`	4D get data fuction where bounds checking is NOT performed.
`static java.lang.String`	`getBufferTypeStr(int type)`	Returns the string for a particular buffer type.
`byte`	`getByte(int position)`	Version of get that does NOT perform bounds checking
`byte`	`getByte(int[] position)`	nD get data fuction where bounds checking is NOT performed.
`byte`	`getByte(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`byte`	`getByte(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`byte`	`getByte(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`byte`	`getByteBiLinear(float x, float y)`	version of get that performs bi-linear interpoloation.
`byte`	`getByteTriLinear(float x, float y, float z)`	version of get that performs tri-linear interpoloation.
`java.lang.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.
`ModelStorageBase.DataType`	`getDataType()`	Accessor that returns the image buffer type as an enum.
`double`	`getDouble(int position)`	The interpolated value from the data array.ersion of get that does NOT perform bounds checking.
`double`	`getDouble(int[] position)`	nD get data fuction where bounds checking is NOT performed.
`double`	`getDouble(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`double`	`getDouble(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`double`	`getDouble(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`double`	`getDoubleBiLinear(float x, float y)`	version of get that performs bi-linear interpoloation.
`double`	`getDoubleTriLinear(float x, float y, float z)`	version of get that performs tri-linear interpoloation.
`int[]`	`getExtents()`	Accessor that returns the extents of the image.
`int[]`	`getExtents(int orientation)`	Returns the image extents translated into the Patient-Coordinate systsm:
`int[]`	`getExtents(int[] aiAxisOrder)`	Returns the image extents translated into the Patient-Coordinate system:
`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.
`int`	`getFilterType()`	returns type of filter - low, high, bandpass, or bandstop. - TO BE MOVED
`float`	`getFloat(int position)`	Version of get that does NOT perform bounds checking.
`float`	`getFloat(int[] position)`	nD get data function where bounds checking is NOT performed.
`float`	`getFloat(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`float`	`getFloat(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`float`	`getFloat(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`float`	`getFloatBiLinear(float x, float y)`	version of get that performs bi-linear interpoloation.
`float`	`getFloatC(int x, int y, int c)`	2D color get data fuction where bounds checking is NOT performed.
`float`	`getFloatC(int x, int y, int z, int c)`	3D color get data fuction where bounds checking is NOT performed.
`float`	`getFloatC(int x, int y, int z, int t, int c)`	4D get data fuction where bounds checking is NOT performed.
`float`	`getFloatTriLinear(float x, float y, float z)`	version of get that performs tri-linear interpoloation.
`float`	`getFloatTriLinearBounds(float x, float y, float z)`	Get a value using tri-linear interpoloation.
`float`	`getFloatTriLinearBounds(float x, float y, float z, int c)`	Get a value using tri-linear interpoloation.
`float`	`getFloatTriLinearBoundsTime(float x, float y, float z, int t)`	Get a value using tri-linear interpoloation.
`float`	`getFreq1()`	returns frequency 1 of filter.
`float`	`getFreq2()`	returns frequency 2 of filter.
`float`	`getFreqU()`	returns frequency U of filter.
`float`	`getFreqV()`	returns frequency V of filter.
`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, ...).
`int`	`getInt(int position)`	Version of get that does NOT perform bounds checking.
`int`	`getInt(int[] position)`	nD get data fuction where bounds checking is NOT performed.
`int`	`getInt(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`int`	`getInt(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`int`	`getInt(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`int`	`getIntBiLinear(float x, float y)`	version of get that performs bi-linear interpoloation.
`int`	`getIntTriLinear(float x, float y, float z)`	Version of get that performs tri-linear interpoloation.
`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.
`long`	`getLong(int position)`	Version of get that does NOT perform bounds checking.
`long`	`getLong(int[] position)`	nD get data fuction where bounds checking is NOT performed.
`long`	`getLong(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`long`	`getLong(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`long`	`getLong(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`long`	`getLongBiLinear(float x, float y)`	version of get that performs bi-linear interpoloation.
`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.
`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:
`boolean`	`getOriginalCropCheckbox()`	DOCUMENT ME!
`boolean`	`getOriginalDoCrop()`	DOCUMENT ME!
`int[]`	`getOriginalEnd()`	DOCUMENT ME!
`double`	`getOriginalEpsilon()`
`int[]`	`getOriginalExtents()`	Accessor that returns the original extents of the image.
`int`	`getOriginalFilterConstruction()`	returns integer telling filter construction method.
`int`	`getOriginalFilterOrder()`	returns integer telling filter order. - TO BE MOVED
`int`	`getOriginalKernelDimension()`	returns kernel diameter chosen on forward FFT.
`double`	`getOriginalRs()`	Decibels stopband is down in Elliptic
`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:
`short`	`getShort(int position)`	Version of get that does NOT perform bounds checking.
`short`	`getShort(int[] position)`	nD get data fuction where bounds checking is NOT performed.
`short`	`getShort(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`short`	`getShort(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`short`	`getShort(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`short`	`getShortBiLinear(float x, float y)`	version of get that performs bi-linear interpoloation.
`short`	`getShortTriLinear(float x, float y, float z)`	version of get that performs tri-linear interpoloation.
`float`	`getSigmaU()`	returns standard deviation U of filter.
`float`	`getSigmaV()`	returns standard deviation V of filter.
`int`	`getSize()`	Accessor that returns the total size(length) of the data array.
`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()`
`java.util.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.
`float`	`getTheta()`	Returns roation angle theta in radians of filter.
`java.lang.Number`	`getTriLinear(float x, float y, float z)`	version of get that performs tri-linear interpoloation.
`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
`java.lang.String`	`getTypeString()`	Accessor that returns the image type.
`short`	`getUByte(int position)`	version of get that does NOT perform bounds checking.
`short`	`getUByte(int[] position)`	nD get data fuction where bounds checking is NOT performed.
`short`	`getUByte(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`short`	`getUByte(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`short`	`getUByte(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`short`	`getUByteBiLinear(float x, float y)`	Version of get that performs bi-linear interpoloation.
`short`	`getUByteTriLinear(float x, float y, float z)`	Version of get that performs tri-linear interpoloation.
`long`	`getUInt(int position)`	version of get that does NOT perform bounds checking.
`long`	`getUInt(int[] position)`	nD get data fuction where bounds checking is NOT performed.
`long`	`getUInt(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`long`	`getUInt(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`long`	`getUInt(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`long`	`getUIntBiLinear(float x, float y)`	version of get that performs bi-linear interpoloation.
`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:
`int`	`getUShort(int position)`	version of get that does NOT perform bounds checking.
`int`	`getUShort(int[] position)`	nD get data fuction where bounds checking is NOT performed.
`int`	`getUShort(int x, int y)`	2D get data fuction where bounds checking is NOT performed.
`int`	`getUShort(int x, int y, int z)`	3D get data fuction where bounds checking is NOT performed.
`int`	`getUShort(int x, int y, int z, int t)`	4D get data fuction where bounds checking is NOT performed.
`int`	`getUShortBiLinear(float x, float y)`	Version of get that performs bi-linear interpoloation.
`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:
`void`	`importComplexData(int start, float[] valuesR, float[] valuesI, boolean mmFlag, boolean logMagDisplay)`	import Complex data (in 2 float units) into data array.
`void`	`importData(int start, boolean[] values, boolean mmFlag)`	Import boolean data into data array.
`void`	`importData(int start, byte[] values, boolean mmFlag)`	Import byte data into data array.
`void`	`importData(int start, double[] values, boolean mmFlag)`	import double data into data array.
`void`	`importData(int start, float[] values, boolean mmFlag)`	import float data into data array.
`void`	`importData(int start, int[] values, boolean mmFlag)`	import integer data into data array.
`void`	`importData(int start, long[] values, boolean mmFlag)`	import long data into data array.
`void`	`importData(int start, short[] values, boolean mmFlag)`	import short data into data array.
`void`	`importData(int start, java.lang.Number[] values, boolean mmFlag)`	import Number data into data array.
`void`	`importData(int start, java.util.BitSet values, boolean mmFlag)`	Import boolean (BitSet) data into data array.
`void`	`importData(java.lang.Object value_array)`	Import Object.
`void`	`importDComplexData(int start, double[] valuesR, double[] valuesI, boolean mmFlag, boolean logMagDisplay)`	import Complex data (in 2 double units) into data array.
`void`	`importRGBData(int color, int alphaIndexStart, byte[] values, boolean mmFlag)`	Import byte data into data array.
`void`	`importRGBData(int color, int alphaIndexStart, float[] values, boolean mmFlag)`	import float data into data array.
`void`	`importRGBData(int color, int alphaIndexStart, short[] values, boolean mmFlag)`	Import byte data into data array.
`void`	`importUData(int start, int[] values, boolean mmFlag)`	import int data into data array.
`void`	`importUData(int start, long[] values, boolean mmFlag)`	import int data into data array.
`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.
`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.
`java.util.BitSet[]`	`removeSurfaceMasks()`	Returns the array of BitSet masks for backup.
`void`	`restoreSurfaceMasks(java.util.BitSet[] masks)`	Restores the mask list from the array.
`void`	`set(int[] position, boolean value)`	nD set data fuction where bounds checking is NOT performed.
`void`	`set(int[] position, byte value)`	nD set data fuction where bounds checking is NOT performed.
`void`	`set(int[] position, double value)`	nD set data fuction where bounds checking is NOT performed.
`void`	`set(int[] position, float value)`	nD set data fuction where bounds checking is NOT performed.
`void`	`set(int[] position, int value)`	nD set data fuction where bounds checking is NOT performed.
`void`	`set(int[] position, long value)`	nD set data fuction where bounds checking is NOT performed.
`void`	`set(int[] position, short value)`	nD set data fuction where bounds checking is NOT performed.
`boolean`	`set(int[] position, java.lang.Number value)`	nD set data fuction where bounds checking is performed.
`void`	`set(int position, boolean value)`	version of set that does NOT perform bounds checking
`void`	`set(int position, byte value)`	Version of set that does NOT perform bounds checking.
`void`	`set(int position, double value)`	version of set that does NOT perform bounds checking.
`void`	`set(int position, float value)`	version of set that does NOT perform bounds checking.
`void`	`set(int position, int value)`	Version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, boolean value)`	2D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, byte value)`	2D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, double value)`	2D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, float value)`	2D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int value)`	2D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, boolean value)`	3D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, byte value)`	3D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, double value)`	3D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, float value)`	3D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, int value)`	3D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, int b, boolean value)`	4D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, int b, byte value)`	4D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, int b, double value)`	4D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, int b, float value)`	4D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, int b, int value)`	4D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, int b, long value)`	4D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, int b, short value)`	4D fast version of set that does NOT perform bounds checking.
`boolean`	`set(int x, int y, int z, int b, java.lang.Number value)`	4D get data fuction where bounds checking is performed.
`void`	`set(int x, int y, int z, long value)`	3D fast version of set that does NOT perform bounds checking.
`void`	`set(int x, int y, int z, short value)`	3D fast version of set that does NOT perform bounds checking.
`boolean`	`set(int x, int y, int z, java.lang.Number value)`	3D set data fuction where bounds checking is performed.
`void`	`set(int x, int y, long value)`	2D fast version of set that does NOT perform bounds checking.
`boolean`	`set(int x, int y, java.lang.Number value)`	2D get data fuction where bounds checking is performed.
`void`	`set(int position, long value)`	version of set that does NOT perform bounds checking.
`boolean`	`set(int position, java.lang.Number value)`	Set that does perform bounds checking.
`void`	`setAll(byte value)`	Sets the entire buffer to value passed to this method.
`void`	`setAll(double value)`	Sets the entire buffer to value passed to this method.
`void`	`setAll(float value)`	Sets the entire buffer to value passed to this method.
`void`	`setAll(int value)`	Sets the entire buffer to value passed to this method.
`void`	`setAll(short value)`	Sets the entire buffer to value passed to this method.
`void`	`setAllUByte(short value)`	Sets the entire buffer to value passed to this method.
`void`	`setAllUShort(int value)`	Sets the entire buffer to value passed to this method.
`void`	`setC(int position, int c, float value)`	color version of setC that does NOT perform bounds checking.
`void`	`setC(int x, int y, int c, float value)`	2D fast color version of set that does NOT perform bounds checking.
`void`	`setC(int x, int y, int z, int c, float value)`	3D fast color version of set that does NOT perform bounds checking.
`boolean`	`setC(int x, int y, int z, int c, java.lang.Number value)`	3D color set data fuction where bounds checking is performed.
`boolean`	`setC(int position, int color, java.lang.Number value)`	Sets the entire buffer to value passed to this method.
`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.
`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.
`void`	`setShort(int x, int y, short value)`	2D fast version of set that does NOT perform bounds checking.
`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!
`void`	`setType(int type)`	Sets the type of data.
`void`	`setType(ModelStorageBase.DataType type)`	Sets the type of data.
`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.
`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.
`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.
`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.
`void`	`setUByte(int position, short value)`	Sets the image voxel at the specified position to the specified value.
`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.
`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.
`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.
`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.
`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.
`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.
`void`	`setUShort(int position, int value)`	Sets the image voxel at the specified position to the specified value.
`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.
`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.
`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 Detail
  - 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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.String ARGB_UINTEGER_STRING
```
    See Also:
    
    Constant Field Values
  - ARGB_FLOAT_STRING
```
public static final java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.util.Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA> m_kColorVector
```
    Surface color vector. - TO BE MOVED - redesigned
  - m_kMaskColorVector
```
private final java.util.Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA[]> m_kMaskColorVector
```
    Surface mask color vector. - TO BE MOVED - redesigned
  - m_kMaskVector
```
private final java.util.Vector<java.util.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 Detail
  - 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 Detail
  - getBufferTypeStr
```
public static java.lang.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,
                           java.util.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 java.lang.Object clone()
```
    Copies the object.
    
    Overrides:
    
    clone in class ModelSerialCloneable
    
    Returns:
    
    Returns the cloned object.
  - convertToFloat
```
public void convertToFloat()
                    throws java.io.IOException
```
    Disposes of old data and constructs a new buffer of the user specific type if the image in NOT locked.
    
    Throws:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportComplexSliceXY
```
public final void exportComplexSliceXY(int slice,
                                       float[] values,
                                       boolean logMagDisplay)
                                throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportData
```
public final java.lang.Object exportData(int start,
                                         int length)
                                  throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(java.lang.Object value_array)
                      throws java.io.IOException
```
    Import Object. Imports Object array that is exported with the exportData function.
    
    Parameters:
    
    value_array - Object storing data.
    
    Throws:
    
    java.io.IOException
  - exportData
```
public final void exportData(int start,
                             int length,
                             java.lang.Number[] values)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportData
```
public final void exportData(int start,
                             int length,
                             java.util.BitSet values)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportData
```
public final void exportData(int start,
                             int length,
                             byte[] values)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportData
```
public final void exportData(int start,
                             int length,
                             short[] values)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportData
```
public final void exportData(int start,
                             int length,
                             int[] values)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportData
```
public final void exportData(int start,
                             int length,
                             long[] values)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportData
```
public final void exportData(int start,
                             int length,
                             float[] values)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportData
```
public final void exportData(int start,
                             int length,
                             double[] values)
                      throws java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportDataNoLock
```
public final void exportDataNoLock(int start,
                                   int length,
                                   java.lang.Number[] values)
                            throws java.io.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:
    
    java.io.IOException - Throws an error when there is a bounds error.
  - exportDataNoLock
```
public final void exportDataNoLock(int start,
                                   int length,
                                   java.util.BitSet values)
                            throws java.io.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:
    
    java.io.IOException - Throws an error when there is a bounds error.
  - exportDataNoLock
```
public final void exportDataNoLock(int start,
                                   int length,
                                   byte[] values)
                            throws java.io.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:
    
    java.io.IOException - Throws an error when there is a bounds error.
  - exportDataNoLock
```
public final void exportDataNoLock(int start,
                                   int length,
                                   short[] values)
                            throws java.io.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:
    
    java.io.IOException - Throws an error when there is a bounds error.
  - exportDataNoLock
```
public final void exportDataNoLock(int start,
                                   int length,
                                   int[] values)
                            throws java.io.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:
    
    java.io.IOException - Throws an error when there is a bounds error.
  - exportDataNoLock
```
public final void exportDataNoLock(int start,
                                   int length,
                                   long[] values)
                            throws java.io.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:
    
    java.io.IOException - Throws an error when there is a bounds error.
  - exportDataNoLock
```
public final void exportDataNoLock(int start,
                                   int length,
                                   float[] values)
                            throws java.io.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:
    
    java.io.IOException - Throws an error when there is a bounds error.
  - exportDataNoLock
```
public final void exportDataNoLock(int start,
                                   int length,
                                   double[] values)
                            throws java.io.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:
    
    java.io.IOException - Throws an error when there is a bounds error.
  - exportDComplexData
```
public final void exportDComplexData(int start,
                                     int length,
                                     double[] valuesR,
                                     double[] valuesI)
                              throws java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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,
                                 java.util.BitSet imageMask,
                                 java.util.Vector<java.util.BitSet> surfaceMask,
                                 boolean[] surfaceValues)
                          throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - exportDiagonal
```
public final void exportDiagonal(java.util.BitSet duplicateMask,
                                 int tSlice,
                                 int slice,
                                 int[] extents,
                                 WildMagic.LibFoundation.Mathematics.Vector3f[] verts,
                                 float diameter,
                                 boolean bSetZero,
                                 float[] values,
                                 boolean bInterpolate)
                          throws java.io.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:
    
    java.io.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 java.io.IOException
```
    Throws:
    
    java.io.IOException
  - exportDMagData
```
public final void exportDMagData(int start,
                                 int length,
                                 double[] values)
                          throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportMagData
```
public final void exportMagData(int start,
                                int length,
                                float[] values)
                         throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportMagData
```
public final void exportMagData(int start,
                                int length,
                                double[] values)
                         throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportRGBData
```
public final java.lang.Object exportRGBData(int offset,
                                            int start,
                                            int length)
                                     throws java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportSliceXY
```
public final void exportSliceXY(int slice,
                                byte[] values)
                         throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportSliceXY
```
public final void exportSliceXY(int slice,
                                short[] values)
                         throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportSliceXY
```
public final void exportSliceXY(int slice,
                                int[] values)
                         throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportSliceXY
```
public final void exportSliceXY(int slice,
                                long[] values)
                         throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportSliceXY
```
public final void exportSliceXY(int slice,
                                float[] values)
                         throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - exportSliceXY
```
public final void exportSliceXY(int slice,
                                double[] values)
                         throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - get
```
public final java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.util.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 java.lang.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 java.lang.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 java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             java.lang.Number[] values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             java.util.BitSet values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             boolean[] values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             byte[] values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             short[] values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             int[] values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             long[] values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             float[] values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importData
```
public final void importData(int start,
                             double[] values,
                             boolean mmFlag)
                      throws java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importUData
```
public final void importUData(int start,
                              short[] values,
                              boolean mmFlag)
                       throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importUData
```
public final void importUData(int start,
                              int[] values,
                              boolean mmFlag)
                       throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - importUData
```
public final void importUData(int start,
                              long[] values,
                              boolean mmFlag)
                       throws java.io.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:
    
    java.io.IOException - Throws an error when there is a locking or bounds error.
  - reallocate
```
public void reallocate(int type)
                throws java.io.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:
    
    java.io.IOException - throws an exception if the image model is locked.
  - reallocate
```
public void reallocate(int[] dimExtents)
                throws java.io.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:
    
    java.io.IOException - throws an exception if the image model is locked.
  - reallocate
```
public void reallocate(int type,
                       int[] dimExtents)
                throws java.io.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:
    
    java.io.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 java.util.BitSet[] removeSurfaceMasks()
```
    Returns the array of BitSet masks for backup.
    
    Returns:
    
    the BitSet mask array.
  - restoreSurfaceMasks
```
public void restoreSurfaceMasks(java.util.BitSet[] masks)
```
    Restores the mask list from the array.
    
    Parameters:
    
    masks - array of BitSet masks
  - set
```
public final boolean set(int position,
                         java.lang.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,
                         java.lang.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.
    
    position - The index into the data array.
    
    value - The value to stored in 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,
                         java.lang.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,
                         java.lang.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,
                         java.lang.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,
                          java.lang.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,
                          java.lang.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 java.io.IOException
```
    Sets the lockFlag to protect data. When the flag is set no other processes can read or write the data
    
    Throws:
    
    java.io.IOException - Throws an error if image is already locked.
  - setLock
```
public final void setLock(int lockType)
                   throws java.io.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:
    
    java.io.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 java.lang.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 java.lang.Object
    
    Throws:
    
    java.lang.Throwable - Throws an error if the finalization failed.
  - getDataSize
```
public int getDataSize()
```
    Get total buffer length.

Class ModelStorageBase

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

UNLOCKED

RW_LOCKED

W_LOCKED

NEAREST

LINEAR

TAYLOR

BOOLEAN

BYTE

UBYTE

SHORT

USHORT

INTEGER

UINTEGER

LONG

FLOAT

DOUBLE

ARGB

ARGB_USHORT

ARGB_FLOAT

ARGB_UINTEGER

COMPLEX

DCOMPLEX

BOOLEAN_STRING

BYTE_STRING

UBYTE_STRING

SHORT_STRING

USHORT_STRING

INTEGER_STRING

LONG_STRING

FLOAT_STRING

DOUBLE_STRING

ARGB_STRING

ARGB_USHORT_STRING

ARGB_UINTEGER_STRING

ARGB_FLOAT_STRING

COMPLEX_STRING

DCOMPLEX_STRING

UINTEGER_STRING

bufferTypeStr

fileInfo

lastMin

lastMax

bufferType

data

dataSize

dimExtents

dimOriginalExtents

filterType

freq1

freq2

freqU

freqV

haveWindowed

image25D

lockStatus

logMagDisp

m_bConvolve

m_bRadiologicalView

m_kColorVector

m_kMaskColorVector

m_kMaskVector

min

max

minA

maxA

minR

maxR

minG

maxG

minB

maxB