maspack.image.nifti

Class NiftiImage

java.lang.Object

maspack.image.nifti.NiftiImage

All Implemented Interfaces:

java.lang.Cloneable, VolumeImage, Clonable

public class NiftiImage
extends java.lang.Object
implements VolumeImage, Clonable

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NiftiImage.ImageSpace

Constructor Summary

Constructors

Constructor and Description
NiftiImage(java.lang.String title, java.io.File file)
NiftiImage(java.lang.String title, NiftiHeader header, NiftiDataBuffer buff)
NiftiImage(java.lang.String title, java.lang.String fileName)

Method Summary

Modifier and Type	Method and Description
NiftiImage	clone()
boolean	getBinary(int v, int i, int j, int k, int t)
byte	getBlue(int v, int i, int j, int k, int t)
double	getComplex128Imaginary(int v, int i, int j, int k, int t)
double	getComplex128Real(int v, int i, int j, int k, int t)
NiftiDataBuffer	getDataBuffer()
NiftiHeader.DataType	getDataType()
int	getDim(int idx)
float	getFloat32(int v, int i, int j, int k, int t)
double	getFloat64(int v, int i, int j, int k, int t)
byte	getGreen(int v, int i, int j, int k, int t)
NiftiHeader	getHeader()
short	getInt16(int v, int i, int j, int k, int t)
int	getInt32(int v, int i, int j, int k, int t)
long	getInt64(int v, int i, int j, int k, int t)
byte	getInt8(int v, int i, int j, int k, int t)
int	getNumChannels() Number of channels per the voxel (e.g.
int	getNumCols() Number of columns in the image, corresponds to image x-axis
int	getNumRows() Number of rows in the image, corresponds to image y-axis
int	getNumSlices() Number of slices in the image, corresponds to image z-axis
int	getNumTimes()
int	getNumValuesPerVoxel()
int	getNumVoxels() Number of voxels per time instance
int	getPixels(int i, int di, int ni, int j, int dj, int nj, int k, int dk, int nk, int t, int scanline, int pageline, NiftiPixelGenerator voxelator, java.nio.ByteBuffer pixels) Fills a buffer with pixel values from the image
byte	getRed(int v, int i, int j, int k, int t)
java.lang.String	getTitle()
double	getValue(int channel, int col, int row, int slice) Voxel raw value at a given column, row, slice
double	getValue(int v, int i, int j, int k, int t)
Vector3d	getVoxelSpacing()
AffineTransform3d	getVoxelTransform() Determines the most likely transform, checking if Quaternion-based exists first, then Affine, then None.
AffineTransform3d	getVoxelTransform(NiftiImage.ImageSpace method)
NiftiHeader.XFormCode	getVoxelTransformCode(NiftiImage.ImageSpace method)
int	numDimensions()
void	setTitle(java.lang.String title)

Methods inherited from class java.lang.Object

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

Constructor Detail

NiftiImage

public NiftiImage(java.lang.String title,
                  java.lang.String fileName)

NiftiImage

public NiftiImage(java.lang.String title,
                  java.io.File file)

NiftiImage

public NiftiImage(java.lang.String title,
                  NiftiHeader header,
                  NiftiDataBuffer buff)

Method Detail

setTitle

public void setTitle(java.lang.String title)

getTitle

public java.lang.String getTitle()

getVoxelTransform

public AffineTransform3d getVoxelTransform()

Determines the most likely transform, checking if Quaternion-based exists first, then Affine, then None.

Specified by:

getVoxelTransform in interface VolumeImage

Returns:

transform

getVoxelTransformCode

public NiftiHeader.XFormCode getVoxelTransformCode(NiftiImage.ImageSpace method)

getVoxelTransform

public AffineTransform3d getVoxelTransform(NiftiImage.ImageSpace method)

getVoxelSpacing

public Vector3d getVoxelSpacing()

numDimensions

public int numDimensions()

getDim

public int getDim(int idx)

getNumCols

public int getNumCols()

Description copied from interface: VolumeImage

Number of columns in the image, corresponds to image x-axis

Specified by:

getNumCols in interface VolumeImage

Returns:

number of columns

getNumRows

public int getNumRows()

Description copied from interface: VolumeImage

Number of rows in the image, corresponds to image y-axis

Specified by:

getNumRows in interface VolumeImage

Returns:

number of rows in the image

getNumSlices

public int getNumSlices()

Description copied from interface: VolumeImage

Number of slices in the image, corresponds to image z-axis

Specified by:

getNumSlices in interface VolumeImage

Returns:

number of slices

getNumTimes

public int getNumTimes()

getNumVoxels

public int getNumVoxels()

Number of voxels per time instance

Returns:

rows*cols*slices

getNumValuesPerVoxel

public int getNumValuesPerVoxel()

getDataType

public NiftiHeader.DataType getDataType()

getDataBuffer

public NiftiDataBuffer getDataBuffer()

getHeader

public NiftiHeader getHeader()

getValue

public double getValue(int v,
                       int i,
                       int j,
                       int k,
                       int t)

getFloat32

public float getFloat32(int v,
                        int i,
                        int j,
                        int k,
                        int t)

getFloat64

public double getFloat64(int v,
                         int i,
                         int j,
                         int k,
                         int t)

getComplex128Real

public double getComplex128Real(int v,
                                int i,
                                int j,
                                int k,
                                int t)

getComplex128Imaginary

public double getComplex128Imaginary(int v,
                                     int i,
                                     int j,
                                     int k,
                                     int t)

getInt64

public long getInt64(int v,
                     int i,
                     int j,
                     int k,
                     int t)

getInt32

public int getInt32(int v,
                    int i,
                    int j,
                    int k,
                    int t)

getInt16

public short getInt16(int v,
                      int i,
                      int j,
                      int k,
                      int t)

getInt8

public byte getInt8(int v,
                    int i,
                    int j,
                    int k,
                    int t)

getBinary

public boolean getBinary(int v,
                         int i,
                         int j,
                         int k,
                         int t)

getRed

public byte getRed(int v,
                   int i,
                   int j,
                   int k,
                   int t)

getGreen

public byte getGreen(int v,
                     int i,
                     int j,
                     int k,
                     int t)

getBlue

public byte getBlue(int v,
                    int i,
                    int j,
                    int k,
                    int t)

getPixels

public int getPixels(int i,
                     int di,
                     int ni,
                     int j,
                     int dj,
                     int nj,
                     int k,
                     int dk,
                     int nk,
                     int t,
                     int scanline,
                     int pageline,
                     NiftiPixelGenerator voxelator,
                     java.nio.ByteBuffer pixels)

Fills a buffer with pixel values from the image

clone

public NiftiImage clone()

Specified by:

clone in interface Clonable

Overrides:

clone in class java.lang.Object

getValue

public double getValue(int channel,
                       int col,
                       int row,
                       int slice)

Description copied from interface: VolumeImage

Voxel raw value at a given column, row, slice

Specified by:

getValue in interface VolumeImage

Parameters:

channel - channel number

col - column index

row - row index

slice - slice index

Returns:

voxel value

getNumChannels

public int getNumChannels()

Description copied from interface: VolumeImage

Number of channels per the voxel (e.g. grayscale=1, RGBA=4)

Specified by:

getNumChannels in interface VolumeImage

Returns:

number of channels