maspack.image.dicom

Class DicomImage

java.lang.Object

maspack.image.dicom.DicomImage

All Implemented Interfaces:

VolumeImage

public class DicomImage
extends java.lang.Object
implements VolumeImage

Constructor Summary

Constructors

Constructor and Description
DicomImage(java.lang.String title, DicomSlice firstSlice) Creates a new DICOM image, extracting common header information from the provided first slice.

Method Summary

Modifier and Type	Method and Description
boolean	addSlice(DicomSlice slice) Appends a slice to the current DICOM image set.
boolean	compatible(DicomSlice slice) Checks whether the provided slice has compatible image dimensions with the the current image set
void	complete() Finalize DICOM image construction
void	ensureCapacity(int cap) Ensure a minimum capacity for number of slices
double	getColSpacing()
double	getMaxIntensity()
double	getMinIntensity()
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	getPixels(int x, int y, int z, int dx, int dy, int dz, int nx, int ny, int nz, DicomPixelBuffer.PixelType type, int scanline, int pageline, DicomPixelInterpolator interp, java.nio.ByteBuffer pixels) Fills a buffer with pixel values from the image
void	getPixels(int x, int y, int z, int dx, int dy, int dz, int nx, int ny, int nz, DicomPixelBuffer.PixelType type, int scanline, int pageline, DicomPixelInterpolator interp, int[] pixels, int offset) Fills a buffer with pixel values from the image
int	getPixels(int x, int y, int z, int dx, int dy, int dz, int nx, int ny, int nz, int time, DicomPixelBuffer.PixelType type, int scanline, int pageline, DicomPixelInterpolator interp, java.nio.ByteBuffer pixels) Fills a buffer with pixel values from the image
void	getPixels(int x, int y, int z, int dx, int dy, int dz, int nx, int ny, int nz, int time, DicomPixelBuffer.PixelType type, int scanline, int pageline, DicomPixelInterpolator interp, int[] pixels, int offset) Fills a buffer with pixel values from the image
DicomPixelBuffer.PixelType	getPixelType() Determines the type of pixels stored in the image
double	getRowSpacing() Width of a row
DicomSlice	getSlice(int slice) Extracts a DICOM slice at a given index
DicomSlice	getSlice(int timeIdx, int slice) Extracts a DICOM slice at a given time point and slice index
double	getSliceSpacing() Spacing between slices, assuming constant fixed spacing
java.lang.String	getTitle()
RigidTransform3d	getTransform() Spatial location of the first slice
double	getValue(int channel, int col, int row, int slice) Voxel raw value at a given column, row, slice
AffineTransform3d	getVoxelTransform() Transform for converting integer voxel locations into spatial locations Assumes regular fixed slice spacing
int	size()
java.lang.String	toString()
void	trim() Trims the array of slices to match the number currently contained in the image

Methods inherited from class java.lang.Object

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

Constructor Detail

DicomImage

public DicomImage(java.lang.String title,
                  DicomSlice firstSlice)

Creates a new DICOM image, extracting common header information from the provided first slice. The slice is also added to the image.

Parameters:

title - title to use for DICOM image

firstSlice - the first slice, which determines header information

Method Detail

compatible

public boolean compatible(DicomSlice slice)

Checks whether the provided slice has compatible image dimensions with the the current image set

Parameters:

slice - new slice to verify

Returns:

true if compatible

addSlice

public boolean addSlice(DicomSlice slice)

Appends a slice to the current DICOM image set. The order of the image is extracted from header information contained in the slice, based on temporal and slice position indices if possible.

Returns:

true if added

ensureCapacity

public void ensureCapacity(int cap)

Ensure a minimum capacity for number of slices

Parameters:

cap - minimum number of slices to support

trim

public void trim()

Trims the array of slices to match the number currently contained in the image

complete

public void complete()

Finalize DICOM image construction

getPixelType

public DicomPixelBuffer.PixelType getPixelType()

Determines the type of pixels stored in the image

Returns:

byte grayscale, short grayscale, or byte RGB

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getPixels

public int getPixels(int x,
                     int y,
                     int z,
                     int dx,
                     int dy,
                     int dz,
                     int nx,
                     int ny,
                     int nz,
                     int time,
                     DicomPixelBuffer.PixelType type,
                     int scanline,
                     int pageline,
                     DicomPixelInterpolator interp,
                     java.nio.ByteBuffer pixels)

Fills a buffer with pixel values from the image

Parameters:

x - starting x voxel position

y - starting y voxel position

z - starting z voxel position

dx - voxel step in x

dy - voxel step in y

dz - voxel step in z

nx - number of voxels in x direction

ny - number of voxels in y direction

nz - number of voxels in z direction

time - time index

type - pixel output type

scanline - offset between x-y rows

pageline - offset between slices

interp - pixel value interpolator (shifts/scales values to appropriate range)

pixels - pixel buffer to fill

Returns:

the number of bytes written to the pixel buffer

getPixels

public int getPixels(int x,
                     int y,
                     int z,
                     int dx,
                     int dy,
                     int dz,
                     int nx,
                     int ny,
                     int nz,
                     DicomPixelBuffer.PixelType type,
                     int scanline,
                     int pageline,
                     DicomPixelInterpolator interp,
                     java.nio.ByteBuffer pixels)

Fills a buffer with pixel values from the image

Parameters:

x - starting x voxel position

y - starting y voxel position

z - starting z voxel position

dx - voxel step in x

dy - voxel step in y

dz - voxel step in z

nx - number of voxels in x direction

ny - number of voxels in y direction

nz - number of voxels in z direction

type - output pixel type

scanline - xy row offset

pageline - offset between slices

interp - pixel value interpolator (shifts/scales values to appropriate range)

pixels - pixel buffer to fill

Returns:

the number of bytes written to the pixel buffer

getPixels

public void getPixels(int x,
                      int y,
                      int z,
                      int dx,
                      int dy,
                      int dz,
                      int nx,
                      int ny,
                      int nz,
                      int time,
                      DicomPixelBuffer.PixelType type,
                      int scanline,
                      int pageline,
                      DicomPixelInterpolator interp,
                      int[] pixels,
                      int offset)

Fills a buffer with pixel values from the image

Parameters:

x - starting x voxel position

y - starting y voxel position

z - starting z voxel position

dx - voxel step in x

dy - voxel step in y

dz - voxel step in z

nx - number of voxels in x direction

ny - number of voxels in y direction

nz - number of voxels in z direction

time - time index

type - pixel output type

scanline - offset between x-y rows

pageline - offset between slices

interp - pixel value interpolator (shifts/scales values to appropriate range)

pixels - pixel buffer to fill

offset - offset in pixel buffer to populate

getPixels

public void getPixels(int x,
                      int y,
                      int z,
                      int dx,
                      int dy,
                      int dz,
                      int nx,
                      int ny,
                      int nz,
                      DicomPixelBuffer.PixelType type,
                      int scanline,
                      int pageline,
                      DicomPixelInterpolator interp,
                      int[] pixels,
                      int offset)

Fills a buffer with pixel values from the image

Parameters:

x - starting x voxel position

y - starting y voxel position

z - starting z voxel position

dx - voxel step in x

dy - voxel step in y

dz - voxel step in z

nx - number of voxels in x direction

ny - number of voxels in y direction

nz - number of voxels in z direction

type - output pixel type

scanline - xy row offset

pageline - offset between slices

interp - pixel value interpolator (shifts/scales values to appropriate range)

pixels - pixel buffer to fill

offset - offset in pixel buffer to populate

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 y-positions (rows) in each image slice

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 x-positions (columns) in each image slice

getNumTimes

public int getNumTimes()

Returns:

Number of time instances, each representing a 3D DICOM image stack

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 (z-)slices in a single 3D DICOM image stack (for DICOM images with multiple time points, assumes all times have the same number of slices as the image at the first time index)

size

public int size()

Returns:

the total number of slices, including all times

getRowSpacing

public double getRowSpacing()

Width of a row

Returns:

row spacing

getColSpacing

public double getColSpacing()

getSliceSpacing

public double getSliceSpacing()

Spacing between slices, assuming constant fixed spacing

Returns:

slice spacing

getMaxIntensity

public double getMaxIntensity()

Returns:

Maximum intensity value in the entire image set, useful for adjusting an intensity window for display

getMinIntensity

public double getMinIntensity()

Returns:

Minimum intensity value in the entire image set, useful for adjusting an intensity window for display

getSlice

public DicomSlice getSlice(int slice)

Extracts a DICOM slice at a given index

Parameters:

slice - index of slice

Returns:

the DICOM slice at the given index

getSlice

public DicomSlice getSlice(int timeIdx,
                           int slice)

Extracts a DICOM slice at a given time point and slice index

Parameters:

timeIdx - time point (identifies 3D stack)

slice - slice index (identifies z position in stack)

Returns:

the appropriate DICOM slice

getTransform

public RigidTransform3d getTransform()

Spatial location of the first slice

Returns:

the 3D transform of the voxel (0,0,0) in the DICOM image stack

getVoxelTransform

public AffineTransform3d getVoxelTransform()

Transform for converting integer voxel locations into spatial locations Assumes regular fixed slice spacing

Specified by:

getVoxelTransform in interface VolumeImage

Returns:

the 3D affine transform for converting voxels to spatial locations

getTitle

public java.lang.String getTitle()

Returns:

the title of the image

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