com.pixelmed.dicom

Class TiledFramesIndex

java.lang.Object

com.pixelmed.dicom.TiledFramesIndex

public class TiledFramesIndex
extends java.lang.Object

The TiledFramesIndex class ... .

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	columnForFrame
protected int[][]	index
protected boolean	isEncodedInStandardRasterOrder
protected boolean	isEncodedInStandardRasterOrderHasBeenTested
protected boolean	isSparse
protected boolean	isSparseHasBeenTested
protected int	numberOfColumnsOfTiles
protected int	numberOfFrames
protected int	numberOfRowsOfTiles
protected int[]	rowForFrame
protected double	totalPixelMatrixXOffsetInSlideCoordinateSystem
protected double	totalPixelMatrixYOffsetInSlideCoordinateSystem
protected double[][]	xOffsetInSlideCoordinateSystem
protected double[][]	yOffsetInSlideCoordinateSystem
protected double[][]	zOffsetInSlideCoordinateSystem

Constructor Summary

Constructors

Constructor and Description
TiledFramesIndex(AttributeList list) Index the tiles by row and column position
TiledFramesIndex(AttributeList list, boolean extractPhysicalOffsets, boolean buildInverseIndex, boolean ignorePlanePosition) Index the tiles by row and column position
TiledFramesIndex(AttributeList list, boolean extractPhysicalOffsets, boolean buildInverseIndex, boolean ignorePlanePosition, boolean checkPhysicalOffsets, double checkPhysicalOffsetPixelSpacingRelativeThreshold) Index the tiles by row and column position

Method Summary

Modifier and Type	Method and Description
protected void	computeRowAndColumnForFrame()
int	getColumn(int frame) Get the column number for the specified frame
int	getFrameNumber(int row, int column) Get the frame number for the tile at the specified row and column
int	getNumberOfColumnsOfTiles()
int	getNumberOfRowsOfTiles()
int	getRow(int frame) Get the row number for the specified frame
boolean	isEncodedInStandardRasterOrder() Is the encoded matrix of tiles organized in a standard raster pattern?
boolean	isSparse() Is the encoded matrix of tiles sparse?
static void	main(java.lang.String[] arg) Read the DICOM input file as a list of attributes, create and index of the tiled frames, and dump it.
java.lang.String	toString() Dump the contents of the index as a human-readable string.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

columnForFrame

protected int[] columnForFrame

index

protected int[][] index

isEncodedInStandardRasterOrder

protected boolean isEncodedInStandardRasterOrder

isEncodedInStandardRasterOrderHasBeenTested

protected boolean isEncodedInStandardRasterOrderHasBeenTested

isSparse

protected boolean isSparse

isSparseHasBeenTested

protected boolean isSparseHasBeenTested

numberOfColumnsOfTiles

protected int numberOfColumnsOfTiles

numberOfFrames

protected int numberOfFrames

numberOfRowsOfTiles

protected int numberOfRowsOfTiles

rowForFrame

protected int[] rowForFrame

totalPixelMatrixXOffsetInSlideCoordinateSystem

protected double totalPixelMatrixXOffsetInSlideCoordinateSystem

totalPixelMatrixYOffsetInSlideCoordinateSystem

protected double totalPixelMatrixYOffsetInSlideCoordinateSystem

xOffsetInSlideCoordinateSystem

protected double[][] xOffsetInSlideCoordinateSystem

yOffsetInSlideCoordinateSystem

protected double[][] yOffsetInSlideCoordinateSystem

zOffsetInSlideCoordinateSystem

protected double[][] zOffsetInSlideCoordinateSystem

Constructor Detail

TiledFramesIndex

public TiledFramesIndex(AttributeList list)
                 throws DicomException

Index the tiles by row and column position

Parameters:

list - an AttributeList for a Whole Slide Image

Throws:

DicomException - if insufficient or inconsistent information

TiledFramesIndex

public TiledFramesIndex(AttributeList list,
                        boolean extractPhysicalOffsets,
                        boolean buildInverseIndex,
                        boolean ignorePlanePosition)
                 throws DicomException

Index the tiles by row and column position

Parameters:

list - an AttributeList for a Whole Slide Image

extractPhysicalOffsets - extract the physical as well as logical position

buildInverseIndex - build the inverse index rather than waiting until it is needed

ignorePlanePosition - ignore the PlanePositionSequence and assume frame order is normal raster

Throws:

DicomException - if insufficient or inconsistent information

TiledFramesIndex

public TiledFramesIndex(AttributeList list,
                        boolean extractPhysicalOffsets,
                        boolean buildInverseIndex,
                        boolean ignorePlanePosition,
                        boolean checkPhysicalOffsets,
                        double checkPhysicalOffsetPixelSpacingRelativeThreshold)
                 throws DicomException

Index the tiles by row and column position

Parameters:

list - an AttributeList for a Whole Slide Image

extractPhysicalOffsets - extract the physical as well as logical position

buildInverseIndex - build the inverse index rather than waiting until it is needed

ignorePlanePosition - ignore the PlanePositionSequence and assume frame order is normal raster

checkPhysicalOffsets - check that the physical offsets match what is predicted from the origin, logical position and spacing

checkPhysicalOffsetPixelSpacingRelativeThreshold - threshold as fraction of pixel spacing for match

Throws:

DicomException - if insufficient or inconsistent information

Method Detail

computeRowAndColumnForFrame

protected void computeRowAndColumnForFrame()

getColumn

public int getColumn(int frame)

Get the column number for the specified frame

Parameters:

frame - the frame number from 1

Returns:

column the number of the tile along the row direction (which column of tiles), numbered from 0

Throws:

java.lang.ArrayIndexOutOfBoundsException - if frame number is beyond limits of tile array

getFrameNumber

public int getFrameNumber(int row,
                          int column)

Get the frame number for the tile at the specified row and column

Parameters:

row - the number of the tile along the column direction (which row of tiles), numbered from 0

column - the number of the tile along the row direction (which column of tiles), numbered from 0

Returns:

the frame number from 1, or 0 if no frame

Throws:

java.lang.ArrayIndexOutOfBoundsException - if row or column beyond limits of tile array

getNumberOfColumnsOfTiles

public int getNumberOfColumnsOfTiles()

getNumberOfRowsOfTiles

public int getNumberOfRowsOfTiles()

getRow

public int getRow(int frame)

Get the row number for the specified frame

Parameters:

frame - the frame number from 1

Returns:

row the number of the tile along the column direction (which row of tiles), numbered from 0

Throws:

java.lang.ArrayIndexOutOfBoundsException - if frame number is beyond limits of tile array

isEncodedInStandardRasterOrder

public boolean isEncodedInStandardRasterOrder()

Is the encoded matrix of tiles organized in a standard raster pattern?

The standard pattern is all the columns of the first row from left to right, then the second row, etc.

Returns:

true if in the standard raster order

isSparse

public boolean isSparse()

Is the encoded matrix of tiles sparse?

Returns:

true if any tile position does not have an encoded frame

main

public static void main(java.lang.String[] arg)

Read the DICOM input file as a list of attributes, create and index of the tiled frames, and dump it.

Parameters:

arg - array of one string (the filename to read and dump),

toString

public java.lang.String toString()

Dump the contents of the index as a human-readable string.

Overrides:

toString in class java.lang.Object

Returns:

the string