Package gov.nih.mipav.model.file

Class FileCOR

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileCOR

public class FileCOR
extends FileBase

FreeSurfer COR files are used to store 3 dimensional unsigned byte data. Suppose the file base name is table. There is a header file named table-.info/and or table-.info~ which has the header information in ascii. A separate unsigned byte file exists for each slice of the 3D image - table-001, table-002, and so on until the last slice. The default is to have xDim = yDim = zDim = 256 and xResolution = yResolution = zResolution = 0.001 meter. Note that all distances in a COR file represent meters.

The header fields are as follows: imnr0 the first slice number imnr1 the last slice number ptype the data type; 2 for unsigned byte x the x dimension y the y dimension fov the field of view thick the z resolution psiz = a common value for both the x and y resolutions locatn location strtx the minimum x value in meters endx the maximum x value in meters strty the minimum y value in meters endy the maximum y value in meters strtz the minimum z value in meters endz the maximum z value in meters tr T_r te T_e ti T_i xform transform file ras_good_file = 1 if the orientation fields are set, 0 otherwise x_ras x axis orientation y_ras y axis orientation z_ras z axis orientation c_ras volume center coordinates If orientation information is missing, the file is assumed to be coronal with z axis = R to L, y axis = S to I, and z axis = P to A. readInfoImage reads in the header information from the set of FreeSurfer COR volume images and then readImage is called once for each slice that must be read from a COR image file set.

Field Summary

Fields

Modifier and Type	Field	Description
private java.io.File	file	DOCUMENT ME!
private java.lang.String	fileDir	DOCUMENT ME!
private FileInfoCOR	fileInfo	DOCUMENT ME!
private java.lang.String	fileName	DOCUMENT ME!
private boolean	foundEOF	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private int[]	imageExtents	DOCUMENT ME!
private int	imageOrientation	DOCUMENT ME!
private float[]	imgBuffer	DOCUMENT ME!
private float[]	imgResols	DOCUMENT ME!
private ModelLUT	LUT	DOCUMENT ME!
private int[]	orient	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.file.FileBase

BIG_ENDIAN, bitsPerPixel, fileNames, LITTLE_ENDIAN, pBarVisible, raFile, READ, READ_WRITE

Constructor Summary

Constructors

Constructor	Description
FileCOR(java.lang.String fileName, java.lang.String fileDir)	COR reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
FileInfoBase	getFileInfo()	Accessor that returns the file info.
float[]	getImageBuffer()	Accessor that returns the image buffer.
ModelLUT	getModelLUT()	Rreturns LUT if defined.
private java.lang.String[]	parse(java.lang.String inString)	DOCUMENT ME!
void	readImage(int length)	This method reads one slice from the file into byteBuffer and then transfers into the float array imgBuffer.
void	readInfoImage()	DOCUMENT ME!
private java.lang.String	readLine()	Reads lines of the file until a nonnull String results or the end of the file is reached.
void	setFileName(java.lang.String fName)	Accessor to set the file name (used for reading COR multiFile).
void	writeImage(ModelImage image, FileWriteOptions options)	Writes a COR format type image.

Methods inherited from class gov.nih.mipav.model.file.FileBase

addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, floatToBytes, getBufferDouble, getBufferFloat, getBufferInt, getBufferLong, getBufferShort, getBufferUShort, getDataType, getDouble, getFloat, getInt, getLong, getProgressChangeListeners, getRaFile, getSignedShort, getString, getUInt, getUnsignedByte, getUnsignedShort, intToBytes, isBigEndian, isProgressBarVisible, linkProgress, longToBytes, readDouble, readFloat, readInt, readLong, readShort, readString, readUnsignedShort, removeProgressChangeListener, setBigEndian, setBufferFloat, setBufferInt, setBufferLong, setBufferShort, setBufferString, setDataType, setEndianess, shortToBytes, writeBytes, writeDouble, writeFloat, writeInt, writeLong, writeShort

Methods inherited from class java.lang.Object

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

Field Detail

file

private java.io.File file

DOCUMENT ME!

fileDir

private java.lang.String fileDir

DOCUMENT ME!

fileInfo

private FileInfoCOR fileInfo

DOCUMENT ME!

fileName

private java.lang.String fileName

DOCUMENT ME!

foundEOF

private boolean foundEOF

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

imageExtents

private int[] imageExtents

DOCUMENT ME!

imageOrientation

private int imageOrientation

DOCUMENT ME!

imgBuffer

private float[] imgBuffer

DOCUMENT ME!

imgResols

private float[] imgResols

DOCUMENT ME!

LUT

private ModelLUT LUT

DOCUMENT ME!

orient

private int[] orient

DOCUMENT ME!

Constructor Detail

FileCOR

public FileCOR(java.lang.String fileName,
               java.lang.String fileDir)
        throws java.io.IOException

COR reader/writer constructor.

Parameters:

fileName - file name

fileDir - file directory

Throws:

java.io.IOException - if there is an error making the file

Method Detail

finalize

public void finalize()

Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.

Overrides:

finalize in class FileBase

getFileInfo

public FileInfoBase getFileInfo()

Accessor that returns the file info.

Returns:

FileInfoBase containing the file info

getImageBuffer

public float[] getImageBuffer()

Accessor that returns the image buffer.

Returns:

buffer of image.

getModelLUT

public ModelLUT getModelLUT()

Rreturns LUT if defined.

Returns:

the LUT if defined else it is null

readImage

public void readImage(int length)
               throws java.io.IOException

This method reads one slice from the file into byteBuffer and then transfers into the float array imgBuffer.

Parameters:

length - length = imageExtents[0] * imageExtents[1]

Throws:

java.io.IOException - if there is an error reading the file

readInfoImage

public void readInfoImage()
                   throws java.io.IOException

DOCUMENT ME!

Throws:

java.io.IOException - DOCUMENT ME!

setFileName

public void setFileName(java.lang.String fName)

Accessor to set the file name (used for reading COR multiFile).

Parameters:

fName - file name of image to read.

writeImage

public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException

Writes a COR format type image.

Parameters:

image - Image model of data to write.

options - options such as starting and ending slices and times

Throws:

java.io.IOException - if there is an error writing the file

parse

private java.lang.String[] parse(java.lang.String inString)

DOCUMENT ME!

Parameters:

inString - DOCUMENT ME!

Returns:

DOCUMENT ME!

readLine

private java.lang.String readLine()
                           throws java.io.IOException

Reads lines of the file until a nonnull String results or the end of the file is reached.

Returns:

the line read in

Throws:

java.io.IOException - if there is an error reading the file