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

All Methods Instance Methods Concrete Methods
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

Class FileCOR

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

file

fileDir

fileInfo

fileName

foundEOF

image

imageExtents

imageOrientation

imgBuffer

imgResols

LUT

orient

Constructor Detail

FileCOR

Method Detail

finalize

getFileInfo

getImageBuffer

getModelLUT

readImage

readInfoImage

setFileName

writeImage

parse

readLine