java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FileBioRad

public class FileBioRad
extends FileBase

Reads BioRaD pic file format.

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`bufferSize`	DOCUMENT ME!
`private byte[]`	`byteBuffer`	DOCUMENT ME!
`private short`	`byteFormat`	if 1 data is UBYTE, otherwise data is SHORT.
`private int`	`color1`	LUT1 color status.
`private int`	`color2`	LUT2 color status.
`private int`	`dataType`	DOCUMENT ME!
`private short`	`edited`	not used in disk files.
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private int`	`fileID`	always set to 12345 in BioRad pic files.
`private FileInfoBioRad`	`fileInfo`	DOCUMENT ME!
`private FileInfoBioRad`	`fileInfoCopy`
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private java.lang.String`	`fName`	DOCUMENT ME!
`private ModelImage`	`image`	DOCUMENT ME!
`private float[]`	`imgBuffer`	DOCUMENT ME!
`private int[]`	`imgExtents`	DOCUMENT ME!
`private short`	`lens`	Integer part of the lens magnification.
`private float`	`magFactor`	magnification factor.
`private short`	`merged`	merged format.
`private byte[]`	`name`	DOCUMENT ME!
`private int`	`notes`	if 0 no notes are present if nonzero 96 byte notes follow after the image data at the end of the file.
`private short`	`ramp1Max`
`private short`	`ramp1Min`
`private short`	`ramp2Max`	LUT2 ramp max.
`private short`	`ramp2Min`	LUT2 ramp min.
`private boolean`	`readAgain`	DOCUMENT ME!
`private int`	`xDim`	DOCUMENT ME!
`private int`	`yDim`	DOCUMENT ME!
`private int`	`zDim`	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

FileBioRad(java.lang.String fileName, java.lang.String fileDir)
reader/writer constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`private void`	`readBuffer(int slice, float[] buffer)`	Reads a slice of data at a time and stores the results in the buffer.
`ModelImage`	`readImage(boolean one)`	reads the BioRad pic file header and data.

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
  - bufferSize
```
private int bufferSize
```
    DOCUMENT ME!
  - byteBuffer
```
private byte[] byteBuffer
```
    DOCUMENT ME!
  - byteFormat
```
private short byteFormat
```
    if 1 data is UBYTE, otherwise data is SHORT.
  - color1
```
private int color1
```
    LUT1 color status.
  - color2
```
private int color2
```
    LUT2 color status.
  - dataType
```
private int dataType
```
    DOCUMENT ME!
  - edited
```
private short edited
```
    not used in disk files.
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileID
```
private int fileID
```
    always set to 12345 in BioRad pic files.
  - fileInfo
```
private FileInfoBioRad fileInfo
```
    DOCUMENT ME!
  - fileInfoCopy
```
private FileInfoBioRad fileInfoCopy
```
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - fName
```
private java.lang.String fName
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - imgBuffer
```
private float[] imgBuffer
```
    DOCUMENT ME!
  - imgExtents
```
private int[] imgExtents
```
    DOCUMENT ME!
  - lens
```
private short lens
```
    Integer part of the lens magnification.
  - magFactor
```
private float magFactor
```
    magnification factor.
  - merged
```
private short merged
```
    merged format.
  - name
```
private byte[] name
```
    DOCUMENT ME!
  - notes
```
private int notes
```
    if 0 no notes are present if nonzero 96 byte notes follow after the image data at the end of the file.
  - ramp1Max
```
private short ramp1Max
```
  - ramp1Min
```
private short ramp1Min
```
  - ramp2Max
```
private short ramp2Max
```
    LUT2 ramp max.
  - ramp2Min
```
private short ramp2Min
```
    LUT2 ramp min.
  - readAgain
```
private boolean readAgain
```
    DOCUMENT ME!
  - xDim
```
private int xDim
```
    DOCUMENT ME!
  - yDim
```
private int yDim
```
    DOCUMENT ME!
  - zDim
```
private int zDim
```
    DOCUMENT ME!
- Constructor Detail
  - FileBioRad
```
public FileBioRad(java.lang.String fileName,
                  java.lang.String fileDir)
           throws java.io.IOException
```
    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
  - readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException
```
    reads the BioRad pic file header and data.
    
    Parameters:
    
    one - DOCUMENT ME!
    
    Returns:
    
    returns a black and white image
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readBuffer
```
private void readBuffer(int slice,
                        float[] buffer)
                 throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - into the file
    
    buffer - buffer where the info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file

Class FileBioRad

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

bufferSize

byteBuffer

byteFormat

color1

color2

dataType

edited

file

fileDir

fileID

fileInfo

fileInfoCopy

fileName

fName

image

imgBuffer

imgExtents

lens

magFactor

merged

name

notes

ramp1Max

ramp1Min

ramp2Max

ramp2Min

readAgain

xDim

yDim

zDim

Constructor Detail

FileBioRad

Method Detail

finalize

readImage

readBuffer