Package gov.nih.mipav.model.file

Class FileMedVision

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileMedVision

public class FileMedVision
extends FileBase

The class reads MedVision files that have been saved as MAC bin files. The MAC files have needed image resolutions encoded in the in the resource section at the end of the file. MedVision also has method of saving images to the Intel world but pixel resolutions are not stored. Here I decode MAC MedVision files. It is easy to write a Intel MedVision reader or one could directly read in the file using using MIPA because they have a fixed offset and can be read in using the RAW file reader.

Version:

0.1 June 25, 1998

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

• FileIO
• FileInfoMedVision
• FileRaw
• FileRawChunk

Field Summary

Fields

Modifier and Type	Field	Description
static final short	BIT16	DOCUMENT ME!
static final short	BIT8	DOCUMENT ME!
private File	file	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private FileInfoMedVision	fileInfo	DOCUMENT ME!
private FileInfoMedVision	fileInfoCom	DOCUMENT ME!
private String	fileName	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private ViewJProgressBar	progressBar	DOCUMENT ME!
private float[]	resolutions	DOCUMENT ME!
static final short	S16BIT	DOCUMENT ME!
static final short	S8BIT	DOCUMENT ME!
static final short	SIGNED	DOCUMENT ME!
private double[]	slicePosition	DOCUMENT ME!
private double[][]	sliceResolutions	DOCUMENT ME!
static final short	U16BIT	DOCUMENT ME!
static final short	U8BIT	DOCUMENT ME!
static final short	UNSIGNED	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
FileMedVision(String fName, String fDir)	FileMedVision - MedVision reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
private void	copyFileInfoCommon()	copyFileInfoCommon - copy common file info into new header Better must exist but this works.
private boolean	decodeFileHeader(boolean endianess)	readFileHeader - reader image file header that encodes info about image.
private void	decodeResourceFooter(boolean endianess)	decodeResourceFooter - This is the tricky function that decodes the the resource footer at the end of the MAC file The data is coded is very odd manner.
private boolean	decodeSliceHeader(long start, FileInfoMedVision fileInfo, boolean endianess)	decodeSliceHeader - reads image slice header that encodes info about specific image slice.
private double	getMedVisionDouble(boolean endianess)	getMedVisionDouble - extracts double value from MedVision MAC resource fork.
ModelImage	readImage()	readImage - reads a MedVision file in MAC format (i.e., decodes resource info).

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

addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, finalize, 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 Details

BIT8

public static final short BIT8

DOCUMENT ME!

See Also:

• Constant Field Values

BIT16

public static final short BIT16

DOCUMENT ME!

See Also:

• Constant Field Values

SIGNED

public static final short SIGNED

DOCUMENT ME!

See Also:

• Constant Field Values

UNSIGNED

public static final short UNSIGNED

DOCUMENT ME!

See Also:

• Constant Field Values

S8BIT

public static final short S8BIT

DOCUMENT ME!

See Also:

• Constant Field Values

U8BIT

public static final short U8BIT

DOCUMENT ME!

See Also:

• Constant Field Values

S16BIT

public static final short S16BIT

DOCUMENT ME!

See Also:

• Constant Field Values

U16BIT

public static final short U16BIT

DOCUMENT ME!

See Also:

• Constant Field Values

file

private File file

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileInfo

private FileInfoMedVision fileInfo

DOCUMENT ME!

fileInfoCom

private FileInfoMedVision fileInfoCom

DOCUMENT ME!

fileName

private String fileName

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

progressBar

private ViewJProgressBar progressBar

DOCUMENT ME!

resolutions

private float[] resolutions

DOCUMENT ME!

slicePosition

private double[] slicePosition

DOCUMENT ME!

sliceResolutions

private double[][] sliceResolutions

DOCUMENT ME!

Constructor Details

FileMedVision

public FileMedVision(String fName,
 String fDir)

FileMedVision - MedVision reader/writer constructor.

Parameters:

fName - file name

fDir - file directory

Method Details

readImage

public ModelImage readImage()
                     throws IOException

readImage - reads a MedVision file in MAC format (i.e., decodes resource info).

Returns:

image model of the data read in from the file

Throws:

IOException - if there is an error reading the file

See Also:

• FileRawChunk

copyFileInfoCommon

private void copyFileInfoCommon()

copyFileInfoCommon - copy common file info into new header Better must exist but this works.

decodeFileHeader

private boolean decodeFileHeader(boolean endianess)
                          throws IOException

readFileHeader - reader image file header that encodes info about image.

Parameters:

endianess - boolean describing byte order

Returns:

boolean indicating successful read

Throws:

IOException - if there is an error reading the file

See Also:

• FileInfoMedVision

decodeResourceFooter

private void decodeResourceFooter(boolean endianess)
                           throws IOException

decodeResourceFooter - This is the tricky function that decodes the the resource footer at the end of the MAC file The data is coded is very odd manner. I was unable to find MAC documentation and decoded it by "hand"

Parameters:

endianess - boolean describing byte order

Throws:

IOException - if there is an error reading the file

decodeSliceHeader

private boolean decodeSliceHeader(long start,
 FileInfoMedVision fileInfo,
 boolean endianess)
                           throws IOException

decodeSliceHeader - reads image slice header that encodes info about specific image slice.

Parameters:

start - start of file information

fileInfo - file information

endianess - boolean describing byte order

Returns:

boolean indicating successful decoding

Throws:

IOException - if there is an error reading the file

getMedVisionDouble

private double getMedVisionDouble(boolean endianess)
                           throws IOException

getMedVisionDouble - extracts double value from MedVision MAC resource fork.

Parameters:

endianess - describes byte ordering of data

Returns:

returns extracted double

Throws:

IOException - if there is an error reading the file