Package gov.nih.mipav.model.file

Class FileMicroCat

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileMicroCat

public class FileMicroCat
extends FileBase

Author:

Matthew J. McAuliffe

See Also:

• FileIO

Field Summary

Fields

Modifier and Type	Field	Description
private File	file	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private String	fileName	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
FileMicroCat(String fileName, String fileDir)	MicroCat reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
String[]	getFileList(String fileDir, String fileName, boolean quiet)	Looks in the image directory and returns all images with the same suffix as fileName, sorted in lexicographical order.
private String	getKeyString(String str)	DOCUMENT ME!
private String	getValString(String str)	DOCUMENT ME!
FileInfoMicroCat	readHeader()	DOCUMENT ME!
ModelImage	readImage(boolean quiet)	Reads the image as a full 3D dataset.
ModelImage	readImage(boolean quiet, boolean one, String inputName)	Reads the image.
private String	readLine()	Reads lines of the file and strips comments indicated by the : symbol until a nonnull String results or the end of the file is reached.
void	setFileName(String fileName)	Sets the file name.
static String	trimmer(String fName)	Trims the numbers(numerics and some special characters [-, _, .) off the end of a string (file name).

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 Details

file

private File file

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileName

private String fileName

DOCUMENT ME!

Constructor Details

FileMicroCat

public FileMicroCat(String fileName,
 String fileDir)
             throws IOException

MicroCat reader/writer constructor.

Parameters:

fileName - file name

fileDir - file directory

Throws:

IOException - if there is an error making the file

Method Details

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

trimmer

public static String trimmer(String fName)

Trims the numbers(numerics and some special characters [-, _, .) off the end of a string (file name).

Parameters:

fName - File name where the last characters are alpha-numerics indicating the image number.

Returns:

File name without numbers on the end.

getFileList

public String[] getFileList(String fileDir,
 String fileName,
 boolean quiet)

Looks in the image directory and returns all images with the same suffix as fileName, sorted in lexicographical order. Will set the number of images (nImages) for the calling program.

Parameters:

fileDir - Directory to looks for images in.

fileName - File name of the image.

quiet - DOCUMENT ME!

Returns:

An array of the image names to be read in or saved as.

readHeader

public FileInfoMicroCat readHeader()
                            throws IOException

DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readImage

public ModelImage readImage(boolean quiet)
                     throws IOException

Reads the image as a full 3D dataset.

Parameters:

quiet - Flag for printing statements to the screen.

Returns:

The image.

Throws:

IOException - DOCUMENT ME!

readImage

public ModelImage readImage(boolean quiet,
 boolean one,
 String inputName)
                     throws IOException

Reads the image.

Parameters:

quiet - Flag for printing statements to the screen.

one - Flag for reading only 1 image of 3D dataset

inputName - If one is true, contains name of image to read.

Returns:

returns the image

Throws:

IOException - if there is an error reading the file

setFileName

public void setFileName(String fileName)

Sets the file name.

Parameters:

fileName - New file name.

getKeyString

private String getKeyString(String str)

DOCUMENT ME!

Parameters:

str - DOCUMENT ME!

Returns:

DOCUMENT ME!

getValString

private String getValString(String str)

DOCUMENT ME!

Parameters:

str - DOCUMENT ME!

Returns:

DOCUMENT ME!

readLine

private String readLine()
                 throws IOException

Reads lines of the file and strips comments indicated by the : symbol until a nonnull String results or the end of the file is reached.

Returns:

the line read in

Throws:

IOException - if there is an error reading the file