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 java.io.File file
DOCUMENT ME!

private java.lang.String fileDir
DOCUMENT ME!

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`java.lang.String[]`	`getFileList(java.lang.String fileDir, java.lang.String fileName, boolean quiet)`	Looks in the image directory and returns all images with the same suffix as `fileName`, sorted in lexicographical order.
`private java.lang.String`	`getKeyString(java.lang.String str)`	DOCUMENT ME!
`private java.lang.String`	`getValString(java.lang.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, java.lang.String inputName)`	Reads the image.
`private java.lang.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(java.lang.String fileName)`	Sets the file name.
`static java.lang.String`	`trimmer(java.lang.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 Detail
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
- Constructor Detail
  - FileMicroCat
```
public FileMicroCat(java.lang.String fileName,
                    java.lang.String fileDir)
             throws java.io.IOException
```
    MicroCat 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
  - trimmer
```
public static java.lang.String trimmer(java.lang.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 java.lang.String[] getFileList(java.lang.String fileDir,
                                      java.lang.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 java.io.IOException
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readImage
```
public ModelImage readImage(boolean quiet)
                     throws java.io.IOException
```
    Reads the image as a full 3D dataset.
    
    Parameters:
    
    quiet - Flag for printing statements to the screen.
    
    Returns:
    
    The image.
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readImage
```
public ModelImage readImage(boolean quiet,
                            boolean one,
                            java.lang.String inputName)
                     throws java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - setFileName
```
public void setFileName(java.lang.String fileName)
```
    Sets the file name.
    
    Parameters:
    
    fileName - New file name.
  - getKeyString
```
private java.lang.String getKeyString(java.lang.String str)
```
    DOCUMENT ME!
    
    Parameters:
    
    str - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getValString
```
private java.lang.String getValString(java.lang.String str)
```
    DOCUMENT ME!
    
    Parameters:
    
    str - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - readLine
```
private java.lang.String readLine()
                           throws java.io.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:
    
    java.io.IOException - if there is an error reading the file

Modifier and Type	Field	Description
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!

Class FileMicroCat

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

fileName

Constructor Detail

FileMicroCat

Method Detail

finalize

trimmer

getFileList

readHeader

readImage

readImage

setFileName

getKeyString

getValString

readLine