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

```
public class FileFits
extends FileBase
```
Some of this code is derived from FITS.java in ImageJ. In A User's Guide for the Flexible Image Transport System (FITS) Version 4.0, Section 4.1 Indexes and Physical Coordinates, the text says, "Historically, astronomers have generally assumed that the index point in a FITS file represents the center of a pixel. This interpretation is endorsed by GC. It differs from the common practice in computer graphics of treating the center of a pixel as a half-integral point." For CRPIXn in FITS: The center of the first pixel is 1 and the center of the last pixel is NAXISn. In MIPAV the center of the first pixel is 0.5 and the center of the last pixel is NAXISn - 0.5. So subtract 0.5 to go from FITS to MIPAV. " ...recommend that FITS writers order pixels starting in the lower left hand corner of the image, with the first axis increasing to the right, as in the rectangular coordinate x-axis, and the second increasing upward (the y-axis)." MIPAV uses the upper left hand corner as the origin and has the y axis going downward. Therefore, the image is flipped after reading and flipped before writing.

ImageJ disclaimer:

ImageJ is being developed at the National Institutes of Health by an employee of the Federal Government in the course of his official duties. Pursuant to Title 17, Section 105 of the United States Code, this software is not subject to copyright protection and is in the public domain. ImageJ is an experimental system. NIH assumes no responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic.

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`BLANK`	DOCUMENT ME!
`private boolean`	`endianess`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoFits`	`fileInfo`	DOCUMENT ME!
`private FileInfoFits`	`fileInfoCopy`
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private AlgorithmFlip`	`flipAlgo`
`private boolean`	`haveBlank`	DOCUMENT ME!
`private ModelImage`	`image`	DOCUMENT ME!
`(package private) int[]`	`imgExtents`	DOCUMENT ME!
`private boolean`	`isColorPlanar2D`
`private ModelLUT`	`LUT`	DOCUMENT ME!
`(package private) int`	`nDimensions`	DOCUMENT ME!
`private int`	`numberSlices`	DOCUMENT ME!
`(package private) int`	`sourceType`	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

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`ModelLUT`	`getModelLUT()`	returns LUT if defined.
`private void`	`readBuffer(int slice, float[] buffer, float scaleFact, float scaleOffset)`	Reads a slice of data at a time and stores the results in the buffer.
`private void`	`readDBuffer(int slice, double[] buffer, double scaleFact, double scaleOffset)`	Reads a slice of data at a time and stores the results in the buffer.
`ModelImage`	`readImage(boolean one)`	reads the FITS file header and data.
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes a FITS 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
  - imgExtents
```
int[] imgExtents
```
    DOCUMENT ME!
  - nDimensions
```
int nDimensions
```
    DOCUMENT ME!
  - sourceType
```
int sourceType
```
    DOCUMENT ME!
  - BLANK
```
private int BLANK
```
    DOCUMENT ME!
  - endianess
```
private boolean endianess
```
    DOCUMENT ME!
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoFits fileInfo
```
    DOCUMENT ME!
  - fileInfoCopy
```
private FileInfoFits fileInfoCopy
```
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - haveBlank
```
private boolean haveBlank
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - LUT
```
private ModelLUT LUT
```
    DOCUMENT ME!
  - numberSlices
```
private int numberSlices
```
    DOCUMENT ME!
  - isColorPlanar2D
```
private boolean isColorPlanar2D
```
  - flipAlgo
```
private AlgorithmFlip flipAlgo
```
- Constructor Detail
  - FileFits
```
public FileFits(java.lang.String fileName,
                java.lang.String fileDir)
         throws java.io.IOException
```
    FITS 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
  - getModelLUT
```
public ModelLUT getModelLUT()
```
    returns LUT if defined.
    
    Returns:
    
    the LUT if defined else it is null
  - readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException
```
    reads the FITS file header and data.
    
    Parameters:
    
    one - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes a FITS 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
  - readBuffer
```
private void readBuffer(int slice,
                        float[] buffer,
                        float scaleFact,
                        float scaleOffset)
                 throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    buffer - buffer where the info is stored
    
    scaleFact - if 1 data is unscaled
    
    scaleOffset - if 0 don't add offset
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readDBuffer
```
private void readDBuffer(int slice,
                         double[] buffer,
                         double scaleFact,
                         double scaleOffset)
                  throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    buffer - buffer where the info is stored
    
    scaleFact - if 1 data is unscaled
    
    scaleOffset - if 0 don't add offset
    
    Throws:
    
    java.io.IOException - if there is an error reading the file

Class FileFits

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

imgExtents

nDimensions

sourceType

BLANK

endianess

file

fileDir

fileInfo

fileInfoCopy

fileName

haveBlank

image

LUT

numberSlices

isColorPlanar2D

flipAlgo

Constructor Detail

FileFits

Method Detail

finalize

getModelLUT

readImage

writeImage

readBuffer

readDBuffer