Package gov.nih.mipav.model.file

Class FileFits

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

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