Package gov.nih.mipav.model.file

Class FileMRC

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileMRC

public class FileMRC
extends FileBase

Comments from David Mastronarde:
I am not familiar with the latest standards for MRC files, but typically the extra header information has been used to save information about each section in the file. Our own implementation is largely derived from that of the Agard group at UCSF, from which the Deltavision software originates. The Deltavision standard uses two fields called "nreal" and "nint" to describe the number of 4-byte reals and integers stored per section. I deviated from that and used "nint" to hold the number of bytes of data per section, and "nreal" to hold a set of flags describing which kinds of data were present (tilt angle, frame X-Y-Z coordinates for a montage, stage position, magnification, all stored as 2-byte integers.). This information is present only for data acquired on our microscope here.

Field Summary

Fields

Modifier and Type	Field	Description
private int	dataSize	DOCUMENT ME!
private int	destType	DOCUMENT ME!
private boolean	endianess	DOCUMENT ME!
private File	file	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private FileInfoMRC	fileInfo	DOCUMENT ME!
private FileInfoMRC	fileInfoCopy
private String	fileName	DOCUMENT ME!
private int	fileSize	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private int[]	imgExtents	DOCUMENT ME!
private ModelLUT	LUT	DOCUMENT ME!
private int	mode	DOCUMENT ME!
private int	mx	DOCUMENT ME!
private int	my	DOCUMENT ME!
private int	mz	DOCUMENT ME!
private int	numberSlices	DOCUMENT ME!
private int	nx	DOCUMENT ME!
private int	nXStart
private int	ny	DOCUMENT ME!
private int	nYStart
private int	nz	DOCUMENT ME!
private int	nZStart

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
FileMRC(String fileName, String fileDir)	MRC 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)	Reads a slice of data at a time and stores the results in the buffer.
private void	readComplexBuffer(int slice, float[] buffer, float[] buffer2)	Reads a slice of data at a time and stores the results in the buffer.
ModelImage	readImage()	reads the MRC file header and data.
void	writeImage(ModelImage image, FileWriteOptions options)	Writes a MRC 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 Details

dataSize

private int dataSize

DOCUMENT ME!

destType

private int destType

DOCUMENT ME!

endianess

private boolean endianess

DOCUMENT ME!

file

private File file

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileInfo

private FileInfoMRC fileInfo

DOCUMENT ME!

fileInfoCopy

private FileInfoMRC fileInfoCopy

fileName

private String fileName

DOCUMENT ME!

fileSize

private int fileSize

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

imgExtents

private int[] imgExtents

DOCUMENT ME!

LUT

private ModelLUT LUT

DOCUMENT ME!

mode

private int mode

DOCUMENT ME!

mx

private int mx

DOCUMENT ME!

my

private int my

DOCUMENT ME!

mz

private int mz

DOCUMENT ME!

numberSlices

private int numberSlices

DOCUMENT ME!

nx

private int nx

DOCUMENT ME!

ny

private int ny

DOCUMENT ME!

nz

private int nz

DOCUMENT ME!

nXStart

private int nXStart

nYStart

private int nYStart

nZStart

private int nZStart

Constructor Details

FileMRC

public FileMRC(String fileName,
 String fileDir)
        throws IOException

MRC 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

getModelLUT

public ModelLUT getModelLUT()

returns LUT if defined.

Returns:

the LUT if defined else it is null

readImage

public ModelImage readImage()
                     throws IOException

reads the MRC file header and data.

Returns:

DOCUMENT ME!

Throws:

IOException - if there is an error reading the file

writeImage

public void writeImage(ModelImage image,
 FileWriteOptions options)
                throws IOException

Writes a MRC format type image.

Parameters:

image - Image model of data to write.

options - options such as starting and ending slices and times

Throws:

IOException - if there is an error writing the file

readBuffer

private void readBuffer(int slice,
 float[] buffer)
                 throws 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

Throws:

IOException - if there is an error reading the file

readComplexBuffer

private void readComplexBuffer(int slice,
 float[] buffer,
 float[] buffer2)
                        throws 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 real info is stored

buffer2 - buffer where the imaginary info is stored

Throws:

IOException - if there is an error reading the file