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 java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoMRC`	`fileInfo`	DOCUMENT ME!
`private FileInfoMRC`	`fileInfoCopy`
`private java.lang.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(java.lang.String fileName, java.lang.String fileDir)
MRC 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)`	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 Detail
  - dataSize
```
private int dataSize
```
    DOCUMENT ME!
  - destType
```
private int destType
```
    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 FileInfoMRC fileInfo
```
    DOCUMENT ME!
  - fileInfoCopy
```
private FileInfoMRC fileInfoCopy
```
  - fileName
```
private java.lang.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 Detail
  - FileMRC
```
public FileMRC(java.lang.String fileName,
               java.lang.String fileDir)
        throws java.io.IOException
```
    MRC 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()
                     throws java.io.IOException
```
    reads the MRC file header and data.
    
    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 MRC 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)
                 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
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readComplexBuffer
```
private void readComplexBuffer(int slice,
                               float[] buffer,
                               float[] buffer2)
                        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 real info is stored
    
    buffer2 - buffer where the imaginary info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file

Class FileMRC

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

dataSize

destType

endianess

file

fileDir

fileInfo

fileInfoCopy

fileName

fileSize

image

imgExtents

LUT

mode

mx

my

mz

numberSlices

nx

ny

nz

nXStart

nYStart

nZStart

Constructor Detail

FileMRC

Method Detail

finalize

getModelLUT

readImage

writeImage

readBuffer

readComplexBuffer