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

```
public class FileMGH
extends FileBase
```
The class reads MGH files. The 4 by 4 matrix in MGH transforms x,y,z indexes to (right, anterior, superior) coordinates where +x = Right, +y = Anterior, +z = Superior. In MIPAV the 4 by 4 matrix does not imply the axis orientations.
The MGH definition is: [right] = [xr yr zr] [ xsize * x] + [rorigin] [anterior] = [xa ya za] [ ysize * y] + [aorigin] [superior] = [xs ys zs] [ zsize * z] + [sorigin] Now in going to MIPAV a change must occur. MGH has L->R and P->A while MIPAV uses R->L in all axes and A->P in axes 0 and 1 and P->A in axis 2, so this would cause xr, yr, zr, rorigin, xa, ya, za, and aorigin to be multiplied by -1. cr, ca, and cs refer to the center point of the scanner coordinate system.

A 284 byte header always precedes the data buffer In version 1 if the goodRASFlag <= 0, then only the first 30 bytes are read. If the goodRASFlag > 0, then the first 90 bytes are read

Immediately after the data buffer other optional data structures may be found: They are: Recovery time in milliseconds float Flip angle in radians float Echo time in milliseconds float Inversion time in millseconds float Field of view in millimeters float Comment about fov field from Nick Schmansky: The FoV field should be ignored. In discussing this field with Bruce Fischl, and looking more closely at the code, it appears to be a field with a long and inconsistent usage history (in how it is set and where the data originates). We do not rely on it in our binaries. Lastly, tags including the Talairach transform file name and a list of commands used to create this data(provenance info) may be present.

I am not reading the contents of the Talairach transform file for 3 reasons: 1.) This information is probably not very useful. 2.) Every sample file that I obtained from MGH gave the same name: talairach.xfm. If this name is always used, then it is impossible to tell which .mgh file it corresponds to. 3.) The Talairach transform file is a clear ascii file, so it can be easily read with any number of common programs.

See Also:

FileIO, FileInfoMGH, FileRaw

Field Summary

Fields
Modifier and Type	Field	Description
`private int[]`	`axisOrientation`	DOCUMENT ME!
`private int`	`bytesPerValue`	DOCUMENT ME!
`private float`	`ca`	DOCUMENT ME!
`(package private) java.lang.String[]`	`cmdlines`	DOCUMENT ME!
`private float`	`cr`	DOCUMENT ME!
`private float`	`cs`	DOCUMENT ME!
`private int`	`dataType`	DOCUMENT ME!
`private int`	`depth`	DOCUMENT ME!
`private int`	`dof`	DOCUMENT ME!
`private int[]`	`extents`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoMGH`	`fileInfo`	DOCUMENT ME!
`private long`	`fileLength`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private java.io.FileInputStream`	`fis`	DOCUMENT ME!
`private float`	`flipAngle`	DOCUMENT ME!
`private float`	`fov`	DOCUMENT ME!
`private short`	`goodRASFlag`	DOCUMENT ME!
`private boolean`	`gunzip`	DOCUMENT ME!
`private int`	`height`	DOCUMENT ME!
`private ModelImage`	`image`	DOCUMENT ME!
`private TransMatrix`	`matrix`	DOCUMENT ME!
`private static int`	`MAX_CMDS`	DOCUMENT ME!
`private int`	`mghType`	DOCUMENT ME!
`private static int`	`MRI_BITMAP`	DOCUMENT ME!
`private static int`	`MRI_FLOAT`	DOCUMENT ME!
`private static int`	`MRI_INT`	DOCUMENT ME!
`private static int`	`MRI_LONG`	DOCUMENT ME!
`private static int`	`MRI_SHORT`	DOCUMENT ME!
`private static int`	`MRI_TENSOR`	DOCUMENT ME!
`private static int`	`MRI_UCHAR`	DOCUMENT ME!
`(package private) int`	`ncmds`	DOCUMENT ME!
`private int`	`nFrames`	DOCUMENT ME!
`private long`	`optionalStructuresLocation`	DOCUMENT ME!
`private float[]`	`origin`	DOCUMENT ME!
`private float[]`	`resolutions`	DOCUMENT ME!
`private static int`	`TAG_CMDLINE`	DOCUMENT ME!
`private static int`	`TAG_MGH_XFORM`	DOCUMENT ME!
`private static int`	`TAG_OLD_COLORTABLE`	DOCUMENT ME!
`private static int`	`TAG_OLD_MGH_XFORM`	DOCUMENT ME!
`private static int`	`TAG_OLD_SURF_GEOM`	DOCUMENT ME!
`private static int`	`TAG_OLD_USEREALRAS`	DOCUMENT ME!
`private float`	`te`	DOCUMENT ME!
`private float`	`ti`	DOCUMENT ME!
`private float`	`tr`	DOCUMENT ME!
`private int`	`version`	Present version number is 1.
`private int`	`width`	DOCUMENT ME!
`private float`	`xa`	DOCUMENT ME!
`private float`	`xr`	DOCUMENT ME!
`private float`	`xs`	DOCUMENT ME!
`private float`	`ya`	DOCUMENT ME!
`private float`	`yr`	DOCUMENT ME!
`private float`	`ys`	DOCUMENT ME!
`private float`	`za`	DOCUMENT ME!
`private float`	`zr`	DOCUMENT ME!
`private float`	`zs`	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

FileMGH(java.lang.String fName, java.lang.String fDir)
Constructs new file object.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`attachFileInfo(FileInfoMGH fileInfo, ModelImage image)`	DOCUMENT ME!
`void`	`finalize()`	Prepares this class for cleanup.
`static int[]`	`getAxisOrientation(TransMatrix mat)`	Return the 3 axis orientation codes that correspond to the closest standard anatomical orientation of the (i,j,k) axes.
`FileInfoMGH`	`getFileInfo()`	Returns the FileInfoMGH read from the file.
`private int`	`getOffset()`	Helper method to calculate the offset for getting only the middle NIFTI image slice from the 3D file.
`boolean`	`readHeader(java.lang.String imageFileName, java.lang.String fileDir)`	Reads the MGH header and stores the information in fileInfo.
`ModelImage`	`readImage(boolean one)`	Reads a MGH image file by reading the header then making a FileRaw to read the image for all filenames in the file list.
`void`	`readImage(float[] buffer)`	Reads a MGH image file by reading the header then making a FileRaw to read the file.
`private void`	`updateorigins(FileInfoBase[] fileInfo)`	Updates the start locations.
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes a MGH or MGZ 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
  - MRI_UCHAR
```
private static final int MRI_UCHAR
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MRI_INT
```
private static final int MRI_INT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MRI_LONG
```
private static final int MRI_LONG
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MRI_FLOAT
```
private static final int MRI_FLOAT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MRI_SHORT
```
private static final int MRI_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MRI_BITMAP
```
private static final int MRI_BITMAP
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MRI_TENSOR
```
private static final int MRI_TENSOR
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - TAG_OLD_COLORTABLE
```
private static final int TAG_OLD_COLORTABLE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - TAG_OLD_USEREALRAS
```
private static final int TAG_OLD_USEREALRAS
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - TAG_CMDLINE
```
private static final int TAG_CMDLINE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - TAG_OLD_SURF_GEOM
```
private static final int TAG_OLD_SURF_GEOM
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - TAG_OLD_MGH_XFORM
```
private static final int TAG_OLD_MGH_XFORM
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - TAG_MGH_XFORM
```
private static final int TAG_MGH_XFORM
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MAX_CMDS
```
private static final int MAX_CMDS
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - cmdlines
```
java.lang.String[] cmdlines
```
    DOCUMENT ME!
  - ncmds
```
int ncmds
```
    DOCUMENT ME!
  - axisOrientation
```
private int[] axisOrientation
```
    DOCUMENT ME!
  - bytesPerValue
```
private int bytesPerValue
```
    DOCUMENT ME!
  - ca
```
private float ca
```
    DOCUMENT ME!
  - cr
```
private float cr
```
    DOCUMENT ME!
  - cs
```
private float cs
```
    DOCUMENT ME!
  - dataType
```
private int dataType
```
    DOCUMENT ME!
  - depth
```
private int depth
```
    DOCUMENT ME!
  - dof
```
private int dof
```
    DOCUMENT ME!
  - extents
```
private int[] extents
```
    DOCUMENT ME!
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoMGH fileInfo
```
    DOCUMENT ME!
  - fileLength
```
private long fileLength
```
    DOCUMENT ME!
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - fis
```
private java.io.FileInputStream fis
```
    DOCUMENT ME!
  - flipAngle
```
private float flipAngle
```
    DOCUMENT ME!
  - fov
```
private float fov
```
    DOCUMENT ME!
  - goodRASFlag
```
private short goodRASFlag
```
    DOCUMENT ME!
  - gunzip
```
private boolean gunzip
```
    DOCUMENT ME!
  - height
```
private int height
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - matrix
```
private TransMatrix matrix
```
    DOCUMENT ME!
  - mghType
```
private int mghType
```
    DOCUMENT ME!
  - nFrames
```
private int nFrames
```
    DOCUMENT ME!
  - optionalStructuresLocation
```
private long optionalStructuresLocation
```
    DOCUMENT ME!
  - origin
```
private float[] origin
```
    DOCUMENT ME!
  - resolutions
```
private float[] resolutions
```
    DOCUMENT ME!
  - te
```
private float te
```
    DOCUMENT ME!
  - ti
```
private float ti
```
    DOCUMENT ME!
  - tr
```
private float tr
```
    DOCUMENT ME!
  - version
```
private int version
```
    Present version number is 1.
  - width
```
private int width
```
    DOCUMENT ME!
  - xa
```
private float xa
```
    DOCUMENT ME!
  - xr
```
private float xr
```
    DOCUMENT ME!
  - xs
```
private float xs
```
    DOCUMENT ME!
  - ya
```
private float ya
```
    DOCUMENT ME!
  - yr
```
private float yr
```
    DOCUMENT ME!
  - ys
```
private float ys
```
    DOCUMENT ME!
  - za
```
private float za
```
    DOCUMENT ME!
  - zr
```
private float zr
```
    DOCUMENT ME!
  - zs
```
private float zs
```
    DOCUMENT ME!
- Constructor Detail
  - FileMGH
```
public FileMGH(java.lang.String fName,
               java.lang.String fDir)
```
    Constructs new file object.
    
    Parameters:
    
    fName - File name.
    
    fDir - File directory.
- 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
  - getFileInfo
```
public FileInfoMGH getFileInfo()
```
    Returns the FileInfoMGH read from the file.
    
    Returns:
    
    File info read from file, or null if it has not been read.
  - readHeader
```
public boolean readHeader(java.lang.String imageFileName,
                          java.lang.String fileDir)
                   throws java.io.IOException
```
    Reads the MGH header and stores the information in fileInfo.
    
    Parameters:
    
    imageFileName - File name of image.
    
    fileDir - Directory.
    
    Returns:
    
    Flag to confirm a successful read.
    
    Throws:
    
    java.io.IOException - if there is an error reading the header
    
    See Also:
    
    FileInfoMGH
  - readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException,
                            java.lang.OutOfMemoryError
```
    Reads a MGH image file by reading the header then making a FileRaw to read the image for all filenames in the file list. Only the one file directory (currently) supported.
    
    Parameters:
    
    one - flag indicating one image of a 3D dataset should be read in.
    
    Returns:
    
    The image.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
    
    java.lang.OutOfMemoryError
    
    See Also:
    
    FileRaw
  - readImage
```
public void readImage(float[] buffer)
               throws java.io.IOException,
                      java.lang.OutOfMemoryError
```
    Reads a MGH image file by reading the header then making a FileRaw to read the file. Image data is left in buffer. If the fileInfo cannot be found, the header will be located and read first. Image is not 'flipped', and neither units of measure nor orientation are set.
    
    Parameters:
    
    buffer - Image buffer to store image data into.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
    
    java.lang.OutOfMemoryError
    
    See Also:
    
    FileRaw
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes a MGH or MGZ 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
  - attachFileInfo
```
private void attachFileInfo(FileInfoMGH fileInfo,
                            ModelImage image)
```
    DOCUMENT ME!
    
    Parameters:
    
    fileInfo - -- a NIFTI file Info that has already been read
    
    image - -- a ModelImage that the fileInfo needs to be attached to
  - getAxisOrientation
```
public static int[] getAxisOrientation(TransMatrix mat)
```
    Return the 3 axis orientation codes that correspond to the closest standard anatomical orientation of the (i,j,k) axes.
    
    Parameters:
    
    mat - 4x4 matrix that transforms (i,j,k) indexes to x,y,z coordinates where +x =Left, +y = Posterior, +z = Superior Only the upper-left 3x3 corner of the matrix is used This routine finds the permutation of (x,y,z) which has the smallest angle to the (i,j,k) axes directions, which are columns of the input matrix Errors: The codes returned will be zero.
    
    Returns:
    
    DOCUMENT ME!
  - getOffset
```
private int getOffset()
```
    Helper method to calculate the offset for getting only the middle NIFTI image slice from the 3D file.
    
    Returns:
    
    offset
  - updateorigins
```
private void updateorigins(FileInfoBase[] fileInfo)
```
    Updates the start locations. Each image has a fileinfo where the start locations are stored. Note that the start location for the Z (3rd) dimension change with the change is the slice. The origin is in the upper left corner and we are using the right hand rule. + x -> left to right; + y -> top to bottom and + z -> into screen.
    
    Parameters:
    
    fileInfo - DOCUMENT ME!

Class FileMGH

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

MRI_UCHAR

MRI_INT

MRI_LONG

MRI_FLOAT

MRI_SHORT

MRI_BITMAP

MRI_TENSOR

TAG_OLD_COLORTABLE

TAG_OLD_USEREALRAS

TAG_CMDLINE

TAG_OLD_SURF_GEOM

TAG_OLD_MGH_XFORM

TAG_MGH_XFORM

MAX_CMDS

cmdlines

ncmds

axisOrientation

bytesPerValue

ca

cr

cs

dataType

depth

dof

extents

file

fileDir

fileInfo

fileLength

fileName

fis

flipAngle

fov

goodRASFlag

gunzip

height

image

matrix

mghType

nFrames

optionalStructuresLocation

origin

resolutions

te

ti

tr

version

width

xa

xr

xs

ya

yr

ys

za

zr

zs

Constructor Detail

FileMGH

Method Detail

finalize

getFileInfo

readHeader

readImage

readImage

writeImage

attachFileInfo

getAxisOrientation

getOffset

updateorigins