Package gov.nih.mipav.model.file

Class FileSPM

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileSPM

public class FileSPM
extends FileBase

The class reads and writes SPM files.

See Also:

• FileIO
• FileInfoSPM
• Note that there are actually 3 variants of Analyze, all using .img and .hdr files, with very slight differences: Mayo Analyze 7.5, SPM99, and SPM2 Variant differences: Location 0 is an int32 with sizeof_hdr. In Non-SPM2, always 348, used to test whether the file is big-endian or little-endian. SPM2 can be 348 or greater. If SPM2 > 348, indicates extended header. The user could change .img to .spm to indicate SPM99 or SPM2. The .hdr extension would remain unchanged.

  Original Mayo Analyze 7.5, SPM99, and SPM2 all have at location 60 a uchar[8] for cal_units and at location 68 an int16 for unused1. However, MIPAV analyze only preserves at location 60 a uchar[4] for cal_units and has hacked locations 64, 66, and 68 with short integers for axis orientation. MIPAV calls these locations unused1, unused2, and unused3. Note that MIPAV's unused3 is at the same location as unused1 in any original format.

  Original Mayo Analyze 7.5 has at locations 112, 116, and 112 3 unused floats, funused1, funused2, and funused3. SPM99 and SPM2 have at location 112 a float scale factor. SPM2 has at location 116 a float dcoff, which is an intensity zero-intercept. MIPAV analyze has hacked these 3 locations to store 3 floats giving the x-origin, y-origin, and z-origin locations.

  Mayo Analyze 7.5 has at location 253 a uchar[10] called originator. SPM99 and SPM2 have at location 253 5-int16 called origin[0] thru origin[4]. In SPM99 X, Y, and Z are near the anterior commissure. If the first 3 shorts of a 3D image are set to 0, 0, 0, the origin is assumed to be at the center of the volume, since in SPM the corner voxel is at 1, 1, 1. The position(x,y,z) in mm. is determined by the distance(x,y,z) from the origin multiplied by the vox_units(x,y,z).

  In SPM the signed byte datatype was added with DT_BYTE = 130. MIPAV ANALYZE uses UNSIGNED_SHORT = 6 while SPM uses DT_UNSIGNED_SHORT = 132. The SPM standard also provides for an unsigned int = 136. Note that in SPM while DATA = datatype * 256 for swapped bytes, only datatype and not DATA is written to the file, so in this program we need never consider the multiplicative factors of 256.

  The most obvious way to test for whether a file is Mayo or SPM would be to see if location 112 is a funused1 = 0 or a nonzero scale factor, but this is complicated by the MIPAV hacking at 112 to store the x-origin location as a float. Asking the users what variant there analyze file is would probably cause massive confusion, so it is probably best for MIPAV just to default to the hacked 7.5 code in FileAnalyze unless a pressing need arises.

Field Summary

Fields

Modifier and Type	Field	Description
private byte[]	bufferByte	DOCUMENT ME!
private File	dataFile
private String	dataFileName
private static final int	DT_BINARY	DOCUMENT ME!
private static final int	DT_BYTE	DOCUMENT ME!
private static final int	DT_COMPLEX	DOCUMENT ME!
private static final int	DT_DOUBLE	DOCUMENT ME!
private static final int	DT_FLOAT	DOCUMENT ME!
private static final int	DT_NONE	DOCUMENT ME!
private static final int	DT_RGB	DOCUMENT ME!
private static final int	DT_SIGNED_INT	DOCUMENT ME!
private static final int	DT_SIGNED_SHORT	DOCUMENT ME!
private static final int	DT_UNSIGNED_CHAR	DOCUMENT ME!
private static final int	DT_UNSIGNED_INT	DOCUMENT ME!
private static final int	DT_UNSIGNED_SHORT	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private FileInfoSPM	fileInfo	DOCUMENT ME!
private String	fileName	DOCUMENT ME!
private File	headerFile	DOCUMENT ME!
private String	headerFileName
private int	headerSize	DOCUMENT ME!
private ModelImage	image	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
FileSPM(String fName, String fDir)	Constructs new file object.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
void	flipTopBottom(float[] buffer, FileInfoSPM fileInfo)	Flips image.
void	flipTopBottom(ModelImage image)	Flips image.
FileInfoSPM	getFileInfo()	Returns the FileInfoSPM read from the file.
private int	getOffset(FileInfoSPM fileInfo)	Helper method to calculate the offset for getting only the middle SPM image slice from the 3D file.
static boolean	isSPM(String absolutePath)	Determines whether this file is SPM file or not based on three fields of the header file: sizeof_hdr, extent and regular.
boolean	readHeader()	DOCUMENT ME!
ModelImage	readImage(boolean one)	Reads an SPM 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 an SPM image file by reading the header then making a FileRaw to read the file.
void	reOrgInfo(ModelImage image, FileInfoSPM fileInfo)	Takes the image and sets it to SPM defaults, using the specified info.
protected void	updateUnitsOfMeasure(FileInfoSPM fileInfo)	updates the units of Measure in the file info based on the voxUnits from an SPM Header.
protected void	updateUnitsOfMeasure(FileInfoSPM fileInfo, ModelImage image)	updates the units of Measure in the file info based on the voxUnits from an SPM Header.
private boolean	writeHeader(ModelImage image, int nImagesSaved, int nTimeSaved, String fileName, String fileDir)	Writes an SPM header to a separate file.
void	writeHeader3DTo2D(ModelImage image, String fileName, String fileDir, FileWriteOptions options)	DOCUMENT ME!
void	writeHeader4DTo3D(ModelImage image, String fileName, String fileDir, FileWriteOptions options)	DOCUMENT ME!
void	writeImage(ModelImage image, FileWriteOptions options)	Writes an SPM 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

DT_NONE

private static final int DT_NONE

DOCUMENT ME!

See Also:

• Constant Field Values

DT_BINARY

private static final int DT_BINARY

DOCUMENT ME!

See Also:

• Constant Field Values

DT_BYTE

private static final int DT_BYTE

DOCUMENT ME!

See Also:

• Constant Field Values

DT_UNSIGNED_CHAR

private static final int DT_UNSIGNED_CHAR

DOCUMENT ME!

See Also:

• Constant Field Values

DT_SIGNED_SHORT

private static final int DT_SIGNED_SHORT

DOCUMENT ME!

See Also:

• Constant Field Values

DT_UNSIGNED_SHORT

private static final int DT_UNSIGNED_SHORT

DOCUMENT ME!

See Also:

• Constant Field Values

DT_SIGNED_INT

private static final int DT_SIGNED_INT

DOCUMENT ME!

See Also:

• Constant Field Values

DT_UNSIGNED_INT

private static final int DT_UNSIGNED_INT

DOCUMENT ME!

See Also:

• Constant Field Values

DT_FLOAT

private static final int DT_FLOAT

DOCUMENT ME!

See Also:

• Constant Field Values

DT_COMPLEX

private static final int DT_COMPLEX

DOCUMENT ME!

See Also:

• Constant Field Values

DT_DOUBLE

private static final int DT_DOUBLE

DOCUMENT ME!

See Also:

• Constant Field Values

DT_RGB

private static final int DT_RGB

DOCUMENT ME!

See Also:

• Constant Field Values

bufferByte

private byte[] bufferByte

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileInfo

private FileInfoSPM fileInfo

DOCUMENT ME!

fileName

private String fileName

DOCUMENT ME!

headerSize

private int headerSize

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

headerFileName

private String headerFileName

headerFile

private File headerFile

DOCUMENT ME!

dataFileName

private String dataFileName

dataFile

private File dataFile

Constructor Details

FileSPM

public FileSPM(String fName,
 String fDir)

Constructs new file object.

Parameters:

fName - File name.

fDir - File directory.

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

isSPM

public static boolean isSPM(String absolutePath)
                     throws FileNotFoundException,
IOException

Determines whether this file is SPM file or not based on three fields of the header file: sizeof_hdr, extent and regular.

Parameters:

absolutePath - the file name.

Returns:

true if the file is ANALYZE file.

Throws:

FileNotFoundException - thrown when the file can't be found.

IOException - thrown when the I/O error happens.

flipTopBottom

public void flipTopBottom(ModelImage image)
                   throws IOException

Flips image. SPM stores its data "upside down".

Parameters:

image - Image to flip.

Throws:

IOException - DOCUMENT ME!

flipTopBottom

public void flipTopBottom(float[] buffer,
 FileInfoSPM fileInfo)
                   throws IOException

Flips image. SPM stores its data "upside down".

Parameters:

buffer - Buffer holding image to flip.

fileInfo - File info structure for image to flip.

Throws:

IOException - DOCUMENT ME!

getFileInfo

public FileInfoSPM getFileInfo()

Returns the FileInfoSPM read from the file.

Returns:

File info read from file, or null if it has not been read.

readHeader

public boolean readHeader()
                   throws IOException

DOCUMENT ME!

Returns:

true if read successfully

Throws:

IOException - DOCUMENT ME!

readImage

public ModelImage readImage(boolean one)
                     throws IOException,
OutOfMemoryError

Reads an SPM 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:

IOException - if there is an error reading the file

OutOfMemoryError

See Also:

• FileRaw

readImage

public void readImage(float[] buffer)
               throws IOException,
OutOfMemoryError

Reads an SPM 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:

IOException - if there is an error reading the file

OutOfMemoryError

See Also:

• FileRaw

reOrgInfo

public void reOrgInfo(ModelImage image,
 FileInfoSPM fileInfo)

Takes the image and sets it to SPM defaults, using the specified info.

Parameters:

image - Image to set to SPM defaults.

fileInfo - File info structure to change.

writeHeader3DTo2D

public void writeHeader3DTo2D(ModelImage image,
 String fileName,
 String fileDir,
 FileWriteOptions options)
                       throws IOException

DOCUMENT ME!

Parameters:

image - DOCUMENT ME!

fileName - DOCUMENT ME!

fileDir - DOCUMENT ME!

options - DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

writeHeader4DTo3D

public void writeHeader4DTo3D(ModelImage image,
 String fileName,
 String fileDir,
 FileWriteOptions options)
                       throws IOException

DOCUMENT ME!

Parameters:

image - DOCUMENT ME!

fileName - DOCUMENT ME!

fileDir - DOCUMENT ME!

options - DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

writeImage

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

Writes an SPM format type image.

Parameters:

image - Image model of data to write.

Throws:

IOException - if there is an error writing the file

See Also:

• FileInfoSPM
• FileRaw

updateUnitsOfMeasure

protected void updateUnitsOfMeasure(FileInfoSPM fileInfo)

updates the units of Measure in the file info based on the voxUnits from an SPM Header. This version simply updates a single FileInfo. It does not have an image to attach to.

Parameters:

fileInfo - -- an SPM file Info that has already been read

updateUnitsOfMeasure

protected void updateUnitsOfMeasure(FileInfoSPM fileInfo,
 ModelImage image)

updates the units of Measure in the file info based on the voxUnits from an SPM Header.

Parameters:

fileInfo - -- an SPM file Info that has already been read

image - -- a ModelImage that the fileInfo needs to be attached to

getOffset

private int getOffset(FileInfoSPM fileInfo)

Helper method to calculate the offset for getting only the middle SPM image slice from the 3D file.

Parameters:

fileInfo - File info.

Returns:

offset

writeHeader

private boolean writeHeader(ModelImage image,
 int nImagesSaved,
 int nTimeSaved,
 String fileName,
 String fileDir)
                     throws IOException

Writes an SPM header to a separate file.

Parameters:

image - Image model of data to write.

fileName - File name.

fileDir - File directory.

Returns:

Flag to confirm a successful read.

Throws:

IOException - if there is an error

See Also:

• FileInfoSPM