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 java.io.File`	`dataFile`
`private java.lang.String`	`dataFileName`
`private static int`	`DT_BINARY`	DOCUMENT ME!
`private static int`	`DT_BYTE`	DOCUMENT ME!
`private static int`	`DT_COMPLEX`	DOCUMENT ME!
`private static int`	`DT_DOUBLE`	DOCUMENT ME!
`private static int`	`DT_FLOAT`	DOCUMENT ME!
`private static int`	`DT_NONE`	DOCUMENT ME!
`private static int`	`DT_RGB`	DOCUMENT ME!
`private static int`	`DT_SIGNED_INT`	DOCUMENT ME!
`private static int`	`DT_SIGNED_SHORT`	DOCUMENT ME!
`private static int`	`DT_UNSIGNED_CHAR`	DOCUMENT ME!
`private static int`	`DT_UNSIGNED_INT`	DOCUMENT ME!
`private static int`	`DT_UNSIGNED_SHORT`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoSPM`	`fileInfo`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private java.io.File`	`headerFile`	DOCUMENT ME!
`private java.lang.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(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
`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(java.lang.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, java.lang.String fileName, java.lang.String fileDir)`	Writes an SPM header to a separate file.
`void`	`writeHeader3DTo2D(ModelImage image, java.lang.String fileName, java.lang.String fileDir, FileWriteOptions options)`	DOCUMENT ME!
`void`	`writeHeader4DTo3D(ModelImage image, java.lang.String fileName, java.lang.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 Detail
  - 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 java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoSPM fileInfo
```
    DOCUMENT ME!
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - headerSize
```
private int headerSize
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - headerFileName
```
private java.lang.String headerFileName
```
  - headerFile
```
private java.io.File headerFile
```
    DOCUMENT ME!
  - dataFileName
```
private java.lang.String dataFileName
```
  - dataFile
```
private java.io.File dataFile
```
- Constructor Detail
  - FileSPM
```
public FileSPM(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
  - isSPM
```
public static boolean isSPM(java.lang.String absolutePath)
                     throws java.io.FileNotFoundException,
                            java.io.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:
    
    java.io.FileNotFoundException - thrown when the file can't be found.
    
    java.io.IOException - thrown when the I/O error happens.
  - flipTopBottom
```
public void flipTopBottom(ModelImage image)
                   throws java.io.IOException
```
    Flips image. SPM stores its data "upside down".
    
    Parameters:
    
    image - Image to flip.
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - flipTopBottom
```
public void flipTopBottom(float[] buffer,
                          FileInfoSPM fileInfo)
                   throws java.io.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:
    
    java.io.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 java.io.IOException
```
    DOCUMENT ME!
    
    Returns:
    
    true if read successfully
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException,
                            java.lang.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:
    
    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 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:
    
    java.io.IOException - if there is an error reading the file
    
    java.lang.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,
                              java.lang.String fileName,
                              java.lang.String fileDir,
                              FileWriteOptions options)
                       throws java.io.IOException
```
    DOCUMENT ME!
    
    Parameters:
    
    image - DOCUMENT ME!
    
    fileName - DOCUMENT ME!
    
    fileDir - DOCUMENT ME!
    
    options - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeHeader4DTo3D
```
public void writeHeader4DTo3D(ModelImage image,
                              java.lang.String fileName,
                              java.lang.String fileDir,
                              FileWriteOptions options)
                       throws java.io.IOException
```
    DOCUMENT ME!
    
    Parameters:
    
    image - DOCUMENT ME!
    
    fileName - DOCUMENT ME!
    
    fileDir - DOCUMENT ME!
    
    options - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes an SPM format type image.
    
    Parameters:
    
    image - Image model of data to write.
    
    Throws:
    
    java.io.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,
                            java.lang.String fileName,
                            java.lang.String fileDir)
                     throws java.io.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:
    
    java.io.IOException - if there is an error
    
    See Also:
    
    FileInfoSPM

Class FileSPM

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

DT_NONE

DT_BINARY

DT_BYTE

DT_UNSIGNED_CHAR

DT_SIGNED_SHORT

DT_UNSIGNED_SHORT

DT_SIGNED_INT

DT_UNSIGNED_INT

DT_FLOAT

DT_COMPLEX

DT_DOUBLE

DT_RGB

bufferByte

fileDir

fileInfo

fileName

headerSize

image

headerFileName

headerFile

dataFileName

dataFile

Constructor Detail

FileSPM

Method Detail

finalize

isSPM

flipTopBottom

flipTopBottom

getFileInfo

readHeader

readImage

readImage

reOrgInfo

writeHeader3DTo2D

writeHeader4DTo3D

writeImage

updateUnitsOfMeasure

updateUnitsOfMeasure

getOffset

writeHeader