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

```
public class FileAnalyze
extends FileBase
```
The class reads and writes Analyze Version 7.5.x files. 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. 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 120 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, but MIPAV does not used the unsigned int data type. Note that in SPM while DATA = datatype * 256 for swapped bytes, only datatype and not DATA is written to the file. 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 just to default to the hacked 7.5 code here unless a pressing need arises.

Version:

0.1 Oct 14, 1997

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

FileIO, FileInfoAnalyze, FileRaw

Field Summary

Fields
Modifier and Type	Field	Description
`private byte[]`	`bufferImageHeader`	Storage buffer for the header.
`static java.lang.String[]`	`EXTENSIONS`	The extensions of ANALYZE file.
`private static int`	`EXTENTS`	The extent size of the ANALYZE file.
`private java.lang.String`	`fileDir`	File directory of the image.
`private java.io.File`	`fileHeader`	Reference to the header file (*.hdr).
`private FileInfoAnalyze`	`fileInfo`	Reference to the file info. for an Analyze header
`private java.lang.String`	`fileName`	File name of the image.
`static int`	`HEADER_SIZE`	The size of the header, always 348 for Analyze images.
`private int`	`headerSize`	Header size for an Analyze image is 348.
`private ModelImage`	`image`	The image read in from the file.
`private float`	`vox_offset`	Voxel offset tag used to read in the image.
`private boolean`	`zerofunused`	If true, zero funused fields

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
`FileAnalyze(java.lang.String[] fileNames)`	Creates a new FileAnalyze object.
`FileAnalyze(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`	`absoluteValue(ModelImage image)`	Take the absolute value of image.
`void`	`finalize()`	Prepares this class for cleanup.
`void`	`flipTopBottom(float[] buffer, FileInfoAnalyze fileInfo)`	Flips image.
`static void`	`flipTopBottom(ModelImage image)`	Flips image.
`static java.lang.String[]`	`getCompleteFileNameList(java.lang.String absolutePath)`	Returns the complete list of file names according to given file name.
`FileInfoAnalyze`	`getFileInfo()`	Returns the FileInfoAnalyze read from the file.
`java.lang.String`	`getHeaderFile()`	Returns the header file.
`static java.lang.String`	`getHeaderFile(java.lang.String[] fileNames)`	Returns the header file (ends in .hdr) as a string.
`java.lang.String[]`	`getImageFiles()`	Returns the image file list.
`static java.lang.String[]`	`getImageFiles(java.lang.String[] fileNames)`	Returns the image file list.
`private int`	`getOffset(FileInfoAnalyze fileInfo)`	Helper method to calculate the offset for getting only the middle analyze image slice from the 3D file.
`static int`	`isAnalyzeOrSPM(java.lang.String absolutePath)`	Determines whether this file is ANALYZE file or not based on three fields of the header file: sizeof_hdr, extent and regular.
`static boolean`	`isHeaderFile(java.lang.String absolutePath)`	Return true if the file specified by absolutePath is header file of ANALYZE.
`static boolean`	`isImageFile(java.lang.String absolutePath)`	Return true if the file specified by absolutePath is image file of ANALYZE.
`boolean`	`readHeader(java.lang.String imageFileName, java.lang.String fileDir)`	Reads the analyze header and stores the information in fileInfo.
`ModelImage`	`readImage(boolean one)`	Reads an analyze 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 analyze image file by reading the header then making a FileRaw to read the file.
`void`	`reOrgInfo(ModelImage image, FileInfoAnalyze fileInfo)`	Takes the image and sets it to analyze defaults, using the specified info.
`void`	`setZerofunused(boolean zerofunused)`
`private void`	`updateStartLocations(FileInfoBase[] fileInfo)`	Updates the start locations.
`private void`	`updateUnitsOfMeasure(FileInfoAnalyze fileInfo, ModelImage image)`	Updates the units of Measure in the file info based on the voxUnits from an Analyze Header.
`private boolean`	`writeHeader(ModelImage image, int nImagesSaved, int nTimeSaved, java.lang.String fileName, java.lang.String fileDir)`	Writes an Analyze header to a separate file.
`private void`	`writeHeader3DTo2D(ModelImage image, java.lang.String fileName, java.lang.String fileDir, FileWriteOptions options)`	This method is used when saving a 3D image in an array of 2D files.
`private void`	`writeHeader4DTo3D(ModelImage image, java.lang.String fileName, java.lang.String fileDir, FileWriteOptions options)`	This method is used when saving a 4D image in an array of 3D files.
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes an analyze 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
  - EXTENSIONS
```
public static final java.lang.String[] EXTENSIONS
```
    The extensions of ANALYZE file.
  - HEADER_SIZE
```
public static final int HEADER_SIZE
```
    The size of the header, always 348 for Analyze images.
    
    See Also:
    
    Constant Field Values
  - EXTENTS
```
private static final int EXTENTS
```
    The extent size of the ANALYZE file.
    
    See Also:
    
    Constant Field Values
  - bufferImageHeader
```
private byte[] bufferImageHeader
```
    Storage buffer for the header.
  - fileDir
```
private java.lang.String fileDir
```
    File directory of the image.
  - fileHeader
```
private java.io.File fileHeader
```
    Reference to the header file (*.hdr).
  - fileInfo
```
private FileInfoAnalyze fileInfo
```
    Reference to the file info. for an Analyze header
  - fileName
```
private java.lang.String fileName
```
    File name of the image.
  - headerSize
```
private int headerSize
```
    Header size for an Analyze image is 348.
  - image
```
private ModelImage image
```
    The image read in from the file.
  - vox_offset
```
private float vox_offset
```
    Voxel offset tag used to read in the image.
  - zerofunused
```
private boolean zerofunused
```
    If true, zero funused fields
- Constructor Detail
  - FileAnalyze
```
public FileAnalyze(java.lang.String[] fileNames)
```
    Creates a new FileAnalyze object.
    
    Parameters:
    
    fileNames - DOCUMENT ME!
  - FileAnalyze
```
public FileAnalyze(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
  - setZerofunused
```
public void setZerofunused(boolean zerofunused)
```
    Parameters:
    
    zerofunused -
  - flipTopBottom
```
public static final void flipTopBottom(ModelImage image)
                                throws java.io.IOException
```
    Flips image. Analyze stores its data "upside down".
    
    Parameters:
    
    image - Image to flip.
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - getCompleteFileNameList
```
public static java.lang.String[] getCompleteFileNameList(java.lang.String absolutePath)
```
    Returns the complete list of file names according to given file name.
    
    Parameters:
    
    absolutePath - one file name of ANALYZE.
    
    Returns:
    
    the complete list of file names.
  - getHeaderFile
```
public static java.lang.String getHeaderFile(java.lang.String[] fileNames)
```
    Returns the header file (ends in .hdr) as a string.
    
    Parameters:
    
    fileNames - DOCUMENT ME!
    
    Returns:
    
    The header file (ends in .hdr)
  - getImageFiles
```
public static java.lang.String[] getImageFiles(java.lang.String[] fileNames)
```
    Returns the image file list.
    
    Parameters:
    
    fileNames - DOCUMENT ME!
    
    Returns:
    
    the image file list.
  - isAnalyzeOrSPM
```
public static int isAnalyzeOrSPM(java.lang.String absolutePath)
                          throws java.io.FileNotFoundException,
                                 java.io.IOException
```
    Determines whether this file is ANALYZE file or not based on three fields of the header file: sizeof_hdr, extent and regular. Note that all Mayo Analyze 7.5 and all SPM99 variants will pass this test. SPM2 variants with a regular header size of 348 will also pass. Only SPM2 files with an extended header > 348 in size will fail.
    
    Parameters:
    
    absolutePath - the file name.
    
    Returns:
    
    FileUtility.ANALYZE, FileUtility.SPM, or FileUtility.UNDEFINED
    
    Throws:
    
    java.io.FileNotFoundException - thrown when the file can't be found.
    
    java.io.IOException - thrown when the I/O error happens.
  - isHeaderFile
```
public static boolean isHeaderFile(java.lang.String absolutePath)
```
    Return true if the file specified by absolutePath is header file of ANALYZE.
    
    Parameters:
    
    absolutePath - the file name including path information.
    
    Returns:
    
    true if the specified file is header file.
  - isImageFile
```
public static boolean isImageFile(java.lang.String absolutePath)
```
    Return true if the file specified by absolutePath is image file of ANALYZE.
    
    Parameters:
    
    absolutePath - the file name including path information.
    
    Returns:
    
    true if the specified file is image file.
  - absoluteValue
```
public void absoluteValue(ModelImage image)
                   throws java.io.IOException
```
    Take the absolute value of image.
    
    Parameters:
    
    image - Image to take absolute value of.
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - flipTopBottom
```
public void flipTopBottom(float[] buffer,
                          FileInfoAnalyze fileInfo)
                   throws java.io.IOException
```
    Flips image. Analyze 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 FileInfoAnalyze getFileInfo()
```
    Returns the FileInfoAnalyze read from the file.
    
    Returns:
    
    File info read from file, or null if it has not been read.
  - getHeaderFile
```
public java.lang.String getHeaderFile()
```
    Returns the header file.
    
    Returns:
    
    DOCUMENT ME!
  - getImageFiles
```
public java.lang.String[] getImageFiles()
```
    Returns the image file list.
    
    Returns:
    
    the image file list.
  - readHeader
```
public boolean readHeader(java.lang.String imageFileName,
                          java.lang.String fileDir)
                   throws java.io.IOException
```
    Reads the analyze 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:
    
    FileInfoAnalyze
  - readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException,
                            java.lang.OutOfMemoryError
```
    Reads an analyze 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 analyze 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,
                      FileInfoAnalyze fileInfo)
```
    Takes the image and sets it to analyze defaults, using the specified info.
    
    Parameters:
    
    image - Image to set to analyze defaults.
    
    fileInfo - File info structure to change.
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes an analyze 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:
    
    FileInfoAnalyze, FileRaw
  - getOffset
```
private int getOffset(FileInfoAnalyze fileInfo)
```
    Helper method to calculate the offset for getting only the middle analyze image slice from the 3D file.
    
    Parameters:
    
    fileInfo - File info.
    
    Returns:
    
    offset
  - updateStartLocations
```
private void updateStartLocations(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!
  - updateUnitsOfMeasure
```
private void updateUnitsOfMeasure(FileInfoAnalyze fileInfo,
                                  ModelImage image)
```
    Updates the units of Measure in the file info based on the voxUnits from an Analyze Header.
    
    Parameters:
    
    fileInfo - -- an Analyze file Info that has already been read
    
    image - -- a ModelImage that the fileInfo needs to be attached to
  - writeHeader
```
private boolean writeHeader(ModelImage image,
                            int nImagesSaved,
                            int nTimeSaved,
                            java.lang.String fileName,
                            java.lang.String fileDir)
                     throws java.io.IOException
```
    Writes an Analyze 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:
    
    FileInfoAnalyze
  - writeHeader3DTo2D
```
private void writeHeader3DTo2D(ModelImage image,
                               java.lang.String fileName,
                               java.lang.String fileDir,
                               FileWriteOptions options)
                        throws java.io.IOException
```
    This method is used when saving a 3D image in an array of 2D files. The file name has numbers appended to correctly order the images.
    
    Parameters:
    
    image - the image dataset to be saved
    
    fileName - the file name
    
    fileDir - the file directory
    
    options - file options indicate how to save the image
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeHeader4DTo3D
```
private void writeHeader4DTo3D(ModelImage image,
                               java.lang.String fileName,
                               java.lang.String fileDir,
                               FileWriteOptions options)
                        throws java.io.IOException
```
    This method is used when saving a 4D image in an array of 3D files. The file name has numbers appended to correctly order the images.
    
    Parameters:
    
    image - the image dataset to be saved
    
    fileName - the file name
    
    fileDir - the file directory
    
    options - file options indicate how to save the image
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!

Class FileAnalyze

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

EXTENSIONS

HEADER_SIZE

EXTENTS

bufferImageHeader

fileDir

fileHeader

fileInfo

fileName

headerSize

image

vox_offset

zerofunused

Constructor Detail

FileAnalyze

FileAnalyze

Method Detail

finalize

setZerofunused

flipTopBottom

getCompleteFileNameList

getHeaderFile

getImageFiles

isAnalyzeOrSPM

isHeaderFile

isImageFile

absoluteValue

flipTopBottom

getFileInfo

getHeaderFile

getImageFiles

readHeader

readImage

readImage

reOrgInfo

writeImage

getOffset

updateStartLocations

updateUnitsOfMeasure

writeHeader

writeHeader3DTo2D

writeHeader4DTo3D