java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FileXML
  - - gov.nih.mipav.model.file.FileImageXML

```
public class FileImageXML
extends FileXML
```
File class for reading/writing Image.XML file headers and their associated images. The XML reader uses the image.xsd schema for parsing. Inherits from FileXML, which parses the image.xml file based on the image.xsd

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`FileImageXML.LUValue`	Stores LUT information (red, green, blue, alpha).
`private class`	`FileImageXML.MyXMLHandler`	Used by the XML Parser to parse the xml header.
`class`	`FileImageXML.Thumbnail`	Holds an AWT Image and an int[] array of data for an XML Thumbnail image the thumbnail is stored in the XML's header so that it may be read in independently from the actual image data. when an XML file is saved, the user has the option to also saved a reduced resolution (max 64x64) image into the XML's header using standard XML tagging

Nested classes/interfaces inherited from class gov.nih.mipav.model.file.FileXML
FileXML.XMLAttributes

Field Summary

Fields
Modifier and Type	Field	Description
`private java.util.Enumeration<XMLPSet>`	`additionalSets`	A listing of all the additional `PSets` to be written into the saved file.
`private java.util.Vector<VOI>`	`annotationVector`	DOCUMENT ME!
`private double[]`	`bValues`
`private java.lang.String[]`	`dataFileName`
`private static java.lang.String[]`	`datasetAttributesStr`	array of strings representing the tags under in the xml schema.
`private DTIParameters`	`dtiparams`
`private int`	`functionIndex`	Index of LUT function when reading xml header.
`private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector2f>`	`functionVector`	Vector to store the LUT functions when reading xml header.
`private double[][]`	`gradients`
`private ModelImage`	`image`	Model Image associated with the file.
`private java.lang.String`	`imageFileName`	Name of the RAW (or IMG) file associated with the XML header.
`private static java.lang.String[]`	`imageStr`	array of strings representing the tags under in the xml schema.
`private static java.lang.String[]`	`investigatorsStr`	array of strings representing the tags under in the xml schema.
`private java.lang.String`	`linkedFilename`	Name of the file linked to this file (separate from fileName).
`private ModelLUT`	`LUT`	Lookup Table associated with the file (grayscale).
`private java.util.Vector<FileImageXML.LUValue>`	`lutVector`	Vector to store LUT values when reading xml header.
`private java.util.Vector<TransMatrix>`	`matrixVector`	Vector to hold matrices while they are being read in for the header (until they are added to the image
`private ModelRGB`	`modelRGB`	RGB lookup table associated with the file.
`private int`	`numVolumes`
`private static java.lang.String[]`	`parameterStr`	array of strings representing the tags under in the xml schema.
`private java.lang.String`	`rawExtension`	The extension to give to the RAW file associated with the XML header.
`private static java.lang.String[]`	`scanAttributesStr`	array of strings representing the tags under in the xml schema.
`private static java.lang.String[]`	`setStr`	array of strings representing the tags under in the xml schema.
`private static java.lang.String[]`	`subjectInformationStr`	array of strings representing the tags under in the xml schema.
`private static java.lang.String[]`	`surfaceStr`	array of strings representing the tags under in the xml schema.
`private FileImageXML.Thumbnail`	`thumbnail`	Thumbnail data and AWT Image.
`private static java.lang.String[]`	`voiStr`	array of strings representing the tags under in the xml schema.

Fields inherited from class gov.nih.mipav.model.file.FileXML
bw, fileDir, fileInfo, fileName, m_kHandler, MIPAV_HEADER, pInterface, TAB, tabLevel, W3C_XML_SCHEMA, XML_ENCODING, XML_HEADER

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

FileImageXML(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`	`addFunctionToLUT()`	Adds the LUT functions collected within the functionVector.
`private void`	`addFunctionToRGB()`	Adds the ModelRGB functions contained within the functionVector.
`private void`	`addLUValue(java.lang.String s)`	Adds LUValue for either LUT or modelRGB.
`private void`	`addPointToFunction(java.lang.String s)`	Adds a point to the function associated with the LUT or modelRGB.
`void`	`clearAdditionalSets()`	Convenience method to clear any additional sets of the enumerated list that might be written into the header file.
`void`	`finalize()`	Prepares class for cleanup.
`static void`	`flipTopBottom(float[] buffer, FileInfoImageXML xmlInfo)`	Flips image.
`static void`	`flipTopBottom(ModelImage img)`	Flips image.
`java.util.Enumeration<XMLPSet>`	`getAdditionalSets()`	Returns the enumerated list of additional sets to be written into the header file.
`java.lang.String[]`	`getDataFileName()`	Accessor that returns the array of data file names
`FileInfoImageXML`	`getFileInfo()`	Returns the FileInfoXML read from the file.
`private java.lang.String`	`getFormattedThumbnailLine(int[] data, int index)`	Returns a String for writing the thumbnail data (r,g,b) to the XML header.
`private byte[]`	`getFullBuffer(java.io.InputStream in, byte[] buff, int off, int fullBufferSize)`
`ModelLUT`	`getModelLUT()`	Gets the LUT.
`ModelRGB`	`getModelRGB()`	Gets the modelRGB.
`private static int`	`getOffset(FileInfoImageXML xmlInfo)`	Helper method to calculate the offset for getting only the middle analyze image slice from the 3D file.
`FileImageXML.Thumbnail`	`getThumbnail()`	Returns the thumbnail associated with the xml file (saved in header).
`float[][]`	`readHeader(java.lang.String headerFileName, java.lang.String headerDir, TalairachTransformInfo talairach)`	Reads and parses an XML header.
`ModelImage`	`readImage(boolean one)`	Reads an XML image file by reading the XML header then making a FileRaw to read the image for all filenames in the file list.
`void`	`readImage(float[] buffer)`	Reads an XML image file by reading the header then making a FileRaw to read the file.
`void`	`setAdditionalSets(java.util.Enumeration<XMLPSet> moreSets)`	Method to replace the enumerated list of additional sets to be written into the header file.
`void`	`setFileName(java.lang.String fName)`	Accessor to set the file name (used when reading XML multiFile).
`private void`	`setLUT()`	Sets up the LUT based on the values read into the lutVector.
`void`	`setModelLUT(ModelLUT lut)`	Sets the model LUT.
`void`	`setModelRGB(ModelRGB modelRGB)`	Sets the model RGB.
`void`	`setRawExtension(java.lang.String ext)`	Changes the extension of the image data file associated with this XML header.
`private void`	`setRGB()`	sets up the model RGB while parsing XML header after all LUValues have been saved in the LUT vector.
`void`	`setThumbnailData(int xDim, int yDim, int[] data)`	Sets the thumbnail data (array of shorts).
`private void`	`updateOriginInfo(FileInfoImageXML[] xmlInfo)`	Updates the start locations.
`boolean`	`writeHeader(ModelImage img, FileWriteOptions options, java.lang.String headerName, java.lang.String headerDir, boolean changeDims)`	Writes the XML header information out to the given filename and path.
`private void`	`writeHeader3DTo2D(ModelImage img, java.lang.String headerName, java.lang.String headerDir, FileWriteOptions options)`	Method to save off the header from a 4D image into 3D header files sequentially named (similar to the method in FileRaw).
`private void`	`writeHeader4DTo3D(ModelImage img, java.lang.String headerName, java.lang.String headerDir, FileWriteOptions options)`	Method to save off the header from a 4D image into 3D header files sequentially named (similar to the method in FileRaw).
`void`	`writeImage(ModelImage img, FileWriteOptions options)`	Writes an XML image with the given options.
`private void`	`writeSet(java.io.BufferedWriter bw, java.util.Enumeration<XMLPSet> setEnum)`	`writeSet` is a helper method, to allow writing set data out to the `BufferedWriter` with any enumeration.

Methods inherited from class gov.nih.mipav.model.file.FileXML
closedTag, closedTag, closedTag, openTag, readHeader, setPBar

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
  - imageStr
```
private static final java.lang.String[] imageStr
```
    array of strings representing the tags under in the xml schema.
  - datasetAttributesStr
```
private static final java.lang.String[] datasetAttributesStr
```
    array of strings representing the tags under in the xml schema.
  - subjectInformationStr
```
private static final java.lang.String[] subjectInformationStr
```
    array of strings representing the tags under in the xml schema.
  - scanAttributesStr
```
private static final java.lang.String[] scanAttributesStr
```
    array of strings representing the tags under in the xml schema.
  - investigatorsStr
```
private static final java.lang.String[] investigatorsStr
```
    array of strings representing the tags under in the xml schema.
  - setStr
```
private static final java.lang.String[] setStr
```
    array of strings representing the tags under in the xml schema.
  - parameterStr
```
private static final java.lang.String[] parameterStr
```
    array of strings representing the tags under in the xml schema.
  - voiStr
```
private static final java.lang.String[] voiStr
```
    array of strings representing the tags under in the xml schema.
  - surfaceStr
```
private static final java.lang.String[] surfaceStr
```
    array of strings representing the tags under in the xml schema.
  - additionalSets
```
private java.util.Enumeration<XMLPSet> additionalSets
```
    A listing of all the additional PSets to be written into the saved file.
  - annotationVector
```
private java.util.Vector<VOI> annotationVector
```
    DOCUMENT ME!
  - functionIndex
```
private int functionIndex
```
    Index of LUT function when reading xml header.
  - functionVector
```
private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector2f> functionVector
```
    Vector to store the LUT functions when reading xml header.
  - matrixVector
```
private java.util.Vector<TransMatrix> matrixVector
```
    Vector to hold matrices while they are being read in for the header (until they are added to the image
  - image
```
private ModelImage image
```
    Model Image associated with the file.
  - imageFileName
```
private java.lang.String imageFileName
```
    Name of the RAW (or IMG) file associated with the XML header.
  - linkedFilename
```
private java.lang.String linkedFilename
```
    Name of the file linked to this file (separate from fileName).
  - LUT
```
private ModelLUT LUT
```
    Lookup Table associated with the file (grayscale).
  - lutVector
```
private java.util.Vector<FileImageXML.LUValue> lutVector
```
    Vector to store LUT values when reading xml header.
  - modelRGB
```
private ModelRGB modelRGB
```
    RGB lookup table associated with the file.
  - rawExtension
```
private java.lang.String rawExtension
```
    The extension to give to the RAW file associated with the XML header. May be changed to .img if the XML header links to an Analyze image (and will need to be flipped when the image is read back in).
  - thumbnail
```
private FileImageXML.Thumbnail thumbnail
```
    Thumbnail data and AWT Image.
  - dataFileName
```
private java.lang.String[] dataFileName
```
  - dtiparams
```
private DTIParameters dtiparams
```
  - numVolumes
```
private int numVolumes
```
  - gradients
```
private double[][] gradients
```
  - bValues
```
private double[] bValues
```
- Constructor Detail
  - FileImageXML
```
public FileImageXML(java.lang.String fName,
                    java.lang.String fDir)
```
    Constructs new file object.
    
    Parameters:
    
    fName - File name.
    
    fDir - File directory.
- Method Detail
  - flipTopBottom
```
public static final void flipTopBottom(ModelImage img)
                                throws java.io.IOException
```
    Flips image. Analyze stores its data "upside down". Used if reading in an XML header attached to an .img raw data file.
    
    Parameters:
    
    img - Image to flip.
    
    Throws:
    
    java.io.IOException - if there is a problem importing or exporting the image
  - flipTopBottom
```
public static final void flipTopBottom(float[] buffer,
                                       FileInfoImageXML xmlInfo)
```
    Flips image. Analyze stores its data "upside down". Used if reading in an XML header attached to an .img raw data file.
    
    Parameters:
    
    buffer - Buffer holding image to flip.
    
    xmlInfo - File info structure for image to flip.
  - clearAdditionalSets
```
public void clearAdditionalSets()
```
    Convenience method to clear any additional sets of the enumerated list that might be written into the header file.
  - finalize
```
public void finalize()
```
    Prepares class for cleanup.
    
    Overrides:
    
    finalize in class FileXML
  - getAdditionalSets
```
public java.util.Enumeration<XMLPSet> getAdditionalSets()
```
    Returns the enumerated list of additional sets to be written into the header file.
    
    Returns:
    
    the additional parameter sets that will be written out to the header
  - getFileInfo
```
public FileInfoImageXML getFileInfo()
```
    Returns the FileInfoXML read from the file.
    
    Returns:
    
    File info read from file, or null if it has not been read.
  - getModelLUT
```
public ModelLUT getModelLUT()
```
    Gets the LUT.
    
    Returns:
    
    ModelLUT the LUT
  - getModelRGB
```
public ModelRGB getModelRGB()
```
    Gets the modelRGB.
    
    Returns:
    
    ModelRGB the modelRGB
  - getThumbnail
```
public FileImageXML.Thumbnail getThumbnail()
```
    Returns the thumbnail associated with the xml file (saved in header).
    
    Returns:
    
    Thumbnail
  - getDataFileName
```
public java.lang.String[] getDataFileName()
```
    Accessor that returns the array of data file names
    
    Returns:
  - readHeader
```
public float[][] readHeader(java.lang.String headerFileName,
                            java.lang.String headerDir,
                            TalairachTransformInfo talairach)
                     throws java.io.IOException
```
    Reads and parses an XML header.
    
    Parameters:
    
    headerFileName - file name of xml header
    
    headerDir - directory
    
    talairach - the talairach transform info to fill out if contained within the header
    
    Returns:
    
    double array containing resolutions (for setting resolutions per FileInfoImageXML)
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException,
                            java.lang.OutOfMemoryError
```
    Reads an XML image file by reading the XML 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 - if there is a problem allocating memory for the image
    
    See Also:
    
    FileRaw
  - getFullBuffer
```
private byte[] getFullBuffer(java.io.InputStream in,
                             byte[] buff,
                             int off,
                             int fullBufferSize)
```
  - readImage
```
public void readImage(float[] buffer)
               throws java.io.IOException,
                      java.lang.OutOfMemoryError
```
    Reads an XML 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.
    
    Parameters:
    
    buffer - Image buffer to store image data into. It is equal to the header length.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
    
    java.lang.OutOfMemoryError - if there was a problem allocating enough memory
    
    See Also:
    
    FileRaw
  - setAdditionalSets
```
public void setAdditionalSets(java.util.Enumeration<XMLPSet> moreSets)
```
    Method to replace the enumerated list of additional sets to be written into the header file. Any existing value is lost.
    
    Parameters:
    
    moreSets - additional parameter sets to be written
  - setFileName
```
public void setFileName(java.lang.String fName)
```
    Accessor to set the file name (used when reading XML multiFile).
    
    Parameters:
    
    fName - file name of image to read.
  - setModelLUT
```
public void setModelLUT(ModelLUT lut)
```
    Sets the model LUT.
    
    Parameters:
    
    lut - ModelLUT the LUT
  - setModelRGB
```
public void setModelRGB(ModelRGB modelRGB)
```
    Sets the model RGB.
    
    Parameters:
    
    modelRGB - ModelRGB the modelRGB
  - setRawExtension
```
public void setRawExtension(java.lang.String ext)
```
    Changes the extension of the image data file associated with this XML header.
    
    Parameters:
    
    ext - the new file extension (such as .img)
  - setThumbnailData
```
public void setThumbnailData(int xDim,
                             int yDim,
                             int[] data)
```
    Sets the thumbnail data (array of shorts).
    
    Parameters:
    
    xDim - the buffer length in the x dimension
    
    yDim - the buffer length in the y dimension
    
    data - the thumbnail data
  - writeHeader
```
public boolean writeHeader(ModelImage img,
                           FileWriteOptions options,
                           java.lang.String headerName,
                           java.lang.String headerDir,
                           boolean changeDims)
                    throws java.io.IOException
```
    Writes the XML header information out to the given filename and path.
    
    Parameters:
    
    img - image associated with header
    
    options - the options to use when writing out the file
    
    headerName - file name to write to
    
    headerDir - name of directory to write to
    
    changeDims - if true indicates that the image is changing dimensionality (e.g., 3D to 2D)
    
    Returns:
    
    if header write was successful
    
    Throws:
    
    java.io.IOException - if a file I/O problem is encoutered while writing the header
  - writeImage
```
public void writeImage(ModelImage img,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes an XML image with the given options.
    
    Parameters:
    
    img - Model image to be written to disk
    
    options - tells how and where to save file
    
    Throws:
    
    java.io.IOException - if there is a problem writing to the file
  - getOffset
```
private static int getOffset(FileInfoImageXML xmlInfo)
```
    Helper method to calculate the offset for getting only the middle analyze image slice from the 3D file.
    
    Parameters:
    
    xmlInfo - File info.
    
    Returns:
    
    offset
  - addFunctionToLUT
```
private void addFunctionToLUT()
```
    Adds the LUT functions collected within the functionVector.
  - addFunctionToRGB
```
private void addFunctionToRGB()
```
    Adds the ModelRGB functions contained within the functionVector.
  - addLUValue
```
private void addLUValue(java.lang.String s)
```
    Adds LUValue for either LUT or modelRGB.
    
    Parameters:
    
    s - String
  - addPointToFunction
```
private void addPointToFunction(java.lang.String s)
```
    Adds a point to the function associated with the LUT or modelRGB.
    
    Parameters:
    
    s - String
  - getFormattedThumbnailLine
```
private java.lang.String getFormattedThumbnailLine(int[] data,
                                                   int index)
```
    Returns a String for writing the thumbnail data (r,g,b) to the XML header.
    
    Parameters:
    
    data - int[] array of int thumbnail data
    
    index - int index of thumbnail data (which line)
    
    Returns:
    
    String a formatted string containing comma separated thumbnail information
  - setLUT
```
private void setLUT()
```
    Sets up the LUT based on the values read into the lutVector.
  - setRGB
```
private void setRGB()
```
    sets up the model RGB while parsing XML header after all LUValues have been saved in the LUT vector.
  - updateOriginInfo
```
private void updateOriginInfo(FileInfoImageXML[] xmlInfo)
```
    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:
    
    xmlInfo - the file info to update
  - writeHeader3DTo2D
```
private void writeHeader3DTo2D(ModelImage img,
                               java.lang.String headerName,
                               java.lang.String headerDir,
                               FileWriteOptions options)
                        throws java.io.IOException
```
    Method to save off the header from a 4D image into 3D header files sequentially named (similar to the method in FileRaw).
    
    Parameters:
    
    img - Image to be saved
    
    headerName - Name of file
    
    headerDir - Directory for file
    
    options - File write options (contains # of digits and start #)
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeHeader4DTo3D
```
private void writeHeader4DTo3D(ModelImage img,
                               java.lang.String headerName,
                               java.lang.String headerDir,
                               FileWriteOptions options)
                        throws java.io.IOException
```
    Method to save off the header from a 4D image into 3D header files sequentially named (similar to the method in FileRaw).
    
    Parameters:
    
    img - Image to be saved
    
    headerName - name of file
    
    headerDir - directory for file
    
    options - file write options
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeSet
```
private void writeSet(java.io.BufferedWriter bw,
                      java.util.Enumeration<XMLPSet> setEnum)
```
    writeSet is a helper method, to allow writing set data out to the BufferedWriter with any enumeration.
    
    Parameters:
    
    bw - The writer to which we will write the data.
    
    setEnum - An enumerated list of set data.

Class FileImageXML

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.model.file.FileXML

Field Summary

Fields inherited from class gov.nih.mipav.model.file.FileXML

Fields inherited from class gov.nih.mipav.model.file.FileBase

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.file.FileXML

Methods inherited from class gov.nih.mipav.model.file.FileBase

Methods inherited from class java.lang.Object

Field Detail

imageStr

datasetAttributesStr

subjectInformationStr

scanAttributesStr

investigatorsStr

setStr

parameterStr

voiStr

surfaceStr

additionalSets

annotationVector

functionIndex

functionVector

matrixVector

image

imageFileName

linkedFilename

LUT

lutVector

modelRGB

rawExtension

thumbnail

dataFileName

dtiparams

numVolumes

gradients

bValues

Constructor Detail

FileImageXML

Method Detail

flipTopBottom

flipTopBottom

clearAdditionalSets

finalize

getAdditionalSets

getFileInfo

getModelLUT

getModelRGB

getThumbnail

getDataFileName

readHeader

readImage

getFullBuffer

readImage

setAdditionalSets

setFileName

setModelLUT

setModelRGB

setRawExtension

setThumbnailData

writeHeader

writeImage

getOffset

addFunctionToLUT

addFunctionToRGB

addLUValue

addPointToFunction

getFormattedThumbnailLine

setLUT

setRGB

updateOriginInfo

writeHeader3DTo2D

writeHeader4DTo3D

writeSet