Package gov.nih.mipav.model.file

Class FileImageXML

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 Enumeration<XMLPSet>	additionalSets	A listing of all the additional PSets to be written into the saved file.
private Vector<VOI>	annotationVector	DOCUMENT ME!
private double[]	bValues
private String[]	dataFileName
private static final String[]	datasetAttributesStr	array of strings representing the tags under invalid input: '<'Dataset-attributes> in the xml schema.
private DTIParameters	dtiparams
private int	functionIndex	Index of LUT function when reading xml header.
private 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 String	imageFileName	Name of the RAW (or IMG) file associated with the XML header.
private static final String[]	imageStr	array of strings representing the tags under in the xml schema.
private static final String[]	investigatorsStr	array of strings representing the tags under in the xml schema.
private String	linkedFilename	Name of the file linked to this file (separate from fileName).
private ModelLUT	LUT	Lookup Table associated with the file (grayscale).
private Vector<FileImageXML.LUValue>	lutVector	Vector to store LUT values when reading xml header.
private 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 final String[]	parameterStr	array of strings representing the tags under in the xml schema.
private String	rawExtension	The extension to give to the RAW file associated with the XML header.
private static final String[]	scanAttributesStr	array of strings representing the tags under invalid input: '<'Scan-attributes> in the xml schema.
private static final String[]	setStr	array of strings representing the tags under in the xml schema.
private static final String[]	subjectInformationStr	array of strings representing the tags under invalid input: '<'Subject-information> in the xml schema.
private static final String[]	surfaceStr	array of strings representing the tags under in the xml schema.
private FileImageXML.Thumbnail	thumbnail	Thumbnail data and AWT Image.
private static final 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(String fName, String fDir)	Constructs new file object.

Method Summary

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(String s)	Adds LUValue for either LUT or modelRGB.
private void	addPointToFunction(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 final void	flipTopBottom(float[] buffer, FileInfoImageXML xmlInfo)	Flips image.
static final void	flipTopBottom(ModelImage img)	Flips image.
Enumeration<XMLPSet>	getAdditionalSets()	Returns the enumerated list of additional sets to be written into the header file.
String[]	getDataFileName()	Accessor that returns the array of data file names
FileInfoImageXML	getFileInfo()	Returns the FileInfoXML read from the file.
private String	getFormattedThumbnailLine(int[] data, int index)	Returns a String for writing the thumbnail data (r,g,b) to the XML header.
private byte[]	getFullBuffer(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(String headerFileName, 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(Enumeration<XMLPSet> moreSets)	Method to replace the enumerated list of additional sets to be written into the header file.
void	setFileName(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(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, String headerName, String headerDir, boolean changeDims)	Writes the XML header information out to the given filename and path.
private void	writeHeader3DTo2D(ModelImage img, String headerName, 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, String headerName, 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(BufferedWriter bw, 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 Details

imageStr

private static final String[] imageStr

array of strings representing the tags under in the xml schema.

datasetAttributesStr

private static final String[] datasetAttributesStr

array of strings representing the tags under invalid input: '<'Dataset-attributes> in the xml schema.

subjectInformationStr

private static final String[] subjectInformationStr

array of strings representing the tags under invalid input: '<'Subject-information> in the xml schema.

scanAttributesStr

private static final String[] scanAttributesStr

array of strings representing the tags under invalid input: '<'Scan-attributes> in the xml schema.

investigatorsStr

private static final String[] investigatorsStr

array of strings representing the tags under in the xml schema.

setStr

private static final String[] setStr

array of strings representing the tags under in the xml schema.

parameterStr

private static final String[] parameterStr

array of strings representing the tags under in the xml schema.

voiStr

private static final String[] voiStr

array of strings representing the tags under in the xml schema.

surfaceStr

private static final String[] surfaceStr

array of strings representing the tags under in the xml schema.

additionalSets

private Enumeration<XMLPSet> additionalSets

A listing of all the additional PSets to be written into the saved file.

annotationVector

private Vector<VOI> annotationVector

DOCUMENT ME!

functionIndex

private int functionIndex

Index of LUT function when reading xml header.

functionVector

private Vector<WildMagic.LibFoundation.Mathematics.Vector2f> functionVector

Vector to store the LUT functions when reading xml header.

matrixVector

private 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 String imageFileName

Name of the RAW (or IMG) file associated with the XML header.

linkedFilename

private 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 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 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 String[] dataFileName

dtiparams

private DTIParameters dtiparams

numVolumes

private int numVolumes

gradients

private double[][] gradients

bValues

private double[] bValues

Constructor Details

FileImageXML

public FileImageXML(String fName,
 String fDir)

Constructs new file object.

Parameters:

fName - File name.

fDir - File directory.

Method Details

flipTopBottom

public static final void flipTopBottom(ModelImage img)
                                throws 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:

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 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 String[] getDataFileName()

Accessor that returns the array of data file names

Returns:

readHeader

public float[][] readHeader(String headerFileName,
 String headerDir,
 TalairachTransformInfo talairach)
                     throws 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:

IOException - DOCUMENT ME!

readImage

public ModelImage readImage(boolean one)
                     throws IOException,
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:

IOException - if there is an error reading the file

OutOfMemoryError - if there is a problem allocating memory for the image

See Also:

• FileRaw

getFullBuffer

private byte[] getFullBuffer(InputStream in,
 byte[] buff,
 int off,
 int fullBufferSize)

readImage

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

IOException - if there is an error reading the file

OutOfMemoryError - if there was a problem allocating enough memory

See Also:

• FileRaw

setAdditionalSets

public void setAdditionalSets(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(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(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,
 String headerName,
 String headerDir,
 boolean changeDims)
                    throws 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:

IOException - if a file I/O problem is encoutered while writing the header

writeImage

public void writeImage(ModelImage img,
 FileWriteOptions options)
                throws 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:

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(String s)

Adds LUValue for either LUT or modelRGB.

Parameters:

s - String

addPointToFunction

private void addPointToFunction(String s)

Adds a point to the function associated with the LUT or modelRGB.

Parameters:

s - String

getFormattedThumbnailLine

private 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,
 String headerName,
 String headerDir,
 FileWriteOptions options)
                        throws 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:

IOException - DOCUMENT ME!

writeHeader4DTo3D

private void writeHeader4DTo3D(ModelImage img,
 String headerName,
 String headerDir,
 FileWriteOptions options)
                        throws 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:

IOException - DOCUMENT ME!

writeSet

private void writeSet(BufferedWriter bw,
 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.