Package com.xinapse.multisliceimage.UNC

Class UNCImage

java.lang.Object

com.xinapse.multisliceimage.MultiSliceImage

com.xinapse.multisliceimage.UNC.UNCImage

All Implemented Interfaces:

ReadableImage, WritableImage, InfoStorer, AutoCloseable, Cloneable

public class UNCImage
extends MultiSliceImage
implements InfoStorer, AutoCloseable

This class is a representation of a multi-dimensional image in the University of North Carolina (UNC) format. A UNCImage object may be either purely held in memory, or may have its pixel data kept on disk. Note that only big-endian byte ordering is implemented and supported.

Nested Class Summary

Nested classes/interfaces inherited from interface com.xinapse.image.ReadableImage

ReadableImage.Position

Field Summary

Fields

Modifier and Type	Field	Description
static final boolean	DEFAULT_OVERWRITE	The default setting for the whether UNC images can be overwritten.
static final int	N_DIMV	The maximum dimensionality of an image.
static final int	N_HISTOGRAM	The number of entries in an image histogram

Fields inherited from class com.xinapse.multisliceimage.MultiSliceImage

AUDIT_TRAIL_ACTION_TEXT, BIRTH_DATE_NAME, BODY_PART_NAME, COLOUR_MAPPING_NAME, DW_B_MATRIX_NAME, DW_B_VALUE_NAME, DW_GRADIENT_VECTOR_NAME, ECHO_TIME_NAME, ECHO_TRAIN_LENGTH_NAME, FLIP_ANGLE_NAME, FRAME_OF_REFERENCE_UID_NAME, IMAGE_ORIENTATION_PATIENT_NAME, IMAGE_POSITION_PATIENT_NAME, INTENSITY_RESCALE_INTERCEPT_NAME, INTENSITY_RESCALE_SLOPE_NAME, INTENSITY_RESCALE_UNITS_NAME, INVERSION_TIME_NAME, LATERALITY_NAME, MODALITY_NAME, mode, PATIENT_ID_NAME, PATIENT_NAME_NAME, PATIENT_POSITION_NAME, PATIENT_SEX_NAME, pixArray, PIXEL_SPACING_NAME, PIXEL_X_SIZE_NAME, PIXEL_Y_SIZE_NAME, PIXEL_Z_SIZE_NAME, PULSE_SEQUENCE_NAME, randomAccessFile, REPETITION_TIME_NAME, SAT_PULSE_FREQ_OFFSET_PPM_NAME, SCAN_DATE_NAME, SCANNING_SEQUENCE_NAME, SEQUENCE_VARIANT_NAME, SERIES_DESCRIPTION_NAME, SERIES_INSTANCE_UID_NAME, SERIES_NUMBER_NAME, SLICE_THICKNESS_NAME, STORAGE_CLASS_UID_NAME, STUDY_ID_NAME, STUDY_INSTANCE_UID_NAME, TIME_BETWEEN_FRAMES_NAME, TRIGGER_DELAY_NAME

Constructor Summary

Constructors

Constructor	Description
UNCImage()	Creates an uninitialised instance of a UNCImage.
UNCImage(UNCPixFormat pixform, int dimc, int[] dimv)	Creates an in-memory UNCImage with the given type of pixel and dimensions.
UNCImage(DataInputStream s, boolean skipPixelData)	Creates an in-memory UNCImage, loading all information from the data input stream.
UNCImage(File f, UNCPixFormat pixform, int dimc, int[] dimv)	Creates a disk-based UNCImage with the given type of pixel and dimensions.
UNCImage(String fileName, UNCPixFormat pixform, int dimc, int[] dimv)	Creates a disk-based UNCImage with the given type of pixel and dimensions.

Method Summary

Modifier and Type	Method	Description
void	anonymise(String patientName, String patientID, Date birthDate, boolean patSex, String patAddr, String patInsurancePlanID, String accessionNumber, boolean patOther, String physicianName, String physicianAddr, String institutionName, String institutionAddr, String deptName, String stationName, String telNumber, boolean removePrivateElements)	Anonymise this WritableImage.
void	appendAuditInfo(String name, String value)	Appends audit trail information to this image.
void	appendInfoList(InfoList list)	Appends an InfoList to the existing general file info of this image.
void	appendInfoList(InfoList list, int dim, int n)	Appends an InfoList to that existing for a specific dimension of this image.
void	close()	Closes a UNCImage and frees up resources.
void	copyInfo(UNCImage toImage)	Copies all the info fields to another image.
void	disposeImageData()	Gives this image the option to free up resources by removing access to image data.
com.xinapse.dicom.BodyPart	getBodyPart()	By default, body part recording is not supported, so this method always returns null.
ByteOrder	getByteOrder()	Returns the byte order for this image.
int	getBytesPerPixel()	Returns the number of bytes per pixel for this image.
static String	getCommonName()	Returns the common name for this type of image.
WritableImage	getCopy()	Returns a copy of this WritableImage.
String	getDescription()	Returns a String description of this image.
String	getDescription(int slice)	Returns a String description of this one particular slice of this image.
int	getDimc()	Returns the dimensionality of this image.
int[]	getDims()	Returns the dimensions (numbers of samples in each image dimension) of this image.
int[]	getDimv()	Returns the dimensions of this image.
Integer	getEchoTrainLength()	Returns the scan echo train length for this image.
int	getFileDataOffset()	Returns the byte offset into the disk-based file format where pixel data begins.
Float	getFlipAngle()	Returns the excitation pulse flip angle for this image.
float[]	getFrameDWBMatrix(int frame)	Returns the diffusion-weighting b-matrix for one frame of this image.
Float	getFrameDWbValue(int frame)	Returns the diffusion-weighting b-value for one frame of this 4-D image.
org.jogamp.vecmath.Vector3f	getFrameDWGradientVector(int frame)	Returns the diffusion-weighting gradient-vector for one frame of this image 4-D image.
String	getFrameInfo(String name, int frame)	Returns a String representing the value of this information item in a particular frame of this image.
InfoList	getFrameInfoList(int frame)	Returns an InfoList object applying to a particular frame of this image.
Float	getFrameTriggerDelayMS(int frame)	Returns the trigger delay, in milliseconds, for one frame of this image.
String	getHTMLDescription()	Returns a String description of this image in HTML format.
String	getHTMLDescription(int slice)	Returns a String description of a slice of this image in HTML format.
org.jogamp.vecmath.Vector3f[]	getImageOrientationPatient()	Returns the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient (L,P,S) coordinates.
org.jogamp.vecmath.Vector3f[]	getImageOrientationPatient(int slice)	Returns the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient coordinates.
org.jogamp.vecmath.Point3f	getImagePositionPatient()	Returns the coordinates of the center of the first pixel of the image, in mm, in patient coordinates.
org.jogamp.vecmath.Point3f	getImagePositionPatient(int slice)	Returns the coordinates of the center of the first pixel of the specified slice of this image, in mm, in patient coordinates.
String	getImageTypeName()	Returns the normal human readable name for this type of image.
String	getInfo(String name)	Returns a string representing the value of this information item in the general image information.
String	getInfo(String name, int dim, int n)	Returns a String representing the value of this information item in a particular dimension of this image.
InfoList	getInfoList()	Returns an InfoList object which is the general info for this image.
InfoList	getInfoList(int dim, int n)	Returns an InfoList object applying to a particular dimension/element for this image.
float[]	getIntensityRescale()	Returns the values m and b in the relationship between pixel intensity (I) values and the output units specified in getRescaleUnits() in the expression: Output units = m*I + b.
com.xinapse.dicom.Laterality	getLaterality()	By default, laterality recording is not supported, so this method returns Laterality.BOTH.
Double	getMax()	Returns the maximum pixel intensity in the image.
Double	getMin()	Returns the minimum pixel intensity in the image.
ColourMapping	getNativeColourMapping()	Returns a ColourMapping if this image has an associated colour mapping.
String	getNativeHeader()	Returns a String showing the 'native' header for this image.
int	getNCols()	Returns the number of image columns in this image.
int	getNDim()	Returns the MultiSliceImage dimensionality of this image.
int	getNFrames()	Returns the number of frames in a multi-frame image.
int	getNRows()	Returns the number of image rows in this image.
int	getNSlices()	Returns the number of physical slice locations in this image.
Date	getPatientDoB()	Returns the patient date of birth for this image.
String	getPatientID()	Returns the patient ID for this image.
String	getPatientName()	Returns the patient name for this image.
PatientPosition	getPatientPosition()	Returns the position in which the patient is lying in the scanning equipment.
com.xinapse.dicom.Sex	getPatientSex()	Returns the patient sex for this image.
float	getPixelXSize()	Returns the pixel size in the x (horizontal) direction for this image.
float	getPixelYSize()	Returns the pixel size in the y (vertical) direction for this image.
float	getPixelZSize()	Returns the separation between the centres of image planes for this image.
UNCPixFormat	getPixformat()	Returns the pixel format (pixformat) of this image.
static boolean	getPreferredOverwrite()	Returns whether the user prefers to overwrite UNC images.
static PreviewIcon	getPreviewIcon(File f, boolean withImagePreview)	Returns the PreviewIcon for a UNC image, or null if the supplied File does not represent a UNC image.
String	getPulseSequence()	Returns the name of the pulse sequence with which this image was collected.
com.xinapse.dicom.RescaleUnits	getRescaleUnits()	Returns the output units of Intensity Rescale Slope and Intensity Rescale Intercept, retrieved by getIntensityRescale().
Float	getSaturationFreqOffsetPPM()	Returns the scan saturation frequency offset for this image if it has a single saturation frequency offset in parts-per-million.
Float	getSaturationFreqOffsetPPM(int index)	Returns the scan saturation frequency offset for one dimension index of this image in parts-per-million.
Date	getScanDate()	Returns the scan Date for this image.
PulseSequenceType	getScanningSequence()	Returns the DICOM Scanning Sequence with which this image was collected.
Float	getScanTE()	Returns the scan echo time for this image if it has a single echo-time.
Float	getScanTE(int index)	Returns the scan echo time for one dimension index of this image.
Float	getScanTI()	Returns the scan inversion time for this image.
Float	getScanTR()	Returns the scan repetition time for this image.
PulseSequenceVariant	getSequenceVariant()	Returns the DICOM Scanning Sequence Variant with which this image was collected.
String	getSeriesDescription()	Returns a short description of the series (scan), such as is provided by the DICOM series description.
Integer	getSeriesNumber()	Returns the series number for this ReadableImage.
float[]	getSliceDWBMatrix(int slice)	Returns the diffusion-weighting b-matrix for one slice of this image.
Float	getSliceDWbValue(int slice)	Returns the diffusion-weighting b-value for one slice of this image.
org.jogamp.vecmath.Vector3f	getSliceDWGradientVector(int slice)	Returns the diffusion-weighting gradient-vector for one slice of this image.
String	getSliceInfo(String name, int slice)	Returns a String representing the value of this information item in a particular slice of this image.
InfoList	getSliceInfoList(int slice)	Returns an InfoList object applying to a particular slice of this image.
Float	getSliceThickness()	Returns the slice thickness (in mm).
Float	getSliceTriggerDelayMS(int slice)	Returns the trigger delay, in milliseconds, for one slice of this image.
PixelDataType	getStoredPixelDataType()	Returns a PixelDataType representing the data type of this image, as the pixel values are stored on disk.
String	getStudyID()	Returns the study ID for this ReadableImage.
float	getTimeBetweenFrames()	Returns the time between frames in a 4- or higher dimensional image.
String	getTitle()	Returns the title of this image.
int	getTotalNSlices()	Returns the total number of slices in this image.
boolean	isOpen()	Tests whether this image is still open.
static boolean	isUNCImage(File f)	Returns true if the File is a UNC Image File.
static boolean	isUNCImage(String fileName)	Returns true if the fileName is the name of a UNC Image file.
static boolean	isUNCImage(URL url)	Returns true if the URL produces a UNCImage input stream.
static UNCImage	newInstance(File f, String mode)	Opens an existing disk-based UNC image.
static UNCImage	newInstance(InputStream s)	Creates an in-memory UNCImage, loading information from an input stream.
static UNCImage	newInstance(InputStream s, boolean skipPixelData)	Creates an in-memory UNCImage, loading information from the input stream.
static UNCImage	newInstance(String fileName, String mode)	Opens an existing disk-based UNC image.
static UNCImage	newInstance(URL url)	Creates an in-memory UNCImage, loading all information from a URL.
static UNCImage	newInstance(URL url, boolean skipPixelData)	Creates an in-memory UNCImage, loading information from a URL.
void	putFrameInfo(InfoList infoList, int frame)	Adds all the items in an InfoList to the frame-specific information.
void	putFrameInfo(String name, String value, int frame)	Adds an item to the frame-specific information.
void	putInfo(String name, float value)	Adds an item to the general file info.
void	putInfo(String name, float value, int dim, int n)	Adds an item to the dimension-specific information.
void	putInfo(String name, int value)	Adds an item to the general file info.
void	putInfo(String name, int value, int dim, int n)	Adds an item to the dimension-specific information.
void	putInfo(String name, String value)	Adds an item to the general file info.
void	putInfo(String name, String value, int dim, int n)	Adds an item to the dimension-specific information.
void	putPix(Object pix, int[] pixIdx)	Puts a single pixel value to the image.
void	putPix(Object array, int[] lowIdx, int[] highIdx)	Put pixel values from a specified array to this image.
void	putSlice(Object array, int slice)	Puts the pixel values to one slice of an n-dimensional image, where n > 1.
void	putSliceInfo(InfoList infoList, int slice)	Adds all the items in an InfoList to the slice-specific information.
void	putSliceInfo(String name, String value, int slice)	Adds an item to the slice-specific information.
void	removeInfo(String name)	Removes an item from the general file information.
void	removeInfo(String name, int dim, int n)	Removes an item from the dimension-specific information.
static void	savePreferredOverwrite(boolean b)	Saves whether the user prefers to overwrite UNC images.
void	setBodyPart(com.xinapse.dicom.BodyPart bodyPart)	By default, body part recording is not supported, so this method does nothing.
void	setEchoTrainLength(Integer etl)	Sets the echo train length for this image.
void	setFlipAngle(Float flipAngle)	Sets the excitation pulse flip angle for this image.
void	setFrameDWBMatrix(float[] bMatrix, int frame)	Sets the diffusion-weighting B-matrix for one "frame" of this 4-D image.
void	setFrameDWbValue(float bValue, int frame)	Sets the diffusion-weighting b-value for one "frame" of this 4-D image.
void	setFrameDWGradientVector(org.jogamp.vecmath.Vector3f gradVec, int frame)	Sets the diffusion-weighting gradient vector for one "frame" of this 4-D image.
void	setFrameInfoList(InfoList list, int frame)	Sets a new InfoList a specific frame of this image.
void	setFrameTriggerDelayMS(float delay, int frame)	Sets the trigger delay (in milliseconds) for one "frame" of this 4-D image.
void	setImageOrientationPatient(org.jogamp.vecmath.Vector3f[] orientation, int slice)	Sets the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient (LPS) coordinates.
void	setImageOrientationPositionPatient(org.jogamp.vecmath.Vector3f[] orientation, org.jogamp.vecmath.Point3f position, boolean force)	Sets the direction cosines of the row, column and slice directions of the image, the coordinates of the center of the first pixel of the image, in patient (LPS) coordinates.
void	setImagePositionPatient(org.jogamp.vecmath.Point3f position, int slice)	Sets the coordinates of the center of the first pixel of the image, in mm, in patient (LPS) coordinates, for one slice of this image.
void	setInfoList(InfoList list)	Sets a new InfoList to the general file info of this image.
void	setInfoList(InfoList list, int dim, int n)	Sets a new InfoList a specific dimension of this image.
void	setIntensityRescale(float rescaleSlope, float rescaleIntercept)	Sets the values m and b in the relationship between pixel intensity (I) values and the output units specified in WritableImage.setRescaleUnits(com.xinapse.dicom.RescaleUnits) in the expression: Output units = m*I + b.
void	setLaterality(com.xinapse.dicom.Laterality laterality)	By default, laterality recording is not supported, so this method does nothing.
void	setMinMax(int min, int max)	Sets the min and max pixel intensity fields for this UNCImage.
void	setNativeColourMapping(ColourMapping colourMapping)	Sets the ColourMapping for this image.
void	setPatientDoB(Date patientDoB)	Sets the patient's date of birth for this image.
void	setPatientID(String patientID)	Sets the patient ID for this image.
void	setPatientName(String patientName)	Attempts to set the patient name for this image.
void	setPatientPosition(PatientPosition position)	Sets the position in which the patient is lying in the scanning equipment for this WritableImage.
void	setPatientSex(com.xinapse.dicom.Sex sex)	Sets the patient sex for this image.
void	setPixelSpacing(Float[] spacing)	Sets the distance (in mm) between pixel centres in the row, column and slice directions of the image, and the time between movie frames (for 4-D images) in seconds.
void	setPixelXSize(float width)	Sets the pixel size in the x (horizontal) direction for this image.
void	setPixelYSize(float height)	Sets the pixel size in the y (vertical) direction for this image.
void	setPixelZSize(float thickness)	Sets the pixel size in the z (slice) direction for this image.
void	setPulseSequence(String seqName)	Sets the pulse sequence name for this image.
void	setRescaleUnits(com.xinapse.dicom.RescaleUnits units)	Sets the rescale units.
void	setSaturationFreqOffsetPPM(Float freqOffset)	Sets the saturation frequency offset in PPM for this image.
void	setSaturationFreqOffsetPPM(Float freqOffset, int index)	Sets the saturation frequency offset for one dimension index of this image.
void	setScanDate(Date scanDate)	Sets the scan date/time for this image.
void	setScanningSequence(PulseSequenceType seq)	Sets the DICOM scanning sequence for this image.
void	setScanTE(Float TE)	Sets the scan echo time for this image.
void	setScanTE(Float TE, int index)	Sets the scan echo time for one dimension index of this image.
void	setScanTI(Float TI)	Sets the scan inversion time for this image.
void	setScanTR(Float TR)	Sets the scan repetition time for this image.
void	setSequenceVariant(PulseSequenceVariant seqVar)	Sets the DICOM scanning sequence variant for this image.
void	setSeriesDescription(String seriesDescription)	Sets a short description of the series (scan).
void	setSeriesNumber(Integer seriesNumber)	Sets the series number for this image.
void	setSliceDWBMatrix(float[] bMatrix, int slice)	Sets the diffusion-weighting B-matrix for one slice of this image.
void	setSliceDWbValue(float bValue, int index)	Sets the diffusion-weighting b-value for one slice of this image.
void	setSliceDWGradientVector(org.jogamp.vecmath.Vector3f gradVec, int index)	Sets the diffusion-weighting gradient vector for one slice of this image.
void	setSliceInfoList(InfoList list, int slice)	Sets a new InfoList a specific slice of this image.
void	setSliceThickness(Float thickness)	Sets the slice thickness (in mm).
void	setSliceTriggerDelayMS(float delay, int index)	Sets the trigger delay (in milliseconds) for one slice of this image.
void	setStudyID(String studyID)	Sets the study ID for this image.
void	setTimeBetweenFrames(float deltaT)	Sets the time between frames in a 4- or higher dimensional image.
void	setTitle(String newTitle)	Sets the title of this image.
boolean	supportsIntensityRescaling()	Returns true because UNC images support intensity rescaling.
String	toHTML()	Returns an HTML string describing this image.
String	toString()	Returns a string describing this image.
void	write(DataOutputStream s)	Writes this UNCImage to a DataOutputStream.
String	write(String fileName)	Writes this WritableImage to a file (or possibly a pair of header/image files).

Methods inherited from class com.xinapse.multisliceimage.MultiSliceImage

clone, getDateFormat, getFrameDim, getFrameOfReferenceUID, getModality, getMostLikePlane, getPix, getPix, getPix, getPix, getPix, getPresentationPixelDataType, getROIs, getScanDateFormat, getSlice, getSlice, getSliceDim, getStoredPix, getSuggestedFileName, isModified, main, parseMultiValuedString, putPix, putPix, setFrameOfReferenceUID, setIntensityRescale, setMinMax, setModality, setModified, setSeriesInstanceUID, setStudyInstanceUID, setSuggestedFileName

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface com.xinapse.image.ReadableImage

getAffineTransform, getAffineTransform, getNSliceLocations

Methods inherited from interface com.xinapse.image.WritableImage

appendToTitle

Field Details

DEFAULT_OVERWRITE

public static final boolean DEFAULT_OVERWRITE

The default setting for the whether UNC images can be overwritten.

See Also:

• Constant Field Values

N_DIMV

public static final int N_DIMV

The maximum dimensionality of an image.

See Also:

• Constant Field Values

N_HISTOGRAM

public static final int N_HISTOGRAM

The number of entries in an image histogram

See Also:

• Constant Field Values

Constructor Details

UNCImage

public UNCImage()

Creates an uninitialised instance of a UNCImage. Needed so that newInstance() method can be called on the class.

UNCImage

public UNCImage(String fileName,
 UNCPixFormat pixform,
 int dimc,
 int[] dimv)
         throws InvalidImageException,
IOException

Creates a disk-based UNCImage with the given type of pixel and dimensions. dimc should be greater that 1 and less than or equal to nDIMV.

Parameters:

fileName - the name of the file to be created.

pixform - the type of image to be created (e.g. UNCPixFormat.GREY).

dimc - the dimensionality of the image.

dimv - an array of length at least dimc containing the number of picture elements in each dimension. For example, in a 3-dimensional image, dimv[0] is the number of slices, dimv[1] the number of rows, and dimv[2] the number of columns.

Throws:

InvalidImageException - if the image cannot be created.

IOException - if an I/O error occurs.

UNCImage

public UNCImage(File f,
 UNCPixFormat pixform,
 int dimc,
 int[] dimv)
         throws InvalidImageException,
IOException

Creates a disk-based UNCImage with the given type of pixel and dimensions. dimc should be greater that 1 and less than or equal to nDIMV.

Parameters:

f - is File Object representing the path of the file to be created.

pixform - the type of image to be created (e.g. UNCPixFormat.GREY).

dimc - the dimensionality of the image.

dimv - an array of length at least dimc containing the number of picture elements in each dimension. For example, in a 3-dimensional image, dimv[0] is the number of slices, dimv[1] the number of rows, and dimv[2] the number of columns.

Throws:

InvalidImageException - if the image cannot be created.

IOException - if an I/O error occurs.

UNCImage

public UNCImage(UNCPixFormat pixform,
 int dimc,
 int[] dimv)
         throws InvalidImageException

Creates an in-memory UNCImage with the given type of pixel and dimensions. dimc should be greater that 1 and less than or equal to nDIMV.

Parameters:

pixform - the type of image to be created (e.g. UNCPixFormat.GREY).

dimc - the dimensionality of the image.

dimv - an array of length at least dimc containing the number of picture elements in each dimension. For example, in a 3-dimensional image, dimv[0] is the number of slices, dimv[1] the number of rows, and dimv[2] the number of columns.

Throws:

InvalidImageException - if the image cannot be created.

UNCImage

public UNCImage(DataInputStream s,
 boolean skipPixelData)
         throws InvalidImageException

Creates an in-memory UNCImage, loading all information from the data input stream. Optionally skips over loading of the pixel data.

Parameters:

s - the DataInputStream.

skipPixelData - if true then pixel data is not loaded and cannot later be accessed.

Throws:

InvalidImageException - if the image cannot be loaded.

Method Details

newInstance

public static UNCImage newInstance(URL url)
                            throws InvalidImageException,
UNCException,
IOException

Creates an in-memory UNCImage, loading all information from a URL.

Parameters:

url - the URL that will give a UNC image data stream.

Returns:

a new UNCImage loaded from a URL.

Throws:

InvalidImageException - if the image cannot be loaded.

UNCException - if the image cannot be loaded for UNC-specific reasons.

IOException - if an I/O error occurs while loading the image.

newInstance

public static UNCImage newInstance(URL url,
 boolean skipPixelData)
                            throws InvalidImageException,
UNCException,
IOException

Creates an in-memory UNCImage, loading information from a URL. Optionally skips loading of the pixel data into memory. If skipPixelData is true, then the pixel data will not be accessible.

Parameters:

url - the URL that will give a UNC image data stream.

skipPixelData - if true then pixel data is not loaded and cannot later be accessed.

Returns:

a new UNCImage loaded from a URL.

Throws:

InvalidImageException - if the image cannot be loaded.

UNCException - if the image cannot be loaded for UNC-specific reasons.

IOException - if an I/O error occurs while loading the image.

newInstance

public static UNCImage newInstance(String fileName,
 String mode)
                            throws InvalidImageException,
IOException,
FileNotFoundException

Opens an existing disk-based UNC image.

Parameters:

fileName - the name of the image file.

mode - the open mode. Can be either "r" (read-only) or "rw" (read-write).

Returns:

a new UNCImage, loaded from a disk file.

Throws:

InvalidImageException - if the mode is invalid or the image cannot be read.

FileNotFoundException - if the image file doesn't exist.

IOException - if an I/O error occurs.

newInstance

public static UNCImage newInstance(File f,
 String mode)
                            throws InvalidImageException,
IOException,
FileNotFoundException

Opens an existing disk-based UNC image.

Parameters:

f - a File object representing the path to this image file.

mode - the open mode. Can be either "r" (read-only) or "rw" (read-write).

Returns:

a new UNCImage, loaded from a disk file.

Throws:

InvalidImageException - if the mode is invalid or the image cannot be read.

FileNotFoundException - if the image file doesn't exist.

IOException - if an I/O error occurs.

newInstance

public static UNCImage newInstance(InputStream s)
                            throws InvalidImageException

Creates an in-memory UNCImage, loading information from an input stream.

Parameters:

s - the InputStream.

Returns:

a new UNCImage, loaded from an input stream.

Throws:

InvalidImageException - if the image cannot be loaded.

newInstance

public static UNCImage newInstance(InputStream s,
 boolean skipPixelData)
                            throws InvalidImageException

Creates an in-memory UNCImage, loading information from the input stream. Optionally skips over loading of the pixel data.

Parameters:

s - the InputStream.

skipPixelData - if true then pixel data is not loaded and cannot later be accessed.

Returns:

a new UNCImage, loaded from an input stream.

Throws:

InvalidImageException - if the image cannot be loaded.

getByteOrder

public ByteOrder getByteOrder()

Description copied from class: MultiSliceImage

Returns the byte order for this image.

Specified by:

getByteOrder in class MultiSliceImage

Returns:

the byte oder for this image, or null if the byte order is not defined yet (in-memory images only).

isUNCImage

public static boolean isUNCImage(URL url)

Returns true if the URL produces a UNCImage input stream. Returns false otherwise.

Parameters:

url - the URL to be tested

Returns:

true if the URL produces a UNCImage input stream; false otherwise.

getPreviewIcon

public static PreviewIcon getPreviewIcon(File f,
 boolean withImagePreview)

Returns the PreviewIcon for a UNC image, or null if the supplied File does not represent a UNC image.

Parameters:

f - the File to be tested.

withImagePreview - whether a image preview is to be generated. Generating an image preview will take longer than not generating one.

Returns:

a PreviewIcon if the File produces a UNCImage; null otherwise.

isUNCImage

public static boolean isUNCImage(String fileName)

Returns true if the fileName is the name of a UNC Image file. Returns false otherwise.

Parameters:

fileName - the name of a file to be tested.

Returns:

true if a UNCImage file with the specified name exists on disk; false otherwise.

isUNCImage

public static boolean isUNCImage(File f)

Returns true if the File is a UNC Image File. Returns false otherwise.

Parameters:

f - the File to be tested.

Returns:

true if the File is a UNC Image File; false otherwise.

disposeImageData

public void disposeImageData()

Description copied from interface: ReadableImage

Gives this image the option to free up resources by removing access to image data. After this method is called, image data may no longer be accessible, and method calls to access it may result in an Exception being thrown.

Specified by:

disposeImageData in interface ReadableImage

close

public void close()
           throws IOException

Closes a UNCImage and frees up resources. For in-memory UNCImages, this merely explicity frees resources so that the garbage collector can work more efficiently. However, for disk-based images it is essential to apply the close() method. Image data is written to disk during the put() methods, but other information - the title and the info fields are only written to disk by the close() method. If the close() method is not applied to a disk-based UNCImage, then any changes to the title and info fields will be lost. Any further operations to a closed UNCImage are not possible, and may cause an exception to be thrown.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface ReadableImage

Throws:

IOException - if the file cannot be written or closed.

isOpen

public boolean isOpen()

Description copied from interface: ReadableImage

Tests whether this image is still open.

Specified by:

isOpen in interface ReadableImage

Returns:

true if the image is still open for reading and (if opened read/write) writing; false otherwise.

write

public String write(String fileName)
             throws InvalidImageException

Description copied from interface: WritableImage

Writes this WritableImage to a file (or possibly a pair of header/image files).

Specified by:

write in interface WritableImage

Parameters:

fileName - with which the image is to be written.

Returns:

the actual file name to which the image was written.

Throws:

InvalidImageException - if the image cannot be written.

getPreferredOverwrite

public static boolean getPreferredOverwrite()

Returns whether the user prefers to overwrite UNC images.

Returns:

true if the user prefers to overwrite existsing UNC images; false if UNC will not be overwritten.

savePreferredOverwrite

public static void savePreferredOverwrite(boolean b)

Saves whether the user prefers to overwrite UNC images.

Parameters:

b - true if the user prefers to overwrite existsing UNC images; false if UNC are not to be overwritten.

write

public void write(DataOutputStream s)
           throws InvalidImageException

Writes this UNCImage to a DataOutputStream.

Parameters:

s - the DataOutputStream.

Throws:

InvalidImageException - if the image cannot be written.

getBytesPerPixel

public int getBytesPerPixel()

Returns the number of bytes per pixel for this image.

Returns:

the number of bytes per pixel.

getNativeHeader

public String getNativeHeader()

Description copied from interface: ReadableImage

Returns a String showing the 'native' header for this image.

Specified by:

getNativeHeader in interface ReadableImage

Returns:

a String describing the 'native' header for this image.

toString

public String toString()

Returns a string describing this image.

Overrides:

toString in class Object

Returns:

a String that describes the image.

toHTML

public String toHTML()

Returns an HTML string describing this image.

Returns:

a String that describes the image in HTML format.

setMinMax

public void setMinMax(int min,
 int max)
               throws InvalidImageException

Sets the min and max pixel intensity fields for this UNCImage. Also sets the valid flag to true.

Specified by:

setMinMax in interface WritableImage

Specified by:

setMinMax in class MultiSliceImage

Parameters:

min - the minimum pixel value in the image.

max - the maximum pixel value in the image.

Throws:

InvalidImageException - if the image is read-only or if the supplied values are unsuitable for this image.

getDimc

public int getDimc()

Returns the dimensionality of this image.

Returns:

dimc, the dimensionality.

getNDim

public int getNDim()

Returns the MultiSliceImage dimensionality of this image.

Specified by:

getNDim in interface ReadableImage

Returns:

the dimensionality.

getDimv

public int[] getDimv()
              throws IllegalStateException

Returns the dimensions of this image. An integer array of length N_DIMV is returned with elements 0 to dimc-1 containing useful information about the numbers of pixels in each dimension of the image. The lowest array element contain the most slowly-varying image component. For example in a 3-dimensional image, dimv[0] is the number of slices, dimv[1] the number of rows, and dimv[2] the number of columns.

Returns:

dimc an array of image dimensions.

Throws:

IllegalStateException - if there is something strange about the dimensionality of this image.

getDims

public int[] getDims()
              throws IllegalStateException

Description copied from interface: ReadableImage

Returns the dimensions (numbers of samples in each image dimension) of this image.

Specified by:

getDims in interface ReadableImage

Returns:

an array with length equal to the image dimensionality, containing the numbers of pixels (samples) in each dimension of the image. By convention, element (nDim-1) contains the number of columns, element (nDim-2) the number of rows, etc. For example, in a 4-dimensional image, dims[0] is the number of frames, dims[1] the number of slices, dims[2] the number of rows and dims[3] the number of columns.

Throws:

IllegalStateException

getPixformat

public UNCPixFormat getPixformat()

Returns the pixel format (pixformat) of this image.

Returns:

a UNCPixFormat representing a particular pixel format.

getStoredPixelDataType

public PixelDataType getStoredPixelDataType()

Description copied from interface: ReadableImage

Returns a PixelDataType representing the data type of this image, as the pixel values are stored on disk.

Specified by:

getStoredPixelDataType in interface ReadableImage

Returns:

the PixelDataType representing the data type of this image as stored on disk.

getFileDataOffset

public int getFileDataOffset()

Returns the byte offset into the disk-based file format where pixel data begins.

Specified by:

getFileDataOffset in class MultiSliceImage

Returns:

the byte offset to the start of pixel data for images that are written to disk.

getTitle

public String getTitle()

Returns the title of this image.

Specified by:

getTitle in interface ReadableImage

Returns:

the title String.

setTitle

public void setTitle(String newTitle)

Sets the title of this image. If the new title String is longer than is allowed by the UNC format, then it is truncated before being applied. If the image is read-only, then this method does nothing.
N.B. For disk-based images, the changes in the title will not be reflected on disk unless the close() method is called.

Specified by:

setTitle in interface WritableImage

Parameters:

newTitle - the new title to be assigned to this image.

putPix

public void putPix(Object array,
 int[] lowIdx,
 int[] highIdx)
            throws IllegalStateException

Description copied from class: MultiSliceImage

Put pixel values from a specified array to this image. array is an array of the correct type of element for this image from which pixel values will be copied; it must be cast to an Object and must have the right number of elements to copy to the pixel values requested. The lowIdx and highIdx int arrays should have at least nDim elements, and the elements specify the pixel number range for each dimension. For example, if an image has nDim = 3, and dims[] = {5, 256, 256}, then pixels for the middle slices 4 will be returned by setting lowIdx to {1, 0, 0} and highIdx to {4, 255, 255}.

Specified by:

putPix in interface WritableImage

Overrides:

putPix in class MultiSliceImage

Parameters:

array - a 1-dimensional array of pixel values of the correct java primitive data type to put to the image.

lowIdx - an array of int specifying the low index of pixel values to put.

highIdx - an array of int specifying the high index of pixel values to put.

Throws:

IllegalStateException - if an error occurs while accessing the pixel values.

putPix

public void putPix(Object pix,
 int[] pixIdx)
            throws IOException

Description copied from class: MultiSliceImage

Puts a single pixel value to the image.

Specified by:

putPix in interface WritableImage

Overrides:

putPix in class MultiSliceImage

Parameters:

pix - the pixel value to put, as a suitable Object.

pixIdx - an int[] of length at least equal to nDim for this image where each element corresponds to an index to the pixel in each dimension. The first element of pixIdx refers to the slowest-varying dimension, and the last relevant element refers to the fastest-varying dimension. For example, for a 3-D image, pixIdx[0] refers to the slice dimension, and pixIdx[2] refers to the column dimension.

Throws:

IOException - if an I/O error occurs while accessing the pixel values.

putSlice

public void putSlice(Object array,
 int slice)
              throws IllegalStateException

Description copied from class: MultiSliceImage

Puts the pixel values to one slice of an n-dimensional image, where n > 1.

N.B.Whenever the radiological orientation of the image can be determined, this method sets pixel values such that when the slice is viewed on-screen, the first pixel in the array belongs at the top left of the screen, and the last pixel in the array belongs at the bottom right of the screen. This is regardless of the sub-class of image (for example, the flipping of Analyze images is taken care of by this method).

Specified by:

putSlice in interface WritableImage

Overrides:

putSlice in class MultiSliceImage

Parameters:

array - a 1-dimensional array of the correct primitive java data type for this image, with dimensions [nRows * nCols] containing the pixel values to put.

slice - the slice number. Must be 0 for a 2-dimensional image or from 0 to dims[0]-1 for a 3-dimensional image.

Throws:

IllegalStateException - if an I/O error occurs while putting the pixel values, or if the array is not of the correct primitive data type for this image.

getInfo

public String getInfo(String name)
               throws InfoNotFoundException

Description copied from interface: InfoStorer

Returns a string representing the value of this information item in the general image information.

For example, if there is a item with a name "pixel_x_size" and a value "0.91162" in the general info, and name "pixel_x_size" is supplied, then this method will return "0.91162".

Specified by:

getInfo in interface InfoStorer

Parameters:

name - the name of this information field.

Returns:

a String representation of the value of this information field.

Throws:

InfoNotFoundException - if the name is not found in the general info.

putInfo

public void putInfo(String name,
 int value)
             throws IOException

Description copied from interface: InfoStorer

Adds an item to the general file info.
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

putInfo in interface InfoStorer

Parameters:

name - the name of the information field to put.

value - an integer value to be associated with this name in the general file information.

Throws:

IOException - if the information cannot be added because of an I/O error.

putInfo

public void putInfo(String name,
 float value)
             throws IOException

Description copied from interface: InfoStorer

Adds an item to the general file info. If an info item with the same name exists, then then value will be overwritten.
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

putInfo in interface InfoStorer

Parameters:

name - the name of the information to put.

value - a floating point value to be associated with this name in the general file information.

Throws:

IOException - if the information cannot be addded because of an I/O error.

putInfo

public void putInfo(String name,
 String value)
             throws IOException

Description copied from interface: InfoStorer

Adds an item to the general file info. If an info item with the same name exists, then then value will be overwritten.
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

putInfo in interface InfoStorer

Parameters:

name - the name of the information to put.

value - a String to be associated with this name in the general file information.

Throws:

IOException - if the information cannot be addded because of an I/O error.

getInfo

public String getInfo(String name,
 int dim,
 int n)
               throws InfoNotFoundException

Description copied from interface: InfoStorer

Returns a String representing the value of this information item in a particular dimension of this image. For example, if there is a item "pixel_x_size=0.91162" in the file info for this dimension, and a name "pixel_x_size" is supplied, then this method will return "0.91162".

Specified by:

getInfo in interface InfoStorer

Parameters:

name - the name of this information item.

dim - the dimension of this image to look for the information. For example in a 3-dimensional image you would look in dimension 0 for slice-specific info.

n - the element to look in. For example in a 3-dimensional image you would look in slice n to info that applied only to slice n.

Returns:

a String representation of the value of this information.

Throws:

InfoNotFoundException - if the name is not found in this dimension/element info.

getSliceInfo

public String getSliceInfo(String name,
 int slice)
                    throws InfoNotFoundException

Description copied from interface: InfoStorer

Returns a String representing the value of this information item in a particular slice of this image.

The slice number is referenced from 0 to (number of slices - 1).

Specified by:

getSliceInfo in interface InfoStorer

Parameters:

name - the name of this information item.

slice - the slice number.

Returns:

a String representation of the value of this information.

Throws:

InfoNotFoundException - if the name is not found for the specified slice.

getFrameInfo

public String getFrameInfo(String name,
 int frame)
                    throws InfoNotFoundException

Description copied from interface: InfoStorer

Returns a String representing the value of this information item in a particular frame of this image.

The frame number is referenced from 0 to (number of frames - 1).

Specified by:

getFrameInfo in interface InfoStorer

Parameters:

name - the name of this information item.

frame - the frame number.

Returns:

a String representation of the value of this information.

Throws:

InfoNotFoundException - if the name is not found for the specified frame.

putInfo

public void putInfo(String name,
 int value,
 int dim,
 int n)
             throws IOException

Description copied from interface: InfoStorer

Adds an item to the dimension-specific information. If an info item with the same name exists, then then value will be overwritten.
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

putInfo in interface InfoStorer

Parameters:

name - the name of the information item to put.

value - an integer value to be associated with this name in the general file information.

dim - the dimension of this image to put the information item. For example in a 3-dimensional image you would put to dimension 0 for slice-specific info.

n - the element to put to. For example in a 3-dimensional image you would put to slice n to info that applied only to slice n.

Throws:

IOException - if the information cannot be addded because of an I/O error.

putInfo

public void putInfo(String name,
 float value,
 int dim,
 int n)
             throws IOException

Description copied from interface: InfoStorer

Adds an item to the dimension-specific information. If an info item with the same name exists, then then value will be overwritten.
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the close() method is called.

Specified by:

putInfo in interface InfoStorer

Parameters:

name - the name of the information item to put.

value - an floating-point value to be associated with this name in the dimension-specific information.

dim - the dimension of this image to put the information. For example in a 3-dimensional image you would put to dimension 0 for slice-specific info.

n - the element to put to. For example in a 3-dimensional image you would put to slice n to info that applied only to slice n.

Throws:

IOException - if the information cannot be addded because of an I/O error.

putInfo

public void putInfo(String name,
 String value,
 int dim,
 int n)
             throws IOException

Description copied from interface: InfoStorer

Adds an item to the dimension-specific information. If an info item with the same name exists, then then value will be overwritten.
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the close() method is called.

Specified by:

putInfo in interface InfoStorer

Parameters:

name - the name of the information item to put.

value - a String value to be associated with this name in the dimension-specific information.

dim - the dimension of this image to put the information. For example in a 3-dimensional image you would put to dimension 0 for slice-specific info.

n - the element to put to. For example in a 3-dimensional image you would put to slice n to info that applied only to slice n.

Throws:

IOException - if the information cannot be addded because of an I/O error.

putSliceInfo

public void putSliceInfo(InfoList infoList,
 int slice)
                  throws IOException

Description copied from interface: InfoStorer

Adds all the items in an InfoList to the slice-specific information. If an info item with the same name exists, then then value will be overwritten.

The slice number is referenced from 0 to (number of slices - 1).
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

putSliceInfo in interface InfoStorer

Parameters:

infoList - the list of InfoItems to put.

slice - the slice number.

Throws:

IOException - if the information cannot be added because of an I/O error.

putFrameInfo

public void putFrameInfo(InfoList infoList,
 int frame)
                  throws IOException

Description copied from interface: InfoStorer

Adds all the items in an InfoList to the frame-specific information. If an info item with the same name exists, then the value will be overwritten.

The frame number is referenced from 0 to (number of frames - 1).
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

putFrameInfo in interface InfoStorer

Parameters:

infoList - the list of InfoItems to put.

frame - the frame number.

Throws:

IOException - if the information cannot be added because of an I/O error.

putSliceInfo

public void putSliceInfo(String name,
 String value,
 int slice)
                  throws IOException

Description copied from interface: InfoStorer

Adds an item to the slice-specific information. If an info item with the same name exists, then then value will be overwritten.

The slice number is referenced from 0 to (number of slices - 1).
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

putSliceInfo in interface InfoStorer

Parameters:

name - the name of the information item to put.

value - a String to be associated with this name in the slice-specific info.

slice - the slice number.

Throws:

IOException - if the information cannot be added because of an I/O error.

putFrameInfo

public void putFrameInfo(String name,
 String value,
 int frame)
                  throws IOException

Description copied from interface: InfoStorer

Adds an item to the frame-specific information. If an info item with the same name exists, then then value will be overwritten.

The frame number is referenced from 0 to (number of frames).
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

putFrameInfo in interface InfoStorer

Parameters:

name - the name of the information item to put.

value - a String to be associated with this name in the frame-specific info.

frame - the frame number.

Throws:

IOException - if the information cannot be added because of an I/O error.

removeInfo

public void removeInfo(String name)
                throws IOException

Description copied from interface: InfoStorer

Removes an item from the general file information. If an info item with the given name is not present in the general info, then this method does nothing.
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

removeInfo in interface InfoStorer

Parameters:

name - the name of the information item to be removed.

Throws:

IOException - if the information cannot be removed.

removeInfo

public void removeInfo(String name,
 int dim,
 int n)
                throws IOException

Description copied from interface: InfoStorer

Removes an item from the dimension-specific information. If an info item with the given name is not present in the dimension-specific, then this method does nothing.
N.B. For disk-based images, the changes in the info will not be reflected on disk unless the ReadableImage.close() method is called.

Specified by:

removeInfo in interface InfoStorer

Parameters:

name - the name of the information item to put.

dim - the dimension of this image to from which to remove the information. For example in a 3-dimensional image you would put to dimension 0 for slice-specific info.

n - the element to from which to remove the info item. For example in a 3-dimensional image you would put to slice n to info that applied only to slice n.

Throws:

IOException - if the information cannot be removed.

copyInfo

public void copyInfo(UNCImage toImage)
              throws IllegalStateException

Copies all the info fields to another image. The general info will be copied to the toImage, overwriting any pre-existing info. Depending on the dimensionality of the two images, the dimension-specific info may also be copied.

Parameters:

toImage - the UNCImage to which info will be copied.

Throws:

IllegalStateException - if the image is read-only.

getInfoList

public InfoList getInfoList()

Description copied from interface: InfoStorer

Returns an InfoList object which is the general info for this image.

Specified by:

getInfoList in interface InfoStorer

Returns:

an InfoList which is the general file info for this InfoStorer.

getInfoList

public InfoList getInfoList(int dim,
 int n)
                     throws IndexOutOfBoundsException

Description copied from interface: InfoStorer

Returns an InfoList object applying to a particular dimension/element for this image.

Specified by:

getInfoList in interface InfoStorer

Parameters:

dim - the dimension for which to get the information list.

n - the element for which to get the information list.

Returns:

an InfoList object from a particular dimension of this InfoStorer.

Throws:

IndexOutOfBoundsException - if the dimensions supplied do not match this image.

getSliceInfoList

public InfoList getSliceInfoList(int slice)
                          throws IndexOutOfBoundsException

Description copied from interface: InfoStorer

Returns an InfoList object applying to a particular slice of this image.

The slice number is referenced from 0 to (number of slices - 1).

Specified by:

getSliceInfoList in interface InfoStorer

Parameters:

slice - the slice number.

Returns:

an InfoList object from a particular slice of this InfoStorer.

Throws:

IndexOutOfBoundsException - if the slice supplied is inappropriate for the dimensions of this image.

getFrameInfoList

public InfoList getFrameInfoList(int frame)
                          throws IndexOutOfBoundsException

Description copied from interface: InfoStorer

Returns an InfoList object applying to a particular frame of this image.

The frame number is referenced from 0 to (number of frames - 1).

Specified by:

getFrameInfoList in interface InfoStorer

Parameters:

frame - the frame number.

Returns:

an InfoList object from a particular frame of this InfoStorer.

Throws:

IndexOutOfBoundsException - if the frame supplied is inappropriate for the dimensions of this image.

setInfoList

public void setInfoList(InfoList list)
                 throws IOException

Description copied from interface: InfoStorer

Sets a new InfoList to the general file info of this image.

Specified by:

setInfoList in interface InfoStorer

Parameters:

list - the InfoList object to set to the general file info for this image.

Throws:

IOException - if the InfoList cannot be set.

setInfoList

public void setInfoList(InfoList list,
 int dim,
 int n)
                 throws IOException

Description copied from interface: InfoStorer

Sets a new InfoList a specific dimension of this image.

Specified by:

setInfoList in interface InfoStorer

Parameters:

list - the InfoList to associate with this image/dimension.

dim - the dimension to which to set the information list.

n - the element to which to set the information list.

Throws:

IOException - if the InfoList cannot be set.

setSliceInfoList

public void setSliceInfoList(InfoList list,
 int slice)
                      throws IOException

Description copied from interface: InfoStorer

Sets a new InfoList a specific slice of this image.

Specified by:

setSliceInfoList in interface InfoStorer

Parameters:

list - the InfoList to associate with this image/slice.

slice - the slice for which to set the information list.

Throws:

IOException - if the InfoList cannot be set.

setFrameInfoList

public void setFrameInfoList(InfoList list,
 int frame)
                      throws IOException

Description copied from interface: InfoStorer

Sets a new InfoList a specific frame of this image.

Specified by:

setFrameInfoList in interface InfoStorer

Parameters:

list - the InfoList to associate with this image/frame.

frame - the frame for which to set the information list.

Throws:

IOException - if the InfoList cannot be set.

appendInfoList

public void appendInfoList(InfoList list)
                    throws IOException

Description copied from interface: InfoStorer

Appends an InfoList to the existing general file info of this image.

Specified by:

appendInfoList in interface InfoStorer

Parameters:

list - the InfoList object to append to the general file info for this image.

Throws:

IOException - if the InfoList cannot be appended because of an I/O error.

appendInfoList

public void appendInfoList(InfoList list,
 int dim,
 int n)
                    throws IllegalStateException

Description copied from interface: InfoStorer

Appends an InfoList to that existing for a specific dimension of this image.

Specified by:

appendInfoList in interface InfoStorer

Parameters:

list - the InfoList to append.

dim - the dimension to which to append the information list.

n - the element to which to append the information list.

Throws:

IllegalStateException

anonymise

public void anonymise(String patientName,
 String patientID,
 Date birthDate,
 boolean patSex,
 String patAddr,
 String patInsurancePlanID,
 String accessionNumber,
 boolean patOther,
 String physicianName,
 String physicianAddr,
 String institutionName,
 String institutionAddr,
 String deptName,
 String stationName,
 String telNumber,
 boolean removePrivateElements)
               throws IOException

Description copied from interface: WritableImage

Anonymise this WritableImage.

Specified by:

anonymise in interface WritableImage

Parameters:

patientName - if non-null, the patient name to substitute.

patientID - if non-null, the patient ID to substitute.

birthDate - if non-null, the birth date to substitute.

patSex - if true, set the sex to "OTHER".

patAddr - if non-null, the address to substitute.

patInsurancePlanID - if non-null, the insurance plan ID to substitute.

accessionNumber - if non-null, the accession number to substitute.

patOther - if true, other patient-related items will be anonymised.

physicianName - if non-null, the physician name to substitute.

physicianAddr - if non-null, the physician's address to substitute.

institutionName - if non-null, the institution name to substitute.

institutionAddr - if non-null, the institution address to substitute.

deptName - if non-null, the department name to substitute.

stationName - if non-null, the station name to substitute.

telNumber - if non-null, the telephone number to substitute for all telephone numbers.

removePrivateElements - if true, all private DICOM elements will be removed.

Throws:

IOException - if an I/O error occurs during anonymisation.

getTotalNSlices

public int getTotalNSlices()

Description copied from interface: ReadableImage

Returns the total number of slices in this image. If the image is less than 3-dimensional, this method returns 1; if it is 3-dimensional, it returns the number of slices; if it is 4- or more dimensional, it sums up the total number of planar slices in each dimension and returns the total. For example a 4-dimensional image with 4 slices and 10 frames, the total number of slices is 40.

Specified by:

getTotalNSlices in interface ReadableImage

Returns:

the number of planar image slices.

getNCols

public int getNCols()

Description copied from interface: ReadableImage

Returns the number of image columns in this image.

Specified by:

getNCols in interface ReadableImage

Returns:

the number of image columns.

getNRows

public int getNRows()

Description copied from interface: ReadableImage

Returns the number of image rows in this image.

Specified by:

getNRows in interface ReadableImage

Returns:

the number of image rows.

getNSlices

public int getNSlices()

Description copied from interface: ReadableImage

Returns the number of physical slice locations in this image. If the image dimensionality is greater than or equal to three, then this method returns the number of samples in the third dimension. If the dimensionality is less than 3 two, it returns 1.

Specified by:

getNSlices in interface ReadableImage

Returns:

the number of physical slice locations.

getNFrames

public int getNFrames()

Description copied from interface: ReadableImage

Returns the number of frames in a multi-frame image. If the image dimensionality is greater than or equal to four, then this method returns the number of samples in the fourth dimension. If the dimensionality is less than 4, it returns 1.

Specified by:

getNFrames in interface ReadableImage

Returns:

the number of image (movie) frames.

getPixelXSize

public float getPixelXSize()
                    throws ParameterNotSetException

Description copied from interface: ReadableImage

Returns the pixel size in the x (horizontal) direction for this image.

Specified by:

getPixelXSize in interface ReadableImage

Returns:

the pixel size in the x (horizontal) direction in mm.

Throws:

ParameterNotSetException - if the pixel size can't be found.

getPixelYSize

public float getPixelYSize()
                    throws ParameterNotSetException

Description copied from interface: ReadableImage

Returns the pixel size in the y (vertical) direction for this image.

Specified by:

getPixelYSize in interface ReadableImage

Returns:

the pixel size in the y (vertical) direction in mm.

Throws:

ParameterNotSetException - if the pixel size can't be found.

getPixelZSize

public float getPixelZSize()
                    throws ParameterNotSetException

Description copied from interface: ReadableImage

Returns the separation between the centres of image planes for this image.

Specified by:

getPixelZSize in interface ReadableImage

Returns:

the pixel size in the z (slice) direction in mm.

Throws:

ParameterNotSetException - if the pixel size can't be found.

getTimeBetweenFrames

public float getTimeBetweenFrames()
                           throws ParameterNotSetException

Description copied from interface: ReadableImage

Returns the time between frames in a 4- or higher dimensional image.

Specified by:

getTimeBetweenFrames in interface ReadableImage

Returns:

the time between frames in seconds.

Throws:

ParameterNotSetException - if the time between frames is not set, or if this image doesn't have a dimensionality of at least 4.

setPixelXSize

public void setPixelXSize(float width)
                   throws IOException

Description copied from class: MultiSliceImage

Sets the pixel size in the x (horizontal) direction for this image.

Specified by:

setPixelXSize in class MultiSliceImage

Parameters:

width - the width of a pixel.

Throws:

IOException - if and I/O error occurs.

setPixelYSize

public void setPixelYSize(float height)
                   throws IOException

Description copied from class: MultiSliceImage

Sets the pixel size in the y (vertical) direction for this image.

Specified by:

setPixelYSize in class MultiSliceImage

Parameters:

height - the height of a pixel.

Throws:

IOException - if an I/O error occurs.

setPixelZSize

public void setPixelZSize(float thickness)
                   throws IOException

Description copied from class: MultiSliceImage

Sets the pixel size in the z (slice) direction for this image.

Specified by:

setPixelZSize in class MultiSliceImage

Parameters:

thickness - the thickness of a pixel.

Throws:

IOException - if an I/O error occurs.

setTimeBetweenFrames

public void setTimeBetweenFrames(float deltaT)
                          throws IOException

Description copied from class: MultiSliceImage

Sets the time between frames in a 4- or higher dimensional image.

Specified by:

setTimeBetweenFrames in class MultiSliceImage

Parameters:

deltaT - the time between frames (in seconds).

Throws:

IOException - if an I/O error occurs.

getImagePositionPatient

public org.jogamp.vecmath.Point3f getImagePositionPatient()

Description copied from interface: ReadableImage

Returns the coordinates of the center of the first pixel of the image, in mm, in patient coordinates. This method will only return if the image pixels form a regular array of pixels with parallel image planes; otherwise a ParameterNotSetException is thrown.

Specified by:

getImagePositionPatient in interface ReadableImage

Returns:

the Left,Posterior,Superior (LPS) coordinates of the first pixel in the image data matrix. Returns null if the position cannot be retrieved from this image.

getImagePositionPatient

public org.jogamp.vecmath.Point3f getImagePositionPatient(int slice)

Description copied from interface: ReadableImage

Returns the coordinates of the center of the first pixel of the specified slice of this image, in mm, in patient coordinates.

Specified by:

getImagePositionPatient in interface ReadableImage

Parameters:

slice - the slice number (indexed from 0) for which to return the pixel coordinates.

Returns:

the Left,Posterior,Superior (LPS) coordinates of the first pixel in the specified slice of this image. Returns null if the position cannot be retrieved from this image.

setImagePositionPatient

public void setImagePositionPatient(org.jogamp.vecmath.Point3f position,
 int slice)

Description copied from interface: WritableImage

Sets the coordinates of the center of the first pixel of the image, in mm, in patient (LPS) coordinates, for one slice of this image.

Specified by:

setImagePositionPatient in interface WritableImage

Parameters:

position - the Left,Posterior,Superior (LPS) coordinates of the first pixel of this specified slice in the image data matrix.

slice - the slice for which to set the position.

getImageOrientationPatient

public org.jogamp.vecmath.Vector3f[] getImageOrientationPatient()

Description copied from interface: ReadableImage

Returns the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient (L,P,S) coordinates.

Specified by:

getImageOrientationPatient in interface ReadableImage

Returns:

a Vector3f[], corresponding to the direction cosines of the image row, column and slice directions in Left,Posterior,Superior (LPS) coordinates. Returns null if the direction cosines cannot be retrieved from this image.

getImageOrientationPatient

public org.jogamp.vecmath.Vector3f[] getImageOrientationPatient(int slice)

Description copied from interface: ReadableImage

Returns the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient coordinates.

Specified by:

getImageOrientationPatient in interface ReadableImage

Parameters:

slice - the slice for which to return the image orientation.

Returns:

a Vector3f[], corresponding to the direction cosines of the image row, column and slice directions in Left,Posterior,Superior (LPS) coordinates. Returns null if the direction cosines cannot be retrieved from this image.

setImageOrientationPositionPatient

public void setImageOrientationPositionPatient(org.jogamp.vecmath.Vector3f[] orientation,
 org.jogamp.vecmath.Point3f position,
 boolean force)

Description copied from class: MultiSliceImage

Sets the direction cosines of the row, column and slice directions of the image, the coordinates of the center of the first pixel of the image, in patient (LPS) coordinates.

N.B. the actual position and orientation set by this method may not be those specified. For example, for NIFTI-1 images, the actual orientation and position may depend on the user Preferences for whether to put pixel values in an order that is compatible with SPM. After using this method, you should use the ReadableImage.getImageOrientationPatient() and ReadableImage.getImagePositionPatient() methods to obtain the real orientation and positions set.

If the orientation or position cannot be set for this image, this method does not report an error.

Specified by:

setImageOrientationPositionPatient in interface WritableImage

Specified by:

setImageOrientationPositionPatient in class MultiSliceImage

Parameters:

orientation - the direction cosines of the image row, column and (optionally) slice directions respectively in Left,Posterior,Superior (LPS) coordinates. If orientation is null, this method will attempt to clear any orientation information, if that is supported by the image format.

position - the Left,Posterior,Superior (LPS) coordinates of the centre of the first pixel in the image data matrix. If position is null, this method will attempt to clear any positional information, if that is supported by the image format.

force - if true, this method will force the orientation and position to be set as requested, regardless of the user Preferences. This can be useful if you read the orientation from an existing image, and you want to set the orientation exactly the same in a new image.

setImageOrientationPatient

public void setImageOrientationPatient(org.jogamp.vecmath.Vector3f[] orientation,
 int slice)
                                throws IndexOutOfBoundsException

Description copied from class: MultiSliceImage

Sets the direction cosines of the row, column and slice directions (for increasing row, column and slice) of the image, in patient (LPS) coordinates.

If the orientation cannot be set for this image, this method does nothing.

Specified by:

setImageOrientationPatient in interface WritableImage

Specified by:

setImageOrientationPatient in class MultiSliceImage

Parameters:

orientation - the direction cosines of the image row, column and (optionally) slice directions respectively in Left,Posterior,Superior (LPS) coordinates.

slice - the slice for which to set the orientation.

Throws:

IndexOutOfBoundsException - if the cosines array does not have the correct dimensions.

setPixelSpacing

public void setPixelSpacing(Float[] spacing)
                     throws IOException

Description copied from interface: WritableImage

Sets the distance (in mm) between pixel centres in the row, column and slice directions of the image, and the time between movie frames (for 4-D images) in seconds. The distances and time should always be positive values.

Specified by:

setPixelSpacing in interface WritableImage

Parameters:

spacing - a Float[] of length up to 4, corresponding to the distance between pixel centres in the row, column, slice and time directions, respectively. Spacing values will only be set for image dimensions where the spacing array is long enough and the array element is non-null. The first element of the array indicates the horizontal pixel size; the second is the vertical pixel size; the third is the pixel depth; fourth is the time between frames.

Throws:

IOException - if the pixel spacing cannot be set for this image.

getSliceThickness

public Float getSliceThickness()

Description copied from interface: ReadableImage

Returns the slice thickness (in mm). This method is necessary because the slice thickness may not be the same as the inter-slice pixel spacing, if there is a gap between slices.

Specified by:

getSliceThickness in interface ReadableImage

Returns:

the slice thickness in mm, or null if the slice thickness is not set, or its value is corrupt.

setSliceThickness

public void setSliceThickness(Float thickness)
                       throws IOException

Description copied from interface: WritableImage

Sets the slice thickness (in mm). This method is necessary because the slice thickness may not be the same as the inter-slice pixel spacing, if there is a gap between slices.

Specified by:

setSliceThickness in interface WritableImage

Parameters:

thickness - the slice thickness in mm, or null to remove the slice thickness information.

Throws:

IOException - if the slice thickness cannot be set for this image.

getStudyID

public String getStudyID()

Description copied from interface: ReadableImage

Returns the study ID for this ReadableImage.

Specified by:

getStudyID in interface ReadableImage

Returns:

the study ID. Returns null if the study ID can't be found.

setStudyID

public void setStudyID(String studyID)

Description copied from interface: WritableImage

Sets the study ID for this image.
N.B. For disk-based images, the changes in the study ID will not be reflected on disk unless the close() method is called.

Specified by:

setStudyID in interface WritableImage

Parameters:

studyID - the new study ID to be assigned to this image.

getPatientPosition

public PatientPosition getPatientPosition()

Description copied from interface: ReadableImage

Returns the position in which the patient is lying in the scanning equipment. For example, PatientPosition.HFS (head-first supine).

Specified by:

getPatientPosition in interface ReadableImage

Returns:

the position in which the patient is lying in the scanning equipment, or null if the patient position cannot be determined.

setPatientPosition

public void setPatientPosition(PatientPosition position)

Description copied from interface: WritableImage

Sets the position in which the patient is lying in the scanning equipment for this WritableImage.

Specified by:

setPatientPosition in interface WritableImage

Parameters:

position - the position in which the patient is lying in the scanning equipment. e.g. PatientPosition.HFS (head-first supine).

supportsIntensityRescaling

public boolean supportsIntensityRescaling()

Returns true because UNC images support intensity rescaling.

Specified by:

supportsIntensityRescaling in interface WritableImage

Returns:

true.

getIntensityRescale

public float[] getIntensityRescale()

Description copied from interface: ReadableImage

Returns the values m and b in the relationship between pixel intensity (I) values and the output units specified in getRescaleUnits() in the expression:
Output units = m*I + b.

Specified by:

getIntensityRescale in interface ReadableImage

Returns:

an array will be of length 2 where the first element is m and the second is b.

setIntensityRescale

public void setIntensityRescale(float rescaleSlope,
 float rescaleIntercept)
                         throws IOException

Description copied from interface: WritableImage

Sets the values m and b in the relationship between pixel intensity (I) values and the output units specified in WritableImage.setRescaleUnits(com.xinapse.dicom.RescaleUnits) in the expression:
Output units = m*I + b.

Specified by:

setIntensityRescale in interface WritableImage

Parameters:

rescaleSlope - the value of m in the expression above.

rescaleIntercept - the value of b in the expression above.

Throws:

IOException - if an I/O error occurs.

getRescaleUnits

public com.xinapse.dicom.RescaleUnits getRescaleUnits()

Description copied from interface: ReadableImage

Returns the output units of Intensity Rescale Slope and Intensity Rescale Intercept, retrieved by getIntensityRescale().

Specified by:

getRescaleUnits in interface ReadableImage

Returns:

the RescaleUnits describing the physical meaning of the pixel intensity units. Returns the RescaleUnits.US if the physical meaning is unknown, or arbitrary.

setRescaleUnits

public void setRescaleUnits(com.xinapse.dicom.RescaleUnits units)
                     throws IOException

Description copied from interface: WritableImage

Sets the rescale units.

Specified by:

setRescaleUnits in interface WritableImage

Parameters:

units - the rescale units.

Throws:

IOException - if the rescale units cannot be set.

appendAuditInfo

public void appendAuditInfo(String name,
 String value)

Description copied from interface: WritableImage

Appends audit trail information to this image.

Specified by:

appendAuditInfo in interface WritableImage

Parameters:

name - a String describing the name of the action that was performed on this image.

value - a String describing the value of the action that was performed on this image.

setPatientName

public void setPatientName(String patientName)
                    throws IOException

Description copied from interface: WritableImage

Attempts to set the patient name for this image. If new patient name String is longer than is allowed by the image format, then it is truncated before being applied. No exception occurs if the image format does not support patient name recording.
N.B. For disk-based images, the changes in the patient name will not be reflected on disk unless the close() method is called.

Specified by:

setPatientName in interface WritableImage

Parameters:

patientName - the new patient name to be assigned to this image.

Throws:

IOException - if the patient name cannot be set.

setPatientID

public void setPatientID(String patientID)
                  throws IOException

Description copied from interface: WritableImage

Sets the patient ID for this image. If the new patient ID String is longer than is allowed by the image format, then it is truncated before being applied. No exception occurs if the image format does not support patient ID recording.
N.B. For disk-based images, the changes in the patient ID will not be reflected on disk unless the close() method is called.

Specified by:

setPatientID in interface WritableImage

Parameters:

patientID - the new patient ID to be assigned to this image.

Throws:

IOException - if the patient ID cannot be set.

setPatientDoB

public void setPatientDoB(Date patientDoB)
                   throws IOException

Description copied from interface: WritableImage

Sets the patient's date of birth for this image. No exception occurs if the image format does not support patient date of birth recording.
N.B. For disk-based images, the changes in the patient's birth date will not be reflected on disk unless the close() method is called.

Specified by:

setPatientDoB in interface WritableImage

Parameters:

patientDoB - the new patient date of birth to be assigned to this image.

Throws:

IOException - if the patient date of birth cannot be set.

setPatientSex

public void setPatientSex(com.xinapse.dicom.Sex sex)
                   throws IOException

Description copied from interface: WritableImage

Sets the patient sex for this image.

Specified by:

setPatientSex in interface WritableImage

Parameters:

sex - the patient sex to be assigned to this image.

Throws:

IOException - if the patient sex cannot be set.

setScanDate

public void setScanDate(Date scanDate)
                 throws IOException

Description copied from interface: WritableImage

Sets the scan date/time for this image.
N.B. For disk-based images, the changes in the scan date will not be reflected on disk unless the close() method is called.

Specified by:

setScanDate in interface WritableImage

Parameters:

scanDate - the new scan date/time to be assigned to this image.

Throws:

IOException - if the scan date cannot be set.

setPulseSequence

public void setPulseSequence(String seqName)
                      throws IOException

Description copied from interface: WritableImage

Sets the pulse sequence name for this image.
N.B. For disk-based images, the changes in the scanning sequence will not be reflected on disk unless the close() method is called.

Specified by:

setPulseSequence in interface WritableImage

Parameters:

seqName - the new name of the pulse sequence to be assigned to this image.

Throws:

IOException - if the pulse sequence name cannot be set.

setScanningSequence

public void setScanningSequence(PulseSequenceType seq)
                         throws IOException

Description copied from interface: WritableImage

Sets the DICOM scanning sequence for this image.
N.B. For disk-based images, the changes in the scanning sequence will not be reflected on disk unless the close() method is called.

Specified by:

setScanningSequence in interface WritableImage

Parameters:

seq - the new scanning sequence to be assigned to this image.

Throws:

IOException - if the scanning sequence cannot be set.

setSequenceVariant

public void setSequenceVariant(PulseSequenceVariant seqVar)
                        throws IOException

Description copied from interface: WritableImage

Sets the DICOM scanning sequence variant for this image.
N.B. For disk-based images, the changes in the scanning sequence variant will not be reflected on disk unless the close() method is called.

Specified by:

setSequenceVariant in interface WritableImage

Parameters:

seqVar - the new scanning sequence variant to be assigned to this image.

Throws:

IOException - if the scanning sequence variant cannot be set.

setSeriesNumber

public void setSeriesNumber(Integer seriesNumber)
                     throws IOException

Description copied from interface: WritableImage

Sets the series number for this image.
N.B. For disk-based images, the changes in the series number will not be reflected on disk unless the close() method is called.

Specified by:

setSeriesNumber in interface WritableImage

Parameters:

seriesNumber - the new series number to be assigned to this image.

Throws:

IOException - if the series number cannot be set.

setSeriesDescription

public void setSeriesDescription(String seriesDescription)
                          throws IOException

Description copied from interface: WritableImage

Sets a short description of the series (scan).
N.B. For disk-based images, the changes in the series description will not be reflected on disk unless the close() method is called.

Specified by:

setSeriesDescription in interface WritableImage

Parameters:

seriesDescription - the new short description of the series, or null if none is available.

Throws:

IOException - if the description cannot be set.

getBodyPart

public com.xinapse.dicom.BodyPart getBodyPart()

Description copied from class: MultiSliceImage

By default, body part recording is not supported, so this method always returns null.

Specified by:

getBodyPart in interface ReadableImage

Overrides:

getBodyPart in class MultiSliceImage

Returns:

null.

setBodyPart

public void setBodyPart(com.xinapse.dicom.BodyPart bodyPart)
                 throws IOException

Description copied from class: MultiSliceImage

By default, body part recording is not supported, so this method does nothing.

Specified by:

setBodyPart in interface WritableImage

Overrides:

setBodyPart in class MultiSliceImage

Parameters:

bodyPart - body the imaged body part.

Throws:

IOException - if body part cannot be set.

getLaterality

public com.xinapse.dicom.Laterality getLaterality()

Description copied from class: MultiSliceImage

By default, laterality recording is not supported, so this method returns Laterality.BOTH.

Specified by:

getLaterality in interface ReadableImage

Overrides:

getLaterality in class MultiSliceImage

Returns:

Laterality.BOTH.

setLaterality

public void setLaterality(com.xinapse.dicom.Laterality laterality)
                   throws IOException

Description copied from class: MultiSliceImage

By default, laterality recording is not supported, so this method does nothing.

Specified by:

setLaterality in interface WritableImage

Overrides:

setLaterality in class MultiSliceImage

Parameters:

laterality - the image laterality.

Throws:

IOException - if laterality cannot be set.

setScanTR

public void setScanTR(Float TR)
               throws IOException

Description copied from interface: WritableImage

Sets the scan repetition time for this image. No exception occurs if the image format does not support scan TR recording.
N.B. For disk-based images, the changes in the scan TR will not be reflected on disk unless the close() method is called.

Specified by:

setScanTR in interface WritableImage

Parameters:

TR - the new scan TR to be assigned to this image. If null, the TR should be unset.

Throws:

IOException - if the scan TR cannot be set.

setScanTI

public void setScanTI(Float TI)
               throws IOException

Description copied from interface: WritableImage

Sets the scan inversion time for this image. No exception occurs if the image format does not support scan TI recording.
N.B. For disk-based images, the changes in the scan TI will not be reflected on disk unless the close() method is called.

Specified by:

setScanTI in interface WritableImage

Parameters:

TI - the new scan TI to be assigned to this image. If null, the TI should be unset.

Throws:

IOException - if the scan TI cannot be set.

setScanTE

public void setScanTE(Float TE)
               throws IOException

Description copied from interface: WritableImage

Sets the scan echo time for this image. No exception occurs if the image format does not support scan TE recording.
N.B. For disk-based images, the changes in the scan TE will not be reflected on disk unless the close() method is called.

Specified by:

setScanTE in interface WritableImage

Parameters:

TE - the new scan TE to be assigned to this image. If null, the TE should be unset.

Throws:

IOException - if the scan TE cannot be set.

setScanTE

public void setScanTE(Float TE,
 int index)
               throws IOException

Description copied from interface: WritableImage

Sets the scan echo time for one dimension index of this image. For 3-D images, the dimension index is the slice dimension. For 4-D (or higher dimensionality) images, the dimension index is the frame dimension. No exception occurs if the image format does not support a scan TE recording.
N.B. For disk-based images, the changes in the scan TE will not be reflected on disk unless the close() method is called.

Specified by:

setScanTE in interface WritableImage

Parameters:

TE - the new scan TE to be assigned to this image.

index - the slice number for which to set the echo time.

Throws:

IOException - if the scan TE cannot be set because of an I/O error.

setSaturationFreqOffsetPPM

public void setSaturationFreqOffsetPPM(Float freqOffset)
                                throws IOException

Description copied from interface: WritableImage

Sets the saturation frequency offset in PPM for this image. No exception occurs if the image format does not support saturation frequency offset recording.
N.B. For disk-based images, the changes in the saturation frequency offset will not be reflected on disk unless the close() method is called.

Specified by:

setSaturationFreqOffsetPPM in interface WritableImage

Parameters:

freqOffset - the new saturation frequency offset to be assigned to this image. If null, the saturation frequency offset should be unset.

Throws:

IOException - if the saturation frequency offset cannot be set.

setSaturationFreqOffsetPPM

public void setSaturationFreqOffsetPPM(Float freqOffset,
 int index)
                                throws IOException

Description copied from interface: WritableImage

Sets the saturation frequency offset for one dimension index of this image. For 3-D images, the dimension index is the slice dimension. For 4-D (or higher dimensionality) images, the dimension index is the frame dimension. No exception occurs if the image format does not support saturation frequency offset recording.
N.B. For disk-based images, the changes in the saturation frequency offset will not be reflected on disk unless the close() method is called.

Specified by:

setSaturationFreqOffsetPPM in interface WritableImage

Parameters:

freqOffset - the new saturation frequency offset to be assigned to this image.

index - the slice number for which to set the saturation frequency offset.

Throws:

IOException - if the saturation frequency offset cannot be set because of an I/O error.

setEchoTrainLength

public void setEchoTrainLength(Integer etl)
                        throws IOException

Description copied from interface: WritableImage

Sets the echo train length for this image. No exception occurs if the image format does not support a echo train length recording.
N.B. For disk-based images, the changes in the echo train length will not be reflected on disk unless the close() method is called.

Specified by:

setEchoTrainLength in interface WritableImage

Parameters:

etl - the new scan echo train length to be assigned to this image. If null, the echo train length is unassigned.

Throws:

IOException - if the echo train length cannot be set because of an I/O error.

setFlipAngle

public void setFlipAngle(Float flipAngle)
                  throws IOException

Description copied from interface: WritableImage

Sets the excitation pulse flip angle for this image. No exception occurs if the image format does not support flip angle recording.
N.B. For disk-based images, the changes in the scan flip angle will not be reflected on disk unless the close() method is called.

Specified by:

setFlipAngle in interface WritableImage

Parameters:

flipAngle - the new scan flip angle to be assigned to this image. If null, the flip angle should be unset.

Throws:

IOException - if the scan flip angle cannot be set.

getPatientName

public String getPatientName()

Description copied from interface: ReadableImage

Returns the patient name for this image.

Specified by:

getPatientName in interface ReadableImage

Returns:

the patient name for this image, or null if the patient name can't be found.

getPatientID

public String getPatientID()

Description copied from interface: ReadableImage

Returns the patient ID for this image.

Specified by:

getPatientID in interface ReadableImage

Returns:

the patientID for this image, or null if the patientID can't be found.

getPatientDoB

public Date getPatientDoB()

Description copied from interface: ReadableImage

Returns the patient date of birth for this image.

Specified by:

getPatientDoB in interface ReadableImage

Returns:

the patient's date of birth for this image, or null if the patient's dob can't be found.

getPatientSex

public com.xinapse.dicom.Sex getPatientSex()

Description copied from interface: ReadableImage

Returns the patient sex for this image.

Specified by:

getPatientSex in interface ReadableImage

Returns:

the patient's sex image, or Sex.OTHER if the patient's sex can't be found.

getScanDate

public Date getScanDate()

Description copied from interface: ReadableImage

Returns the scan Date for this image.

Specified by:

getScanDate in interface ReadableImage

Returns:

the date/time at which this scan was performed, or null if the scan date can't be found.

getPulseSequence

public String getPulseSequence()

Description copied from interface: ReadableImage

Returns the name of the pulse sequence with which this image was collected.

Specified by:

getPulseSequence in interface ReadableImage

Returns:

the name of the pulse sequence used to collect this image.

getScanningSequence

public PulseSequenceType getScanningSequence()

Description copied from interface: ReadableImage

Returns the DICOM Scanning Sequence with which this image was collected.

Specified by:

getScanningSequence in interface ReadableImage

Returns:

the DICOM Scanning Sequence used to collect this image, or null if the scanning sequence isn't available.

getSequenceVariant

public PulseSequenceVariant getSequenceVariant()

Description copied from interface: ReadableImage

Returns the DICOM Scanning Sequence Variant with which this image was collected.

Specified by:

getSequenceVariant in interface ReadableImage

Returns:

the DICOM Scanning Sequence Variant used to collect this image, or null if the sequence variant isn't available.

getSeriesNumber

public Integer getSeriesNumber()

Description copied from interface: ReadableImage

Returns the series number for this ReadableImage.

Specified by:

getSeriesNumber in interface ReadableImage

Returns:

the series number. Returns null if the series number can't be found.

getSeriesDescription

public String getSeriesDescription()

Description copied from interface: ReadableImage

Returns a short description of the series (scan), such as is provided by the DICOM series description.

Specified by:

getSeriesDescription in interface ReadableImage

Returns:

a short description of the series, or null if none is available.

getScanTR

public Float getScanTR()

Description copied from interface: ReadableImage

Returns the scan repetition time for this image.

Specified by:

getScanTR in interface ReadableImage

Returns:

the scan TR for this image, or null if not set for this image.

getScanTI

public Float getScanTI()

Description copied from interface: ReadableImage

Returns the scan inversion time for this image.

Specified by:

getScanTI in interface ReadableImage

Returns:

the scan TI for this image, or null if not set for this image.

getScanTE

public Float getScanTE()

Description copied from interface: ReadableImage

Returns the scan echo time for this image if it has a single echo-time.

Specified by:

getScanTE in interface ReadableImage

Returns:

the scan TE for this image, or null if not set for this image.

getScanTE

public Float getScanTE(int index)
                throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the scan echo time for one dimension index of this image. For 3-D images, the dimension index is the slice dimension. For 4-D (or higher dimensionality) images, the dimension index is the frame dimension.

Specified by:

getScanTE in interface ReadableImage

Parameters:

index - the index for which to return the echo time.

Returns:

the scan TE for the specified index of this image, or null if not set for this image.

Throws:

IndexOutOfBoundsException - if the index is bad for this image.

getSaturationFreqOffsetPPM

public Float getSaturationFreqOffsetPPM()

Description copied from interface: ReadableImage

Returns the scan saturation frequency offset for this image if it has a single saturation frequency offset in parts-per-million.

Specified by:

getSaturationFreqOffsetPPM in interface ReadableImage

Returns:

the scan saturation frequency offset for this image, or null if not set for this image.

getSaturationFreqOffsetPPM

public Float getSaturationFreqOffsetPPM(int index)
                                 throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the scan saturation frequency offset for one dimension index of this image in parts-per-million. For 3-D images, the dimension index is the slice dimension. For 4-D (or higher dimensionality) images, the dimension index is the frame dimension.

Specified by:

getSaturationFreqOffsetPPM in interface ReadableImage

Parameters:

index - the index for which to return the saturation frequency offset.

Returns:

the scan TE for the specified index of this image, or null if not set for this image.

Throws:

IndexOutOfBoundsException - if the index is bad for this image.

getEchoTrainLength

public Integer getEchoTrainLength()

Description copied from interface: ReadableImage

Returns the scan echo train length for this image.

Specified by:

getEchoTrainLength in interface ReadableImage

Returns:

the echo train length for this image, or null if not set for this image.

getFlipAngle

public Float getFlipAngle()

Description copied from interface: ReadableImage

Returns the excitation pulse flip angle for this image.

Specified by:

getFlipAngle in interface ReadableImage

Returns:

the excitation pulse flip angle for this image, or null if not set for this image.

getSliceDWbValue

public Float getSliceDWbValue(int slice)
                       throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the diffusion-weighting b-value for one slice of this image.

Specified by:

getSliceDWbValue in interface ReadableImage

Parameters:

slice - the slice number for which to return the b-value.

Returns:

the diffusion-weighting b-value for the specified slice of this image, or null if the b-value cannot be found, or if the modality used to collect the image doesn't have a b-value defined

Throws:

IndexOutOfBoundsException - if the slice number is bad for this image.

getFrameDWbValue

public Float getFrameDWbValue(int frame)
                       throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the diffusion-weighting b-value for one frame of this 4-D image.

Specified by:

getFrameDWbValue in interface ReadableImage

Parameters:

frame - the frame number for which to return the b-value.

Returns:

the diffusion-weighting b-value for the specified frame of this image, or null if the b-value cannot be found, or if the modality used to collect the image doesn't have a b-value defined

Throws:

IndexOutOfBoundsException - if the frame number is bad for this image, or it isn't a 4-D image.

setSliceDWbValue

public void setSliceDWbValue(float bValue,
 int index)
                      throws IOException

Description copied from interface: WritableImage

Sets the diffusion-weighting b-value for one slice of this image. No exception occurs if the image format does not support recording the b-value.
N.B. For disk-based images, the changes in the b-value will not be reflected on disk unless the close() method is called.

Specified by:

setSliceDWbValue in interface WritableImage

Parameters:

bValue - the new b-value to be assigned to this image.

index - the slice number for which to set the b-value.

Throws:

IOException - if the scan b-value cannot be set.

setFrameDWbValue

public void setFrameDWbValue(float bValue,
 int frame)
                      throws IOException

Description copied from interface: WritableImage

Sets the diffusion-weighting b-value for one "frame" of this 4-D image. No exception occurs if the image format does not support recording the b-value.
N.B. For disk-based images, the changes in the b-value will not be reflected on disk unless the close() method is called.

Specified by:

setFrameDWbValue in interface WritableImage

Parameters:

bValue - the new b-value to be assigned to this image.

frame - the frame number for which to set the b-value.

Throws:

IOException - if the scan b-value cannot be set.

getSliceDWGradientVector

public org.jogamp.vecmath.Vector3f getSliceDWGradientVector(int slice)
                                                     throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the diffusion-weighting gradient-vector for one slice of this image.

Specified by:

getSliceDWGradientVector in interface ReadableImage

Parameters:

slice - the slice number for which to return the gradient-vector.

Returns:

the diffusion-weighting gradient-vector for the specified slice of this image, or null if the gradient vector cannot be found, or if the modality used to collect the image doesn't have a gradient vector defined.

Throws:

IndexOutOfBoundsException - if the slice number is bad for this image.

getFrameDWGradientVector

public org.jogamp.vecmath.Vector3f getFrameDWGradientVector(int frame)
                                                     throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the diffusion-weighting gradient-vector for one frame of this image 4-D image.

Specified by:

getFrameDWGradientVector in interface ReadableImage

Parameters:

frame - the frame number for which to return the gradient-vector.

Returns:

the diffusion-weighting gradient-vector for the specified frame of this image, or null if the gradient vector cannot be found, or if the modality used to collect the image doesn't have a gradient vector defined.

Throws:

IndexOutOfBoundsException - if the frame number is bad for this image, or it isn't a 4-D image.

setSliceDWGradientVector

public void setSliceDWGradientVector(org.jogamp.vecmath.Vector3f gradVec,
 int index)
                              throws IOException

Description copied from interface: WritableImage

Sets the diffusion-weighting gradient vector for one slice of this image. No exception occurs if the image format does not support recording the gradient vector.
N.B. For disk-based images, the changes in the gradient vector will not be reflected on disk unless the close() method is called.

Specified by:

setSliceDWGradientVector in interface WritableImage

Parameters:

gradVec - the new gradient vector to be assigned to this image.

index - the slice number for which to set the gradient vector.

Throws:

IOException - if the scan gradient vector cannot be set.

setFrameDWGradientVector

public void setFrameDWGradientVector(org.jogamp.vecmath.Vector3f gradVec,
 int frame)
                              throws IOException

Description copied from interface: WritableImage

Sets the diffusion-weighting gradient vector for one "frame" of this 4-D image. No exception occurs if the image format does not support recording the gradient vector.
N.B. For disk-based images, the changes in the gradient vector will not be reflected on disk unless the close() method is called.

Specified by:

setFrameDWGradientVector in interface WritableImage

Parameters:

gradVec - the new gradient vector to be assigned to this image.

frame - the frame number for which to set the gradient vector.

Throws:

IOException - if the scan gradient vector cannot be set.

getSliceDWBMatrix

public float[] getSliceDWBMatrix(int slice)
                          throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the diffusion-weighting b-matrix for one slice of this image.

Specified by:

getSliceDWBMatrix in interface ReadableImage

Parameters:

slice - the slice number for which to get the b-matrix.

Returns:

the diffusion-weighting b-matrix for this image if it is a magnetic resonance image, or null if the B-matrix cannot be found, or if the modality used to collect the image doesn't have a B-matrix defined. The 6 unique matrix elements are returned as a float[] with elements in the order bXX, bXY, bXZ, bYY, bYZ, bZZ.

Throws:

IndexOutOfBoundsException - if the slice number is bad for this image.

getFrameDWBMatrix

public float[] getFrameDWBMatrix(int frame)
                          throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the diffusion-weighting b-matrix for one frame of this image.

Specified by:

getFrameDWBMatrix in interface ReadableImage

Parameters:

frame - the frame number for which to get the b-matrix.

Returns:

the diffusion-weighting b-matrix for this image if it is a magnetic resonance image, or null if the B-matrix cannot be found, or if the modality used to collect the image doesn't have a B-matrix defined. The 6 unique matrix elements are returned as a float[] with elements in the order bXX, bXY, bXZ, bYY, bYZ, bZZ.

Throws:

IndexOutOfBoundsException - if the frame number is bad for this image, or it isn't a 4-D image.

setSliceDWBMatrix

public void setSliceDWBMatrix(float[] bMatrix,
 int slice)
                       throws IOException

Description copied from interface: WritableImage

Sets the diffusion-weighting B-matrix for one slice of this image. No exception occurs if the image format does not support recording the B-matrix.
N.B. For disk-based images, the changes in the B-matrix will not be reflected on disk unless the close() method is called.

Specified by:

setSliceDWBMatrix in interface WritableImage

Parameters:

bMatrix - the new B-matrix to be assigned to this image.

slice - the slice number for which to set the B-matrix.

Throws:

IOException - if the scan B-matrix cannot be set.

setFrameDWBMatrix

public void setFrameDWBMatrix(float[] bMatrix,
 int frame)
                       throws IOException,
IndexOutOfBoundsException

Description copied from interface: WritableImage

Sets the diffusion-weighting B-matrix for one "frame" of this 4-D image. No exception occurs if the image format does not support recording the B-matrix.
N.B. For disk-based images, the changes in the B-matrix will not be reflected on disk unless the close() method is called.

Specified by:

setFrameDWBMatrix in interface WritableImage

Parameters:

bMatrix - the new B-matrix to be assigned to this image.

frame - the frame number for which to set the B-matrix.

Throws:

IOException - if the scan B-matrix cannot be set.

IndexOutOfBoundsException - if this is not a 4-D image.

getSliceTriggerDelayMS

public Float getSliceTriggerDelayMS(int slice)
                             throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the trigger delay, in milliseconds, for one slice of this image.

Specified by:

getSliceTriggerDelayMS in interface ReadableImage

Parameters:

slice - the slice number for which to get the trigger delay.

Returns:

the trigger delay (in milliseconds) for this image, or null if the trigger delay cannot be found.

Throws:

IndexOutOfBoundsException - if the slice number is bad for this image, or it isn't a 4-D image.

getFrameTriggerDelayMS

public Float getFrameTriggerDelayMS(int frame)
                             throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns the trigger delay, in milliseconds, for one frame of this image.

Specified by:

getFrameTriggerDelayMS in interface ReadableImage

Parameters:

frame - the frame number for which to get the trigger delay.

Returns:

the trigger delay (in milliseconds) for this image, or null if the trigger delay cannot be found.

Throws:

IndexOutOfBoundsException - if the frame number is bad for this image, or it isn't a 4-D image.

setSliceTriggerDelayMS

public void setSliceTriggerDelayMS(float delay,
 int index)
                            throws IOException

Description copied from interface: WritableImage

Sets the trigger delay (in milliseconds) for one slice of this image. No exception occurs if the image format does not support recording the trigger delay.
N.B. For disk-based images, the changes in the trigger delay will not be reflected on disk unless the close() method is called.

Specified by:

setSliceTriggerDelayMS in interface WritableImage

Parameters:

delay - the new trigger delay (in milliseconds) to be assigned to this image slice.

index - the slice number for which to set the trigger delay.

Throws:

IOException - if the trigger delay cannot be set.

setFrameTriggerDelayMS

public void setFrameTriggerDelayMS(float delay,
 int frame)
                            throws IOException

Description copied from interface: WritableImage

Sets the trigger delay (in milliseconds) for one "frame" of this 4-D image. No exception occurs if the image format does not support recording the trigger delay.
N.B. For disk-based images, the changes in the trigger delay will not be reflected on disk unless the close() method is called.

Specified by:

setFrameTriggerDelayMS in interface WritableImage

Parameters:

delay - the new trigger delay to be assigned to this image.

frame - the frame number for which to set the trigger delay.

Throws:

IOException - if the trigger delay cannot be set.

getDescription

public String getDescription()

Description copied from interface: ReadableImage

Returns a String description of this image.

Specified by:

getDescription in interface ReadableImage

Returns:

a String describing this image.

getDescription

public String getDescription(int slice)
                      throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns a String description of this one particular slice of this image.

Specified by:

getDescription in interface ReadableImage

Parameters:

slice - the slice to describe.

Returns:

a String describing the given slice of this image.

Throws:

IndexOutOfBoundsException

getHTMLDescription

public String getHTMLDescription()

Description copied from interface: ReadableImage

Returns a String description of this image in HTML format.

Specified by:

getHTMLDescription in interface ReadableImage

Returns:

a String describing this image.

getHTMLDescription

public String getHTMLDescription(int slice)
                          throws IndexOutOfBoundsException

Description copied from interface: ReadableImage

Returns a String description of a slice of this image in HTML format.

Specified by:

getHTMLDescription in interface ReadableImage

Parameters:

slice - the slice number.

Returns:

a String describing this image slice.

Throws:

IndexOutOfBoundsException - if the slice is bad for this image.

getNativeColourMapping

public ColourMapping getNativeColourMapping()
                                     throws InvalidColourMappingException

Description copied from interface: ReadableImage

Returns a ColourMapping if this image has an associated colour mapping.

Specified by:

getNativeColourMapping in interface ReadableImage

Returns:

a ColourMapping if this image has an associated colour mapping. Returns null if it does not.

Throws:

InvalidColourMappingException - if this image has an associated ColourMapping, but the ColourMapping cannot be successfully retrieved.

setNativeColourMapping

public void setNativeColourMapping(ColourMapping colourMapping)
                            throws IOException

Description copied from interface: WritableImage

Sets the ColourMapping for this image. No exception occurs if the image format does not support a colour mapping.
N.B. For disk-based images, the changes in the ColourMapping may not be reflected on disk unless the close() method is called.

Specified by:

setNativeColourMapping in interface WritableImage

Parameters:

colourMapping - the new ColourMapping to be assigned to this image.

Throws:

IOException - if the ColourMapping cannot be set for this image.

getMin

public Double getMin()
              throws InvalidImageException

Description copied from interface: ReadableImage

Returns the minimum pixel intensity in the image.

Specified by:

getMin in interface ReadableImage

Returns:

the maximum pixel intensity as a Double, or null if the intensity min hasn't been calculated for this image.

Throws:

InvalidImageException - if the intensity cannot be returned as a Double.

getMax

public Double getMax()
              throws InvalidImageException

Description copied from interface: ReadableImage

Returns the maximum pixel intensity in the image.

Specified by:

getMax in interface ReadableImage

Returns:

the maximum pixel intensity as a Double, or null if the intensity max hasn't been calculated for this image.

Throws:

InvalidImageException - if the intensity cannot be returned as a Double.

getCommonName

public static String getCommonName()

Returns the common name for this type of image.

Returns:

the String "UNC".

getImageTypeName

public String getImageTypeName()

Description copied from interface: WritableImage

Returns the normal human readable name for this type of image.

Specified by:

getImageTypeName in interface WritableImage

Returns:

a String with a one-word description of this type of image.

getCopy

public WritableImage getCopy()
                      throws IOException

Description copied from interface: WritableImage

Returns a copy of this WritableImage.

Specified by:

getCopy in interface ReadableImage

Specified by:

getCopy in interface WritableImage

Returns:

a copy of this ReadableImage.

Throws:

IOException - if the an I/O error occurs whilst copying.