Class NIFTI2Image

java.lang.Object

com.xinapse.multisliceimage.MultiSliceImage

com.xinapse.multisliceimage.analyze.ANZImage

com.xinapse.multisliceimage.analyze.NIFTIImage

com.xinapse.multisliceimage.analyze.NIFTI2Image

All Implemented Interfaces:

ReadableImage, WritableImage, InfoStorer, AutoCloseable

public class NIFTI2Image
extends NIFTIImage
implements InfoStorer, AutoCloseable

This class is a representation of a multi-dimensional image in the NIFTI-2 format, the updated NIFTI format.

Nested Class Summary

Nested classes/interfaces inherited from interface ReadableImage

ReadableImage.Position

Field Summary

Fields inherited from class NIFTIImage

COMPRESSED_EXTENSION, DEFAULT_COMPRESSED, DEFAULT_NIFTI_ONE_FILE, EXTENSION, UPPERCASE_COMPRESSED_EXTENSION, UPPERCASE_EXTENSION

Fields inherited from class ANZImage

COMPRESSED_UPPERCASE_EXTENSION

Fields inherited from class MultiSliceImage

ACCESSION_NUMBER_NAME, 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, IMAGE_TYPE_NAME, INTENSITY_RESCALE_INTERCEPT_NAME, INTENSITY_RESCALE_SLOPE_NAME, INTENSITY_RESCALE_UNITS_NAME, INVERSION_TIME_NAME, LATERALITY_NAME, MODALITY_NAME, PATIENT_ID_NAME, PATIENT_NAME_NAME, PATIENT_POSITION_NAME, PATIENT_SEX_NAME, PIXEL_SPACING_NAME, PIXEL_X_SIZE_NAME, PIXEL_Y_SIZE_NAME, PIXEL_Z_SIZE_NAME, PULSE_SEQUENCE_NAME, 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
NIFTI2Image()	Creates an uninitialised instance of a NIFTI2Image.
NIFTI2Image(long nCols, long nRows, long nSlices, long nFrames, ANZPixFormat dataType)	Creates a new in-memory NIFTI2Image.
NIFTI2Image(ANZPixFormat dataType, Long... dims)	Creates a new in-memory NIFTI2Image.
NIFTI2Image(String fileName, FileAccessMode mode)	Opens an existing NIFTI2Image.

Method Summary

Modifier and Type	Method	Description
static String	getCommonName()	Returns the common name for this type of image.
static void	main(String[] args)	Run the self-test for the NIFTI2Image class.

Methods inherited from class NIFTIImage

addExtendedData, anonymise, appendAuditInfo, appendInfoList, appendInfoList, getBodyPart, getCopy, getDICOMImageType, getEchoTrainLength, getExtendedData, getFlatSliceDescription, getFlipAngle, getFrameDICOMImageType, getFrameDWBMatrix, getFrameDWbValue, getFrameDWGradientVector, getFrameInfo, getFrameInfoList, getFrameSaturationFreqOffsetPPM, getFrameTE, getFrameTriggerDelayMS, getImageOrientationPatient, getImagePositionPatient, getImageTypeName, getInfo, getInfo, getInfoList, getInfoList, getIntensityRescale, getIntent, getLaterality, getNIFTIOneFile, getPatientDoB, getPatientID, getPatientName, getPatientPosition, getPatientSex, getPreferredCompressed, getPreferredNIFTIOneFile, getPreviewIcon, getPulseSequence, getQForm, getRescaleUnits, getSaturationFreqOffsetPPM, getSaveCompressed, getScanDate, getScanningSequence, getScanTE, getScanTI, getScanTR, getSequenceVariant, getSeriesDescription, getSeriesNumber, getSForm, getSFormAffineTransform, getSliceInfo, getSliceInfoList, getSliceThickness, getStudyID, imageExists, putFrameInfo, putFrameInfo, putInfo, putInfo, putInfo, putInfo, putInfo, putInfo, putSliceInfo, putSliceInfo, removeExtendedData, removeInfo, removeInfo, savePreferredCompressed, savePreferredNIFTIOneFile, setBodyPart, setDICOMImageType, setEchoTrainLength, setFlipAngle, setFrameDICOMImageType, setFrameDWBMatrix, setFrameDWbValue, setFrameDWGradientVector, setFrameInfoList, setFrameSaturationFreqOffsetPPM, setFrameTE, setFrameTriggerDelayMS, setImageOrientationPatient, setImagePositionPatient, setInfoList, setInfoList, setIntensityRescale, setIntent, setLaterality, setPatientDoB, setPatientID, setPatientName, setPatientPosition, setPatientSex, setPulseSequence, setQForm, setRescaleUnits, setSaturationFreqOffsetPPM, setScanDate, setScanningSequence, setScanTE, setScanTI, setScanTR, setSequenceVariant, setSeriesDescription, setSeriesNumber, setSForm, setSFormAffineTransform, setSliceInfoList, setSliceThickness, setStudyID, stripExtension, supportsIntensityRescaling, write

Methods inherited from class ANZImage

close, getByteOrder, getDataType, getDescription, getDims, getFileDataOffset, getHeader, getImageOrientationPatient, getImagePositionPatient, getMax, getMin, getNativeColourMapping, getNativeHeader, getNCols, getNDim, getNFrames, getNRows, getNSlices, getPixelXSize, getPixelYSize, getPixelZSize, getStoredPixelDataType, getTimeBetweenFrames, getTitle, getTotalNSlices, isCompressed, isOpen, setDBName, setDescription, setImageOrientationPositionPatient, setMinMax, setNativeColourMapping, setPixelSpacing, setPixelXSize, setPixelYSize, setPixelZSize, setTimeBetweenFrames, setTitle, toString

Methods inherited from class MultiSliceImage

clearModified, disposeImageData, doRescale, doUnRescale, getAccessionNumber, getDateFormat, getFrameOfReferenceUID, getModality, getMostLikePlane, getPix, getPix, getPix, getPix, getPresentationPixelDataType, getRawPix, getROIs, getScanDateFormat, getSlice, getSlice, getStudyInstanceUID, getSuggestedFileName, isModified, putPix, putPix, putPix, putPix, putSlice, setAccessionNumber, setFrameOfReferenceUID, setIntensityRescale, setMinMax, setModality, setModified, setSeriesInstanceUID, setStudyInstanceUID, setSuggestedFileName

Methods inherited from class Object

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

Methods inherited from interface InfoStorer

appendInfoList, appendInfoList, getFloatInfo, getFloatInfo, getFrameInfo, getFrameInfoList, getInfo, getInfo, getInfoList, getInfoList, getIntegerInfo, getSliceInfo, getSliceInfoList, getVectorInfo, putFrameInfo, putFrameInfo, putInfo, putInfo, putInfo, putInfo, putInfo, putInfo, putSliceInfo, putSliceInfo, removeInfo, removeInfo, setFrameInfoList, setInfoList, setInfoList, setSliceInfoList

Methods inherited from interface ReadableImage

getAffineTransform, getAffineTransform, getDescription, getFlatSliceDescription, getFlatSliceHTMLDescription, getHTMLDescription, getNSliceLocations, getPixelSpacingOrDefaults

Methods inherited from interface WritableImage

addBasicAudit, addBasicAudit, appendToTitle

Constructor Details

NIFTI2Image

public NIFTI2Image()

Creates an uninitialised instance of a NIFTI2Image. Needed so that newInstance() method can be called on the class.

NIFTI2Image

public NIFTI2Image(long nCols,
 long nRows,
 long nSlices,
 long nFrames,
 ANZPixFormat dataType)
            throws ANZException

Creates a new in-memory NIFTI2Image. This image exists in memory, and will only be written with an explicit write() method call.

Parameters:

nCols - the number of columns in the image x-direction.

nRows - the number of rows in the image y-direction.

nSlices - the number of slice in the image.

nFrames - the number of frames (time points) in the image.

dataType - the ANZPixFormat for the image.

Throws:

ANZException - if the image cannot be created.

NIFTI2Image

public NIFTI2Image(ANZPixFormat dataType,
 Long... dims)
            throws ANZException

Creates a new in-memory NIFTI2Image. This image exists in memory, and will only be written with an explicit write() method call.

Parameters:

dataType - an ANZPixFormat.

dims - the number of samples in each of the image dimensions. The number of arguments supplied determines the dimensionality of the image.

Throws:

ANZException - if the image cannot be created.

NIFTI2Image

public NIFTI2Image(String fileName,
 FileAccessMode mode)
            throws InvalidImageException,
IOException

Opens an existing NIFTI2Image.

Parameters:

fileName - the name of the image file.

mode - the access mode for the image.

Throws:

InvalidImageException - if the image cannot be opened or loaded, or if mode is invalid.

FileNotFoundException - if the image file doesn't exist.

IOException - if an I/O error occurs.

Method Details

getCommonName

public static String getCommonName()

Returns the common name for this type of image.

Returns:

the String "NIFTI-2".

main

public static void main(String[] args)

Run the self-test for the NIFTI2Image class.

Parameters:

args - a list of images to try to open.