Package gov.nih.mipav.model.file

Class FileInfoNRRD

java.lang.Object

gov.nih.mipav.model.structures.ModelSerialCloneable

gov.nih.mipav.model.file.FileInfoBase

gov.nih.mipav.model.file.FileInfoNRRD

All Implemented Interfaces:

Serializable, Cloneable

public class FileInfoNRRD
extends FileInfoBase

See Also:

• FileNRRD
• Serialized Form

Nested Class Summary

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

FileInfoBase.AxisOrientation, FileInfoBase.ImageOrientation, FileInfoBase.Modality, FileInfoBase.Unit, FileInfoBase.UnitType

Field Summary

Fields

Modifier and Type	Field	Description
private String	contentString	Concise textual description of the information in the array
private String	DWMRI_B_VALUE	"DWMRI_b-value:=b " : This key/value pair gives the (scalar) diffusion-weighting value, in units of s/mm^2.
private String[][]	dwmriGradient	For every index position NNNN along the DWI axis (whichever is the non-spatial axis identified by the "list" or "vector" kind field), either "DWMRI_gradient_NNNN:=x y z " or "DWMRI_B-matrix_NNNN:=xx xy xz yy yz zz " must be given (except if "DWMRI_NEX_NNNN:= M " is used).
private String	encodingString	Data compression - raw, gzip
private String[]	labelString	Axis names such as X, Y, or Z
private String	modalityString	Diffusion weighted MRI is currently the only value that has been seen for modality in our samples.
private float	sliceThickness
private String	spaceString	Possible values are "right-anterior-superior", "left-anterior-superior", "left-posterior-superior", "right-anterior-superior-time", "left-anterior-superior-time", "left-posterior-superior-time", "scanner-xyz", "scanner-xyz-time", "3d-right-handed", "3d-left-handed", "3d-right-handed-time", "3d-left-handed-time"
private float	versionNumber	Version of the NRRD file format being used.

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

ANGSTROMS, ANGSTROMS_STRING, AXIAL, axisOrientation, axisOrientationStr, BIOMAGNETIC_IMAGING, cameraMake, cameraModel, CENTIMETERS, CENTIMETERS_STRING, COLOR_FLOW_DOPPLER, COMPRESSION_BZIP2, COMPRESSION_GZIP, COMPRESSION_NONE, COMPRESSION_ZIP, COMPUTED_RADIOGRAPHY, COMPUTED_TOMOGRAPHY, conversionSpaceTimeUnits, CORONAL, DEGREES, DEGREES_STRING, DIAPHANOGRAPHY, DIGITAL_RADIOGRAPHY, dtiParams, DUPLEX_DOPPLER, ENDOSCOPY, exposureTime, EXTERNAL_CAMERA_PHOTOGRAPHY, FA, fileName, fileSuffix, FNumber, focalLength, focalLength35, GENERAL_MICROSCOPY, HARDCOPY, HOURS, HOURS_STRING, HZ, HZ_STRING, ICG, imageOrientation, INCHES, INCHES_STRING, INTRAORAL_RADIOGRAPHY, ISOSpeedRating, KILOMETERS, KILOMETERS_STRING, LASER_SURFACE_SCAN, MAGNETIC_RESONANCE, MAGNETIC_RESONANCE_ANGIOGRAPHY, MAGNETIC_RESONANCE_SPECTROSCOPY, MAMMOGRAPHY, METERS, METERS_STRING, MICROMETERS, MICROMETERS_STRING, MICROSEC, MICROSEC_STRING, MILES, MILES_STRING, MILLIMETERS, MILLIMETERS_STRING, MILLISEC, MILLISEC_STRING, MILS, MILS_STRING, MINUTES, MINUTES_STRING, modality, NANOMETERS, NANOMETERS_STRING, NANOSEC, NANOSEC_STRING, NUCLEAR_MEDICINE, ORI_A2P_TYPE, ORI_I2S_TYPE, ORI_L2R_TYPE, ORI_P2A_TYPE, ORI_R2L_TYPE, ORI_S2I_TYPE, ORI_UNKNOWN_TYPE, origin, OTHER, PANORAMIC_XRAY, POSITRON_EMISSION_TOMOGRAPHY, PPM, PPM_STRING, RADIO_FLUOROSCOPY, RADIOGRAPHIC_IMAGING, RADIOTHERAPY_DOSE, RADIOTHERAPY_IMAGE, RADIOTHERAPY_PLAN, RADIOTHERAPY_RECORD, RADIOTHERAPY_STRUCTURE_SET, RADS, RADS_STRING, RED_FREE, SAGITTAL, SECONDS, SECONDS_STRING, SINGLE_PHOTON_EMISSION_COMPUTED_TOMOGRAPHY, SLIDE_MICROSCOPY, sUnits, tagDescription, tagName, THERMOGRAPHY, TRANSFORM_ANOTHER_DATASET, TRANSFORM_MNI_152, TRANSFORM_SCANNER_ANATOMICAL, TRANSFORM_TALAIRACH_TOURNOUX, TRANSFORM_UNKNOWN, tUnits, ULTRASOUND, unitsOfMeasure, UNKNOWN_MEASURE, UNKNOWN_MODALITY, UNKNOWN_ORIENT, UNKNOWN_STRING, XRAY_ANGIOGRAPHY

Constructor Summary

Constructors

Constructor	Description
FileInfoNRRD(String name, String directory, int format)	file info storage constructor.

Method Summary

Modifier and Type	Method	Description
void	displayAboutInfo(JDialogBase dlog, TransMatrix matrix)	Displays the file information.
void	setContent(String contentString)	Accessor setting contentString giving textual description of information in the array
void	setDWMRI_B_VALUE(String DWMRI_B_VALUE)	Accessor setting DWMRI_B_VALUE
void	setDwmriGradient(String[][] dwmriGradient)	Accessor setting dwmriGradient
void	setEncoding(String encodingString)	Accessor setting encoding string telling data compression method
void	setLabels(String[] labelString)	Accessor setting labelString for axis names
void	setModality(String modalityString)	Accessor setting modalityString
void	setSliceThickness(float sliceThickness)	Accessor setting sliceThickness
void	setSpace(String spaceString)	Accessor setting spaceString
void	setVersionNumber(float versionNumber)	Accessor setting versionNumber, version of NRRD file format being used.

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

copyCoreInfo, copyCoreInfo, displayAboutInfo, displayPrimaryInfo, finalize, getAboutInfo, getAllSameDimUnits, getAreaUnitsOfMeasureStr, getAxisDirection, getAxisOrientation, getAxisOrientation, getAxisOrientationFromStr, getAxisOrientationStr, getCameraMake, getCameraModel, getCompressionType, getDataType, getDataTypeFromStr, getDTIParameters, getEndianess, getEndianessFromStr, getExposureTime, getExtents, getFileDirectory, getFileFormat, getFileName, getFileSuffix, getFNumber, getFocalLength, getFocalLength35, getImageOrientation, getImageOrientationFromStr, getImageOrientationStr, getIs2_5D, getISOSpeedRating, getLPSOrigin, getLUT, getMax, getMaxB, getMaxG, getMaxR, getMin, getMinB, getMinG, getMinR, getModality, getModalityFromStr, getModalityStr, getModalityStr, getMultiFile, getNumOfBytesPerPixel, getOffset, getOrigin, getOrigin, getOriginalEndianess, getOriginAtSlice, getPhotometric, getPixelPadValue, getPrimaryInfo, getRescaleIntercept, getRescaleSlope, getResolution, getResolutions, getSize, getSliceThickness, getUnitsOfMeasure, getUnitsOfMeasure, getUnitsOfMeasureAbbrevStr, getUnitsOfMeasureAbbrevStr, getUnitsOfMeasureFromStr, getUnitsOfMeasureStr, getUnitsOfMeasureStr, getVolumeUnitsOfMeasureStr, isDicomOrdered, oppositeOrient, sameAxis, setAxisOrientation, setAxisOrientation, setCameraMake, setCameraModel, setCompressionType, setDataType, setDTIParameters, setEndianess, setExposureTime, setExtents, setExtents, setFileDirectory, setFileFormat, setFileName, setFileSuffix, setFNumber, setFocalLength, setFocalLength35, setImageOrientation, setISOSpeedRating, setLUT, setMax, setMaxB, setMaxG, setMaxR, setMin, setMinB, setMinG, setMinR, setModality, setMultiFile, setOffset, setOrigin, setOrigin, setOriginalEndianess, setPhotometric, setPixelPadValue, setRescaleIntercept, setRescaleSlope, setResolutions, setResolutions, setTagDescription, setTagName, setUnitsOfMeasure, setUnitsOfMeasure, setUnitsOfMeasure, setUnitsOfMeasure, toString

Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneable

clone, nativeClone

Methods inherited from class java.lang.Object

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

Field Details

versionNumber

private float versionNumber

Version of the NRRD file format being used.

encodingString

private String encodingString

Data compression - raw, gzip

contentString

private String contentString

Concise textual description of the information in the array

labelString

private String[] labelString

Axis names such as X, Y, or Z

sliceThickness

private float sliceThickness

modalityString

private String modalityString

Diffusion weighted MRI is currently the only value that has been seen for modality in our samples.

DWMRI_B_VALUE

private String DWMRI_B_VALUE

"DWMRI_b-value:=b " : This key/value pair gives the (scalar) diffusion-weighting value, in units of s/mm^2. Example: "DWMRI_b-value:=1000". The effective magnitude of diffusion-weighting for each DWI is determined with some simple calculations based on the individual per-DWI gradient directions or B-matrices.

dwmriGradient

private String[][] dwmriGradient

For every index position NNNN along the DWI axis (whichever is the non-spatial axis identified by the "list" or "vector" kind field), either "DWMRI_gradient_NNNN:=x y z " or "DWMRI_B-matrix_NNNN:=xx xy xz yy yz zz " must be given (except if "DWMRI_NEX_NNNN:= M " is used).

spaceString

private String spaceString

Possible values are "right-anterior-superior", "left-anterior-superior", "left-posterior-superior", "right-anterior-superior-time", "left-anterior-superior-time", "left-posterior-superior-time", "scanner-xyz", "scanner-xyz-time", "3d-right-handed", "3d-left-handed", "3d-right-handed-time", "3d-left-handed-time"

Constructor Details

FileInfoNRRD

public FileInfoNRRD(String name,
 String directory,
 int format)

file info storage constructor.

Parameters:

name - file name

directory - directory

format - file format

Method Details

displayAboutInfo

public void displayAboutInfo(JDialogBase dlog,
 TransMatrix matrix)

Displays the file information.

Specified by:

displayAboutInfo in class FileInfoBase

Parameters:

dlog - dialog box that is written to

matrix - transformation matrix

setVersionNumber

public void setVersionNumber(float versionNumber)

Accessor setting versionNumber, version of NRRD file format being used.

Parameters:

versionNumber -

setEncoding

public void setEncoding(String encodingString)

Accessor setting encoding string telling data compression method

Parameters:

encodingString -

setContent

public void setContent(String contentString)

Accessor setting contentString giving textual description of information in the array

Parameters:

contentString -

setLabels

public void setLabels(String[] labelString)

Accessor setting labelString for axis names

Parameters:

labelString -

setSliceThickness

public void setSliceThickness(float sliceThickness)

Accessor setting sliceThickness

Overrides:

setSliceThickness in class FileInfoBase

Parameters:

sliceThickness -

setModality

public void setModality(String modalityString)

Accessor setting modalityString

Parameters:

modalityString -

setDWMRI_B_VALUE

public void setDWMRI_B_VALUE(String DWMRI_B_VALUE)

Accessor setting DWMRI_B_VALUE

Parameters:

DWMRI_B_VALUE -

setDwmriGradient

public void setDwmriGradient(String[][] dwmriGradient)

Accessor setting dwmriGradient

Parameters:

dwmriGradient -

setSpace

public void setSpace(String spaceString)

Accessor setting spaceString

Parameters:

spaceString -