Package gov.nih.mipav.model.file

Class FileInfoBRUKER

java.lang.Object

gov.nih.mipav.model.structures.ModelSerialCloneable

gov.nih.mipav.model.file.FileInfoBase

gov.nih.mipav.model.file.FileInfoBRUKER

All Implemented Interfaces:

Serializable, Cloneable

public class FileInfoBRUKER
extends FileInfoBase

File information related to the Bruker/Biospin scanner format.

See Also:

• 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 double[][][]	acqGradMat
private String[]	activeReceivers
private int[]	BValuesPerDirection
private double	delayBetweenVolumes
private String	deriveGains
private int	diffusionExperimentsPerDirection
private double[]	diffusionGradientAmplitude
private double[]	diffusionGradientDuration
private double[]	diffusionGradientSeparation
private String	diffusionGradientSwitchingScheme
private String	diffusionMeasurementMode
private double	diffusionModuleDuration
private double	diffusionModuleEchoDelay
private String	diffusionPreparation
private String	directScaledSwitching
private double	echoTime
private double	effectiveSpectralBandwidth
private boolean	haveZResol	Whether the z resolution is set in the acqp or reco files
private double	inversionTime	The inversion time of an MR scan.
private double	maximumPossibleBValue
private String	method
private int	numberOfA0Images
private int	numberOfAverages
private int	numberOfDiffusionDirections
private int	numberOfObjects
private int	numberOfRepetitions
private int	numberOfSegments
private String	patientPosition
private int	PPIAcceleration
private int	recoInpSize
private int	recoSize	The size of the reconstruction
private String	refocusingPulseType
private double	repetitionTime
private String	scanTime
private static final long	serialVersionUID	Use serialVersionUID for interoperability.
private String	showAllParameters
private double	sliceGradient
private double	sliceGradientDuration
private double	sliceGradientLimit
private String	sliceSeparationMode	The slice inversion time of the scan
private double	TESliceSpoilerGradientsAmplitude
private double	TEsliceSpoilerGradientsDuration
private double	TESliceSpoilerGradientsLimit
private int	totalNumberOfDiffusionExperiments
private double	usedSliceThickness
private String	useMultipleReceivers
private double	zeroFillFactorRead

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
FileInfoBRUKER(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.
double[][][]	getAcqGradMat()
boolean	getHaveZResol()	Accessor to get the flag for having a z resolution.
double	getInversionTime()	Gets the inversion time of the scan.
int	getRecoInpSize()
int	getRecoSize()	Gets the size of the reconstruction.
void	setAcqGradMat(double[][][] acqGradMat)
void	setActiveReceivers(String[] activeReceivers)
void	setBValuesPerDirection(int[] BValuesPerDirection)
void	setDelayBetweenVolumes(double delayBetweenVolumes)
void	setDeriveGains(String deriveGains)
void	setDiffusionExperimentsPerDirection(int diffusionExperimentsPerDirection)
void	setDiffusionGradientAmplitude(double[] diffusionGradientAmplitude)
void	setDiffusionGradientDuration(double[] diffusionGradientDuration)
void	setDiffusionGradientSeparation(double[] diffusionGradientSeparation)
void	setDiffusionGradientSwitchingScheme(String diffusionGradientSwitchingScheme)
void	setDiffusionMeasurementMode(String diffusionMeasurementMode)
void	setDiffusionModuleDuration(double diffusionModuleDuration)
void	setDiffusionModuleEchoDelay(double diffusionModuleEchoDelay)
void	setDiffusionPreparation(String diffusionPreparation)
void	setDirectScaledSwitching(String directScaledSwitching)
void	setEchoTime(double echoTime)
void	setEffectiveSpectralBandwidth(double effectiveSpectralBandwidth)
void	setHaveZResol(boolean haveZResol)	Accessor to set the flag for having a z resolution.
void	setInversionTime(double inversionTime)	Accessor to set the inversion time of the scan
void	setMaximumPossibleBValue(double maximumPossibleBValue)
void	setMethod(String method)
void	setNumberOfA0Images(int numberOfA0Images)
void	setNumberOfAverages(int numberOfAverages)
void	setNumberOfDiffusionDirections(int numberOfDiffusionDirections)
void	setNumberOfObjects(int numberOfObjects)
void	setNumberOfRepetitions(int numberOfRepetitions)
void	setNumberOfSegments(int numberOfSegments)
void	setPatientPosition(String patientPosition)
void	setPPIAcceleration(int PPIAcceleration)	\
void	setRecoInpSize(int recoInpSize)
void	setRecoSize(int recoSize)	Accessor to set the reco size.
void	setRefocusingPulseType(String refocusingPulseType)
void	setRepetitionTime(double repetitionTime)
void	setScanTime(String scanTime)
void	setShowAllParameters(String showAllParameters)
void	setSliceGradient(double sliceGradient)
void	setSliceGradientDuration(double sliceGradientDuration)
void	setSliceGradientLimit(double sliceGradientLimit)
void	setSliceSeparationMode(String sliceSeparationMode)	Accessor to set the slice separation mode.
void	setTESliceSpoilerGradientsAmplitude(double TEsliceSpoilerGradientsAmplitude)
void	setTESliceSpoilerGradientsDuration(double TEsliceSpoilerGradientsDuration)
void	setTESliceSpoilerGradientsLimit(double TEsliceSpoilerGradientsLimit)
void	setTotalNumberOfDiffusionExperiments(int totalNumberOfDiffusionExperiments)
void	setUsedSliceThickness(double usedSliceThickness)
void	setUseMultipleReceivers(String useMultipleReceivers)
void	setZeroFillFactorRead(double zeroFillFactorRead)

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, setSliceThickness, 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

serialVersionUID

private static final long serialVersionUID

Use serialVersionUID for interoperability.

See Also:

• Constant Field Values

haveZResol

private boolean haveZResol

Whether the z resolution is set in the acqp or reco files

recoSize

private int recoSize

The size of the reconstruction

recoInpSize

private int recoInpSize

sliceSeparationMode

private String sliceSeparationMode

The slice inversion time of the scan

inversionTime

private double inversionTime

The inversion time of an MR scan.

method

private String method

effectiveSpectralBandwidth

private double effectiveSpectralBandwidth

echoTime

private double echoTime

numberOfSegments

private int numberOfSegments

repetitionTime

private double repetitionTime

delayBetweenVolumes

private double delayBetweenVolumes

numberOfAverages

private int numberOfAverages

numberOfRepetitions

private int numberOfRepetitions

scanTime

private String scanTime

deriveGains

private String deriveGains

diffusionPreparation

private String diffusionPreparation

usedSliceThickness

private double usedSliceThickness

showAllParameters

private String showAllParameters

refocusingPulseType

private String refocusingPulseType

sliceGradientDuration

private double sliceGradientDuration

sliceGradient

private double sliceGradient

sliceGradientLimit

private double sliceGradientLimit

TEsliceSpoilerGradientsDuration

private double TEsliceSpoilerGradientsDuration

TESliceSpoilerGradientsAmplitude

private double TESliceSpoilerGradientsAmplitude

TESliceSpoilerGradientsLimit

private double TESliceSpoilerGradientsLimit

diffusionGradientDuration

private double[] diffusionGradientDuration

diffusionGradientSeparation

private double[] diffusionGradientSeparation

directScaledSwitching

private String directScaledSwitching

diffusionMeasurementMode

private String diffusionMeasurementMode

numberOfDiffusionDirections

private int numberOfDiffusionDirections

diffusionExperimentsPerDirection

private int diffusionExperimentsPerDirection

numberOfA0Images

private int numberOfA0Images

patientPosition

private String patientPosition

acqGradMat

private double[][][] acqGradMat

numberOfObjects

private int numberOfObjects

diffusionGradientSwitchingScheme

private String diffusionGradientSwitchingScheme

maximumPossibleBValue

private double maximumPossibleBValue

BValuesPerDirection

private int[] BValuesPerDirection

diffusionGradientAmplitude

private double[] diffusionGradientAmplitude

totalNumberOfDiffusionExperiments

private int totalNumberOfDiffusionExperiments

diffusionModuleDuration

private double diffusionModuleDuration

diffusionModuleEchoDelay

private double diffusionModuleEchoDelay

useMultipleReceivers

private String useMultipleReceivers

activeReceivers

private String[] activeReceivers

zeroFillFactorRead

private double zeroFillFactorRead

PPIAcceleration

private int PPIAcceleration

Constructor Details

FileInfoBRUKER

public FileInfoBRUKER(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

getHaveZResol

public boolean getHaveZResol()

Accessor to get the flag for having a z resolution.

Returns:

true if has a z resolution.

getRecoSize

public int getRecoSize()

Gets the size of the reconstruction.

Returns:

The reco size.

getRecoInpSize

public int getRecoInpSize()

getInversionTime

public double getInversionTime()

Gets the inversion time of the scan.

Returns:

The inversion time.

setHaveZResol

public void setHaveZResol(boolean haveZResol)

Accessor to set the flag for having a z resolution.

Parameters:

haveZResol - Flag to set.

setRecoSize

public void setRecoSize(int recoSize)

Accessor to set the reco size.

Parameters:

recoSize - Value to set.

setRecoInpSize

public void setRecoInpSize(int recoInpSize)

setSliceSeparationMode

public void setSliceSeparationMode(String sliceSeparationMode)

Accessor to set the slice separation mode.

Parameters:

sliceSeparationMode - Value to set.

setInversionTime

public void setInversionTime(double inversionTime)

Accessor to set the inversion time of the scan

Parameters:

inversionTime - the inversion time of the scan

setMethod

public void setMethod(String method)

setEffectiveSpectralBandwidth

public void setEffectiveSpectralBandwidth(double effectiveSpectralBandwidth)

Parameters:

effectiveSpectralBandwidth -

setEchoTime

public void setEchoTime(double echoTime)

Parameters:

echoTime -

setNumberOfSegments

public void setNumberOfSegments(int numberOfSegments)

setRepetitionTime

public void setRepetitionTime(double repetitionTime)

Parameters:

repetitionTime -

setDelayBetweenVolumes

public void setDelayBetweenVolumes(double delayBetweenVolumes)

Parameters:

delayBetweenVolumes -

setNumberOfAverages

public void setNumberOfAverages(int numberOfAverages)

Parameters:

numberOfAverages -

setNumberOfRepetitions

public void setNumberOfRepetitions(int numberOfRepetitions)

Parameters:

numberOfRepetitions -

setScanTime

public void setScanTime(String scanTime)

Parameters:

scanTime -

setDeriveGains

public void setDeriveGains(String deriveGains)

Parameters:

deriveGains -

setDiffusionPreparation

public void setDiffusionPreparation(String diffusionPreparation)

Parameters:

diffusionPreparation -

setUsedSliceThickness

public void setUsedSliceThickness(double usedSliceThickness)

Parameters:

usedSliceThickness -

setShowAllParameters

public void setShowAllParameters(String showAllParameters)

Parameters:

showAllParameters -

setRefocusingPulseType

public void setRefocusingPulseType(String refocusingPulseType)

Parameters:

refocusingPulseType -

setSliceGradientDuration

public void setSliceGradientDuration(double sliceGradientDuration)

Parameters:

sliceGradientDuration -

setSliceGradient

public void setSliceGradient(double sliceGradient)

Parameters:

sliceGradient -

setSliceGradientLimit

public void setSliceGradientLimit(double sliceGradientLimit)

Parameters:

sliceGradientLimit -

setTESliceSpoilerGradientsDuration

public void setTESliceSpoilerGradientsDuration(double TEsliceSpoilerGradientsDuration)

Parameters:

TEsliceSpoilerGradientsDuration -

setTESliceSpoilerGradientsAmplitude

public void setTESliceSpoilerGradientsAmplitude(double TEsliceSpoilerGradientsAmplitude)

Parameters:

TEsliceSpoilerGradientsAmplitude -

setTESliceSpoilerGradientsLimit

public void setTESliceSpoilerGradientsLimit(double TEsliceSpoilerGradientsLimit)

Parameters:

TEsliceSpoilerGradientsLimit -

setDiffusionGradientDuration

public void setDiffusionGradientDuration(double[] diffusionGradientDuration)

Parameters:

diffusionGradientDuration -

setDiffusionGradientSeparation

public void setDiffusionGradientSeparation(double[] diffusionGradientSeparation)

Parameters:

diffusionGradientSeparation -

setDirectScaledSwitching

public void setDirectScaledSwitching(String directScaledSwitching)

Parameters:

directScaledSwitching -

setDiffusionMeasurementMode

public void setDiffusionMeasurementMode(String diffusionMeasurementMode)

Parameters:

diffusionMeasurementMode -

setNumberOfDiffusionDirections

public void setNumberOfDiffusionDirections(int numberOfDiffusionDirections)

Parameters:

numberOfDiffusionDirections -

setDiffusionExperimentsPerDirection

public void setDiffusionExperimentsPerDirection(int diffusionExperimentsPerDirection)

Parameters:

diffusionExperimentsPerDirection -

setNumberOfA0Images

public void setNumberOfA0Images(int numberOfA0Images)

Parameters:

numberOfA0Images -

setPatientPosition

public void setPatientPosition(String patientPosition)

Parameters:

patientPosition -

setAcqGradMat

public void setAcqGradMat(double[][][] acqGradMat)

Parameters:

acqGradMat -

getAcqGradMat

public double[][][] getAcqGradMat()

Returns:

setNumberOfObjects

public void setNumberOfObjects(int numberOfObjects)

Parameters:

numberOfObjects -

setDiffusionGradientSwitchingScheme

public void setDiffusionGradientSwitchingScheme(String diffusionGradientSwitchingScheme)

Parameters:

diffusionGradientSwitchingScheme -

setMaximumPossibleBValue

public void setMaximumPossibleBValue(double maximumPossibleBValue)

Parameters:

maximumPossibleBValue -

setBValuesPerDirection

public void setBValuesPerDirection(int[] BValuesPerDirection)

Parameters:

BValuesPerDirection -

setDiffusionGradientAmplitude

public void setDiffusionGradientAmplitude(double[] diffusionGradientAmplitude)

Parameters:

diffusionGradientAmplitude -

setTotalNumberOfDiffusionExperiments

public void setTotalNumberOfDiffusionExperiments(int totalNumberOfDiffusionExperiments)

Parameters:

totalNumberOfDiffusionExperiments -

setDiffusionModuleDuration

public void setDiffusionModuleDuration(double diffusionModuleDuration)

Parameters:

diffusionModuleDuration -

setDiffusionModuleEchoDelay

public void setDiffusionModuleEchoDelay(double diffusionModuleEchoDelay)

Parameters:

diffusionModuleEchoDelay -

setUseMultipleReceivers

public void setUseMultipleReceivers(String useMultipleReceivers)

Parameters:

useMultipleReceivers -

setActiveReceivers

public void setActiveReceivers(String[] activeReceivers)

Parameters:

activeReceivers -

setZeroFillFactorRead

public void setZeroFillFactorRead(double zeroFillFactorRead)

Parameters:

zeroFillFactorRead -

setPPIAcceleration

public void setPPIAcceleration(int PPIAcceleration)

\

Parameters:

PPIAcceleration -