Package gov.nih.mipav.model.file

Class FileInfoBRUKER

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable
    public class FileInfoBRUKER
extends FileInfoBase
    File information related to the Bruker/Biospin scanner format.
    See Also:
    Serialized Form

    • Field Detail

      • 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 java.lang.String sliceSeparationMode
        The slice inversion time of the scan

      • inversionTime

        private double inversionTime
        The inversion time of an MR scan.

      • method

        private java.lang.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 java.lang.String scanTime

      • deriveGains

        private java.lang.String deriveGains

      • diffusionPreparation

        private java.lang.String diffusionPreparation

      • usedSliceThickness

        private double usedSliceThickness

      • showAllParameters

        private java.lang.String showAllParameters

      • refocusingPulseType

        private java.lang.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 java.lang.String directScaledSwitching

      • diffusionMeasurementMode

        private java.lang.String diffusionMeasurementMode

      • numberOfDiffusionDirections

        private int numberOfDiffusionDirections

      • diffusionExperimentsPerDirection

        private int diffusionExperimentsPerDirection

      • numberOfA0Images

        private int numberOfA0Images

      • patientPosition

        private java.lang.String patientPosition

      • acqGradMat

        private double[][][] acqGradMat

      • numberOfObjects

        private int numberOfObjects

      • diffusionGradientSwitchingScheme

        private java.lang.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 java.lang.String useMultipleReceivers

      • activeReceivers

        private java.lang.String[] activeReceivers

      • zeroFillFactorRead

        private double zeroFillFactorRead

      • PPIAcceleration

        private int PPIAcceleration

    • Constructor Detail

      • FileInfoBRUKER

        public FileInfoBRUKER​(java.lang.String name,
                      java.lang.String directory,
                      int format)
        File info storage constructor.
        Parameters:
        name - file name
        directory - directory
        format - file format

    • Method Detail

      • 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​(java.lang.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​(java.lang.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​(java.lang.String scanTime)
        Parameters:
        scanTime -

      • setDeriveGains

        public void setDeriveGains​(java.lang.String deriveGains)
        Parameters:
        deriveGains -

      • setDiffusionPreparation

        public void setDiffusionPreparation​(java.lang.String diffusionPreparation)
        Parameters:
        diffusionPreparation -

      • setUsedSliceThickness

        public void setUsedSliceThickness​(double usedSliceThickness)
        Parameters:
        usedSliceThickness -

      • setShowAllParameters

        public void setShowAllParameters​(java.lang.String showAllParameters)
        Parameters:
        showAllParameters -

      • setRefocusingPulseType

        public void setRefocusingPulseType​(java.lang.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​(java.lang.String directScaledSwitching)
        Parameters:
        directScaledSwitching -

      • setDiffusionMeasurementMode

        public void setDiffusionMeasurementMode​(java.lang.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​(java.lang.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​(java.lang.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​(java.lang.String useMultipleReceivers)
        Parameters:
        useMultipleReceivers -

      • setActiveReceivers

        public void setActiveReceivers​(java.lang.String[] activeReceivers)
        Parameters:
        activeReceivers -

      • setZeroFillFactorRead

        public void setZeroFillFactorRead​(double zeroFillFactorRead)
        Parameters:
        zeroFillFactorRead -

      • setPPIAcceleration

        public void setPPIAcceleration​(int PPIAcceleration)
        \
        Parameters:
        PPIAcceleration -