Package gov.nih.mipav.model.file

Class FileGESigna4X

  • public class FileGESigna4X
extends FileBase
    Fixed format header Image data is not compressed Image data fixed offset 14336 bytes Data General host The image files are of fixed layout, described here as a series of 256 by 16 bit word blocks (512 bytes), blocks numbered from 0. The headers start at the following block offsets: block 0 - length 4 blocks - System configuration block 4 - length 2 blocks - Site customization block 6 - length 2 blocks - Study header block 8 - length 2 blocks - Series header block 10 - length 2 blocks - Image header block 12 - length 4 blocks - Raw database header block 16 - length 10 blocks - Pulse sequence description block 26 - length 2 blocks - Pixel map (? not ever used) block 28 - length 256 blocks - Image data The header is a fixed length of 14336 bytes, after which the uncompressed image data starts. 16 bit big endian shorts are used. Ascii strings are FORTRAN style specifications with length in bytes. 4 byte floats are used. Spacing between slices was seen to vary so resolution[2] cannot be obtained by checking the difference between slice spacing. The field called pixel size actually gives 5 * resolution[2]. resolution[0] and resolution[1] can in theory be calculated in 3 different ways with 3 slightly different results. (fov/256)*kludge factor 2, (difference between corners/255) * kludge factor 2, or using the thickness field equals about 10 * resolution[0] = 10 * resolution[1]. Use fov/256 multiplied by a kludge factor of 2 to obtain the right answer. On one run SWAP_PF said Operator selects to swap phase and frequency and PF_SWAPPED said Phase and frequency not swapped, a seeming contradiction. The field strength in the series header was read as -99 gauss. The 6 values for SAT pulse location relative to landmark were all 9999 millimeters. So there are problems.

    • Field Detail

      • systemID

        private java.lang.String systemID

      • systemConfigHospitalName

        private java.lang.String systemConfigHospitalName

      • studyHeaderID

        private java.lang.String studyHeaderID

      • studyHeaderRevisionNumber

        private java.lang.String studyHeaderRevisionNumber

      • studyHeaderBlocks

        private short studyHeaderBlocks

      • MRIProcessName

        private java.lang.String MRIProcessName

      • studyTaskID

        private short studyTaskID

      • rawDataStudyNumber

        private java.lang.String rawDataStudyNumber

      • studyNumber

        private java.lang.String studyNumber

      • rawDataSystemID

        private java.lang.String rawDataSystemID

      • systemGenerationID

        private java.lang.String systemGenerationID

      • studyDate

        private java.lang.String studyDate

      • studyTime

        private java.lang.String studyTime

      • patientName

        private java.lang.String patientName

      • patientID

        private java.lang.String patientID

      • patientAge

        private java.lang.String patientAge

      • patientSex

        private java.lang.String patientSex

      • patientWeight

        private int patientWeight

      • referringPhysician

        private java.lang.String referringPhysician

      • diognostician

        private java.lang.String diognostician

      • operator

        private java.lang.String operator

      • studyDescription

        private java.lang.String studyDescription

      • history

        private java.lang.String history

      • hospitalName

        private java.lang.String hospitalName

      • patientStatus

        private short patientStatus

      • requestedNumber

        private java.lang.String requestedNumber

      • seriesHeaderID

        private java.lang.String seriesHeaderID

      • seriesHeaderRevisionNumber

        private java.lang.String seriesHeaderRevisionNumber

      • seriesRevisionSubnumber

        private int seriesRevisionSubnumber

      • seriesHeaderBlocks

        private short seriesHeaderBlocks

      • seriesProcessName

        private java.lang.String seriesProcessName

      • seriesTaskID

        private short seriesTaskID

      • originalSeriesNumber

        private java.lang.String originalSeriesNumber

      • seriesNumber

        private java.lang.String seriesNumber

      • seriesRawDataSystemID

        private java.lang.String seriesRawDataSystemID

      • seriesSystemGenerationID

        private java.lang.String seriesSystemGenerationID

      • seriesDate

        private java.lang.String seriesDate

      • seriesTime

        private java.lang.String seriesTime

      • seriesDescription

        private java.lang.String seriesDescription

      • seriesType

        private short seriesType

      • coilType

        private short coilType

      • coilName

        private java.lang.String coilName

      • contrastDescription

        private java.lang.String contrastDescription

      • planeType

        private short planeType

      • planeName

        private java.lang.String planeName

      • imageMode

        private short imageMode

      • fieldStrength

        private short fieldStrength

      • pulseSequence

        private short pulseSequence

      • pulseSequenceSubtype

        private short pulseSequenceSubtype

      • fieldOfView

        private float fieldOfView

      • rlCenter

        private float rlCenter

      • apCenter

        private float apCenter

      • siCenter

        private float siCenter

      • orientation

        private short orientation

      • position

        private short position

      • longitudinalAnatomicalReference

        private java.lang.String longitudinalAnatomicalReference

      • verticalAnatomicalReference

        private java.lang.String verticalAnatomicalReference

      • verticalLandmark

        private float verticalLandmark

      • horizontalLandmark

        private float horizontalLandmark

      • tableLocation

        private float tableLocation

      • scanMatrixX

        private short scanMatrixX

      • scanMatrixY

        private short scanMatrixY

      • imageMatrix

        private short imageMatrix

      • imagesAllocated

        private short imagesAllocated

      • gatingType

        private short gatingType

      • pulseSequenceMode

        private short pulseSequenceMode

      • gatingTypeString

        private java.lang.String gatingTypeString

      • seriesPSDName

        private java.lang.String seriesPSDName

      • landmarkCounter

        private int landmarkCounter

      • scanProtocolName

        private java.lang.String scanProtocolName

      • surfaceCoilType

        private short surfaceCoilType

      • suppressionTechnique

        private short suppressionTechnique

      • satSelections

        private short satSelections

      • satSelectionsString

        private java.lang.String satSelectionsString

      • surfaceCoilIntensityCorrection

        private short surfaceCoilIntensityCorrection

      • satXLoc1

        private short satXLoc1

      • satXLoc2

        private short satXLoc2

      • satYLoc1

        private short satYLoc1

      • satYLoc2

        private short satYLoc2

      • satZLoc1

        private short satZLoc1

      • satZLoc2

        private short satZLoc2

      • satXThick

        private short satXThick

      • satYThick

        private short satYThick

      • satZThick

        private short satZThick

      • vasMode

        private short vasMode

      • phaseContrastFlowAxis

        private short phaseContrastFlowAxis

      • gatingType2

        private short gatingType2

      • imageHeaderID

        private java.lang.String imageHeaderID

      • imageHeaderRevisionNumber

        private java.lang.String imageHeaderRevisionNumber

      • imageRevisionSubnumber

        private int imageRevisionSubnumber

      • imageHeaderBlocks

        private short imageHeaderBlocks

      • imageHeaderCreatorProcess

        private java.lang.String imageHeaderCreatorProcess

      • imageHeaderCreatorTask

        private short imageHeaderCreatorTask

      • imageCreationDate

        private java.lang.String imageCreationDate

      • imageCreationTime

        private java.lang.String imageCreationTime

      • imageNumber

        private java.lang.String imageNumber

      • series

        private java.lang.String series

      • imageRawDataSystemID

        private java.lang.String imageRawDataSystemID

      • imageSystemGenerationID

        private java.lang.String imageSystemGenerationID

      • startX

        private float startX

      • endX

        private float endX

      • startY

        private float startY

      • endY

        private float endY

      • startZ

        private float startZ

      • endZ

        private float endZ

      • imageLocation

        private float imageLocation

      • tablePosition

        private float tablePosition

      • thickness

        private float thickness

      • imageSpacing

        private float imageSpacing

      • round

        private short round

      • tr

        private float tr

      • ts

        private float ts

      • te

        private float te

      • ti

        private float ti

      • numberOfEchos

        private short numberOfEchos

      • echoNumber

        private short echoNumber

      • sliceQuantity

        private short sliceQuantity

      • averagesNumber

        private short averagesNumber

      • researchMode

        private short researchMode

      • psdFileName

        private java.lang.String psdFileName

      • psdDay

        private short psdDay

      • psdMonth

        private short psdMonth

      • psdYear

        private short psdYear

      • psdHour

        private short psdHour

      • psdMinute

        private short psdMinute

      • psdSeconds

        private short psdSeconds

      • graphicallyPrescribed

        private short graphicallyPrescribed

      • prescribedSeriesNumbers

        private java.lang.String prescribedSeriesNumbers

      • prescribedImageNumbers

        private java.lang.String prescribedImageNumbers

      • imageShape

        private short imageShape

      • pixelSize

        private float pixelSize

      • defaultWindow

        private short defaultWindow

      • defaultLevel

        private short defaultLevel

      • fileBlocks

        private short fileBlocks

      • excitationsNumber

        private float excitationsNumber

      • peakSAR

        private float peakSAR

      • averageSAR

        private float averageSAR

      • SARMonitored

        private short SARMonitored

      • contiguousSlices

        private short contiguousSlices

      • cardiacHeartRate

        private short cardiacHeartRate

      • totalPostTriggerDelayTime

        private float totalPostTriggerDelayTime

      • arrythmiaRejectionRatio

        private short arrythmiaRejectionRatio

      • cardiacRepTime

        private short cardiacRepTime

      • imagesPerCardiacCycle

        private short imagesPerCardiacCycle

      • scanARRs

        private int scanARRs

      • transmitAttenuatorSetting

        private short transmitAttenuatorSetting

      • receiveAttenuatorSetting

        private short receiveAttenuatorSetting

      • imageFieldStrength

        private int imageFieldStrength

      • imageOffset

        private short imageOffset

      • interImageDelay

        private float interImageDelay

      • psdName

        private java.lang.String psdName

      • flipAngle

        private short flipAngle

      • surfaceCoilsCorrectionType

        private java.lang.String surfaceCoilsCorrectionType

      • scSer

        private java.lang.String scSer

      • scIma

        private java.lang.String scIma

      • extremityCoil

        private short extremityCoil

      • pSeries2

        private java.lang.String pSeries2

      • pImage2

        private java.lang.String pImage2

      • rCenter

        private float rCenter

      • aCenter

        private float aCenter

      • sCenter

        private float sCenter

      • rNormal

        private float rNormal

      • aNormal

        private float aNormal

      • sNormal

        private float sNormal

      • imgTLHC_R

        private float imgTLHC_R

      • imgTLHC_A

        private float imgTLHC_A

      • imgTLHC_S

        private float imgTLHC_S

      • imgTRHC_R

        private float imgTRHC_R

      • imgTRHC_A

        private float imgTRHC_A

      • imgTRHC_S

        private float imgTRHC_S

      • imgBLHC_R

        private float imgBLHC_R

      • imgBLHC_A

        private float imgBLHC_A

      • imgBLHC_S

        private float imgBLHC_S

      • imageHeaderDisclaimer

        private short imageHeaderDisclaimer

      • minimumDelay

        private short minimumDelay

      • cPhase

        private short cPhase

      • TE2

        private float TE2

      • swapPF

        private short swapPF

      • pauseInterval

        private short pauseInterval

      • pauseTime

        private float pauseTime

      • userBitmap

        private short userBitmap

      • user0

        private float user0

      • user1

        private float user1

      • user2

        private float user2

      • user3

        private float user3

      • user4

        private float user4

      • user5

        private float user5

      • user6

        private float user6

      • user7

        private float user7

      • user8

        private float user8

      • user9

        private float user9

      • obliquePlane

        private short obliquePlane

      • contrastUsed

        private short contrastUsed

      • contrastAgent

        private java.lang.String contrastAgent

      • contrastAmount

        private float contrastAmount

      • fileFormat

        private short fileFormat

      • autoCenterFrequency

        private short autoCenterFrequency

      • actualTransmitFrequency

        private int actualTransmitFrequency

      • actualReceiveFrequency

        private int actualReceiveFrequency

      • recommendedTransmitFrequency

        private int recommendedTransmitFrequency

      • recommendedReceiveFrequency

        private int recommendedReceiveFrequency

      • recommendedTransmitAttenuation

        private int recommendedTransmitAttenuation

      • recommendedReceiveAttenuation

        private int recommendedReceiveAttenuation

      • histogramPresent

        private short histogramPresent

      • pfSwapped

        private short pfSwapped

      • R1

        private short R1

      • R2

        private short R2

      • variableBandwidth

        private short variableBandwidth

      • prescanReceiveAttenuation1

        private short prescanReceiveAttenuation1

      • prescanReceiveAttenuation2

        private short prescanReceiveAttenuation2

      • autoManualPrescan

        private short autoManualPrescan

      • changedValuesBitmap

        private short changedValuesBitmap

      • changedValuesString

        private java.lang.String changedValuesString

      • imageType

        private short imageType

      • collapseImage

        private short collapseImage

      • sliceThicknessDisclaimer

        private short sliceThicknessDisclaimer

      • PCVelocityEncoding

        private short PCVelocityEncoding

      • projectionAngle

        private float projectionAngle

      • concatenatedSATSelection

        private short concatenatedSATSelection

      • fractionalEffectiveEcho

        private short fractionalEffectiveEcho

      • echoTrainLength

        private int echoTrainLength

      • sliceMultiplier

        private short sliceMultiplier

      • cardiacPhaseNumber

        private short cardiacPhaseNumber

      • scanAcquisitionNumber

        private short scanAcquisitionNumber

      • vascularImagingFlags

        private short vascularImagingFlags

      • vencScalingFactor

        private float vencScalingFactor

      • byteBuffer

        private byte[] byteBuffer
        DOCUMENT ME!

      • fileDir

        private java.lang.String fileDir
        DOCUMENT ME!

      • fileHeader

        private java.io.File fileHeader
        DOCUMENT ME!

      • fileName

        private java.lang.String fileName
        DOCUMENT ME!

      • orient

        private int[] orient

      • start

        private float[] start

      • endianess

        private boolean endianess

      • width

        private short width

      • height

        private short height

      • compression

        private short compression

      • bitsPerPixel

        private short bitsPerPixel

      • resX

        private float resX

      • resY

        private float resY

    • Constructor Detail

      • FileGESigna4X

        public FileGESigna4X​(java.lang.String fileName,
                     java.lang.String fileDir)
              throws java.io.IOException
        reader/writer constructor.
        Parameters:
        fileName - file name
        fileDir - file directory
        Throws:
        java.io.IOException - if there is an error making the file

    • Method Detail

      • finalize

        public void finalize()
        Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
        Overrides:
        finalize in class FileBase

      • getFileInfo

        public FileInfoGESigna4X getFileInfo()
        DOCUMENT ME!
        Returns:
        FileInfoGESigna4X fileInfo

      • getImageNumber

        public int getImageNumber()
        DOCUMENT ME!
        Returns:
        int image number

      • getPatientName

        public java.lang.String getPatientName()
        Returns:

      • getWidth

        public int getWidth()
        DOCUMENT ME!
        Returns:
        int width

      • getHeight

        public int getHeight()
        DOCUMENT ME!
        Returns:
        int height

      • getImageLocation

        public float getImageLocation()
        Returns:

      • getImgTLHC_R

        public float getImgTLHC_R()
        Returns:

      • getImgTLHC_A

        public float getImgTLHC_A()
        Returns:

      • getImgTLHC_S

        public float getImgTLHC_S()
        Returns:

      • getImgTRHC_R

        public float getImgTRHC_R()
        Returns:

      • getImgTRHC_A

        public float getImgTRHC_A()
        Returns:

      • getImgTRHC_S

        public float getImgTRHC_S()
        Returns:

      • getImgBLHC_R

        public float getImgBLHC_R()
        Returns:

      • getImgBLHC_A

        public float getImgBLHC_A()
        Returns:

      • getImgBLHC_S

        public float getImgBLHC_S()
        Returns:

      • isGESigna4X

        public boolean isGESigna4X()
                    throws java.io.IOException
        Looks for the image header ID "IMAGE HEADER" and number of image header blocks (usually 2 in units of 512 bytes )in GE Signa 4.X file in the File header. If present, the image is GE SIGNA 4.X format.
        Returns:
        boolean true if the image header ID and 2 image header blocks was found in the image header.
        Throws:
        java.io.IOException - Indicates error reading the file

      • readImage

        public void readImage​(float[] buffer)
               throws java.io.IOException
        reads the Signa 4X file header and data.
        Parameters:
        buffer - DOCUMENT ME!
        Throws:
        java.io.IOException - if there is an error reading the file

      • setFileName

        public void setFileName​(java.lang.String fName)
                 throws java.io.IOException
        Accessor that sets the file name and allocates new FileInfo, File and RandomAccess file objects.
        Parameters:
        fName - File name.
        Throws:
        java.io.IOException - if there is an error constructing the files.

      • readBuffer

        private void readBuffer​(float[] buffer)
                 throws java.io.IOException
        Reads a slice of data at a time and stores the results in the buffer.
        Parameters:
        buffer - buffer where the info is stored
        Throws:
        java.io.IOException - DOCUMENT ME!

      • readImageFileData

        public int readImageFileData()
        DOCUMENT ME!
        Returns:
        int size of image file data

      • writeImage

        public void writeImage​(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
        Throws:
        java.io.IOException