Package gov.nih.mipav.model.file

Class FileInfoAnalyze

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable
    public class FileInfoAnalyze
extends FileInfoBase
    This structures contains the information that describes how an analyze image is stored on disk. Analyze Version 7.5. We have extended this format to store image orientation and origin. We have used unused variables to store these data. Almost all programs ignore these variables and should not have any problems reading images saved with MIPAV, except SPM. A new format for MIPAV is now XML based.

    Unused1 - X-axis orientation @see FileInfoBase for static variables that are set. Unused2 - Y-axis orientation // All three unused variables are of short type. Unused3 - Z-axis orientation

    Funused1 - X-axis starting location (origin from upper left-hand corner) Funused2 - Y-axis starting location (origin from upper left-hand corner) Funused3 - Z-axis starting location (origin is the first image slice)

    RGB analyze images are store in chunky format rgb, rgb, rgb ......

    Note that there is a char data_type[10] field and a short datatype field.

    Version:
    1.0 July, 2002
    Author:
    Matthew J. McAuliffe, Ph.D.
    See Also:
    FileAnalyze, Serialized Form

    • Field Detail

      • serialVersionUID

        private static final long serialVersionUID
        Use serialVersionUID for interoperability.
        See Also:
        Constant Field Values

      • DT_NONE

        public static final short DT_NONE
        Analyze file format define use to indicate no image data type.
        See Also:
        Constant Field Values

      • DT_UNKNOWN

        public static final short DT_UNKNOWN
        AAnalyze file format define use to indicate undefined image data type.
        See Also:
        Constant Field Values

      • DT_BINARY

        public static final short DT_BINARY
        Analyze file format define use to indicate binary (1 bit) image data type.
        See Also:
        Constant Field Values

      • DT_UNSIGNED_CHAR

        public static final short DT_UNSIGNED_CHAR
        Analyze file format define use to indicate unsigned byte (char) (8 bit) image data type.
        See Also:
        Constant Field Values

      • DT_SIGNED_SHORT

        public static final short DT_SIGNED_SHORT
        Analyze file format define use to indicate short (16 bit) image data type.
        See Also:
        Constant Field Values

      • DT_UNSIGNED_SHORT

        public static final short DT_UNSIGNED_SHORT
        Analyze file format define use to indicate short (16 bit) image data type.
        See Also:
        Constant Field Values

      • DT_SIGNED_INT

        public static final short DT_SIGNED_INT
        Analyze file format define use to indicate integer (32 bit) image data type.
        See Also:
        Constant Field Values

      • DT_FLOAT

        public static final short DT_FLOAT
        Analyze file format define use to indicate float (32 bit) image data type.
        See Also:
        Constant Field Values

      • DT_COMPLEX

        public static final short DT_COMPLEX
        Analyze file format define use to indicate complex (64 bit) image data type.
        See Also:
        Constant Field Values

      • DT_DOUBLE

        public static final short DT_DOUBLE
        Analyze file format define use to indicate double (64 bit) image data type.
        See Also:
        Constant Field Values

      • DT_RGB

        public static final short DT_RGB
        Analyze file format define use to indicate color (RGB - 24 bits) image data type.
        See Also:
        Constant Field Values

      • DT_ALL

        public static final short DT_ALL
        Analyze file format define use to indicate _ALL_ image data type.
        See Also:
        Constant Field Values

      • UNKNOWN_ORIENT

        public static final byte UNKNOWN_ORIENT
        The data_history substructure is not required, but the orient element is used to indicate individual slice orientation and determines whetther the Analyze Movie program will attempt to flip the images before displaying a movie sequence. 0 - transverse unflipped 1 - coronal unflipped 2 - sagitttal unflipped 3 - transverse flipped 4 - coronal flipped 5 - sagitttal flipped
        See Also:
        Constant Field Values

      • TRANSVERSE_UNFLIPPED

        public static final byte TRANSVERSE_UNFLIPPED
        DOCUMENT ME!
        See Also:
        Constant Field Values

      • CORONAL_UNFLIPPED

        public static final byte CORONAL_UNFLIPPED
        DOCUMENT ME!
        See Also:
        Constant Field Values

      • SAGITTAL_UNFLIPPED

        public static final byte SAGITTAL_UNFLIPPED
        DOCUMENT ME!
        See Also:
        Constant Field Values

      • TRANSVERSE_FLIPPED

        public static final byte TRANSVERSE_FLIPPED
        DOCUMENT ME!
        See Also:
        Constant Field Values

      • SAGITTAL_FLIPPED

        public static final byte SAGITTAL_FLIPPED
        DOCUMENT ME!
        See Also:
        Constant Field Values

      • aux_file

        private java.lang.String aux_file
        DOCUMENT ME!

      • bitpix

        private short bitpix
        Bits per pixel. Valid values include: 1, 8, 16, 32, 64, 24(rgb).

      • cal_max

        private float cal_max
        Range of calibration values.

      • cal_min

        private float cal_min
        Values of 0.0 for both fields imply that no calibration min and max values are used !

      • cal_units

        private java.lang.String cal_units
        Specifies the name of the calibration unit.

      • compressed

        private float compressed
        Indicates if compression is used. Default is -1 indicating no compression

      • data_type

        private java.lang.String data_type
        Unknown use 10 chars.

      • datatype

        private short datatype
        Stores the image data type DT_NONE = 0; DT_UNKNOWN = 0; DT_BINARY = 1; DT_UNSIGNED_CHAR = 2; DT_SIGNED_SHORT = 4; DT_UNSIGNED_SHORT = 4; DT_SIGNED_INT = 8; DT_FLOAT = 16; DT_COMPLEX = 32; DT_DOUBLE = 64; DT_RGB = 128; DT_ALL = 255;

      • db_name

        private java.lang.String db_name
        Name of file with a length of 18 chars.

      • descrip

        private java.lang.String descrip
        String with a max character length of 80 used to describe image.

      • dim_un0

        private short dim_un0
        Unused.

      • exp_date

        private java.lang.String exp_date
        String with a max character length of 10 used to indicate the experiment date.

      • exp_time

        private java.lang.String exp_time
        String with a max character length of 10 used to indicate the experiment time.

      • extents

        private int extents
        Should be 16384.

      • field_skip

        private int field_skip
        Unknown length.

      • funused1

        private float funused1
        MIPAV uses this variable to define the X-axis origin.

      • funused2

        private float funused2
        MIPAV uses this variable to define the Y-axis origin.

      • funused3

        private float funused3
        MIPAV uses this variable to define the Z-axis origin.

      • generated

        private java.lang.String generated
        Unknown use. Length of 10.

      • glmax

        private int glmax
        Maximum pixel values for the entire dataset.

      • glmin

        private int glmin
        Minimum pixel values for the entire database.

      • hist_un0

        private java.lang.String hist_un0
        Unknown use. Length of 3.

      • hkey_un0

        private char hkey_un0
        Unknown use. Length of 1.

      • omax

        private int omax
        Unknown use.

      • omin

        private int omin
        Unknown use.

      • orient

        private byte orient
        DOCUMENT ME!

      • originator

        private java.lang.String originator
        Unknown use. Length of 10.

      • patient_id

        private java.lang.String patient_id
        Patient's ID. Length of 10.

      • regular

        private char regular
        I think it means data has uniform spacing (resolutions).

      • scannum

        private java.lang.String scannum
        Scan ID Length of 10.

      • session_error

        private short session_error
        Unknown use.

      • sizeof_hdr

        private int sizeof_hdr
        Always of length 348.

      • smax

        private int smax
        Unknown use.

      • smin

        private int smin
        Unknown use.

      • start_field

        private int start_field
        Unknown use.

      • unused1

        private short unused1
        MIPAV uses this variable to define the X-axis orientation.

      • unused2

        private short unused2
        MIPAV uses this variable to define the Y-axis orientation.

      • unused3

        private short unused3
        MIPAV uses this variable to define the Z-axis orientation.

      • verified

        private float verified
        Unknown use.

      • views

        private int views
        Unknown use.

      • vols_added

        private int vols_added
        Unknown use.

      • vox_units

        private java.lang.String vox_units
        specifies the spatial units of measure for a voxel.

    • Constructor Detail

      • FileInfoAnalyze

        public FileInfoAnalyze​(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

      • getAuxFile

        public java.lang.String getAuxFile()
        Accessor to the aux_file string.
        Returns:
        String aux_file

      • getBitPix

        public short getBitPix()
        Accessor to the bitpix value.
        Returns:
        short the bitpix value.

      • getCalMax

        public float getCalMax()
        Accessor to cal-max.
        Returns:
        float cal_max

      • getCalMin

        public float getCalMin()
        Accessor to cal_min.
        Returns:
        float cal_min

      • getCalUnits

        public java.lang.String getCalUnits()
        Provides the string for cal units.
        Returns:
        String string for cal_units

      • getCompressed

        public float getCompressed()
        Provides the compressed value.
        Returns:
        float compressed

      • getDataTypeCode

        public short getDataTypeCode()
        Accessor to coded datatype value.
        Returns:
        short datatype

      • getDataTypeName

        public java.lang.String getDataTypeName()
        Accessor to the 10 character string of data-type.
        Returns:
        String returns data_type

      • getDBname

        public java.lang.String getDBname()
        Accessor to DB_name.
        Returns:
        String database name

      • getDescription

        public java.lang.String getDescription()
        Accessor to the current analyze-image description.
        Returns:
        String description

      • getDim

        public short getDim()
        Accessor to the dim_un0.
        Returns:
        Returns the dim_un0 variable.

      • getExperimentDate

        public java.lang.String getExperimentDate()
        Provides the current experiment date string.
        Returns:
        String the experiment date.

      • getExperimentTime

        public java.lang.String getExperimentTime()
        Provides the current experiment time string.
        Returns:
        String the experiment time

      • getFieldSkip

        public int getFieldSkip()
        Provides the current field_skip value.
        Returns:
        int the field_skip value

      • getFileExtents

        public int getFileExtents()
        Analyze _extents_ value of 16,384.
        Returns:
        The extents value which always seems to be 16,384.

      • getFunused1

        public float getFunused1()
        MIPAV hack to the ANALYZE standard. Retrieves start locaiton from x-axis. To be stored as Funused1.
        Returns:
        float funused1

      • getFunused2

        public float getFunused2()
        MIPAV hack to the ANALYZE standard. Retrieves start locaiton from y-axis. To be stored as Funused2.
        Returns:
        float funused2

      • getFunused3

        public float getFunused3()
        MIPAV hack to the ANALYZE standard. Retrieves start location from z-axis. To be stored as Funused3.
        Returns:
        float funused3

      • getGenerated

        public java.lang.String getGenerated()
        Provides the current generated string.
        Returns:
        String generated string

      • getGLmax

        public int getGLmax()
        Provides the value of glmax.
        Returns:
        int glmax

      • getGLmin

        public int getGLmin()
        Provides the value of glmin.
        Returns:
        int glmin

      • getHist

        public java.lang.String getHist()
        Accessor to get the Analyze's hist_un0 string.
        Returns:
        Returns the hist_un0 string.

      • getHkey

        public char getHkey()
        Accessor to get the Analyze's hkey_un0 string.
        Returns:
        Returns the hkey_un0 string.

      • getOmax

        public int getOmax()
        Provides current omax value.
        Returns:
        int the omax value

      • getOmin

        public int getOmin()
        Provides current omin value.
        Returns:
        int the omin value

      • getOrientation

        public byte getOrientation()
        Provides the current orientation value.
        Returns:
        byte orientation value

      • getOriginator

        public java.lang.String getOriginator()
        Provides the current originator string.
        Returns:
        String originator string

      • getPatientID

        public java.lang.String getPatientID()
        Provides the current patient id.
        Returns:
        String the patient id

      • getRegular

        public char getRegular()
        Provides the value of regular character.
        Returns:
        char value of regular character

      • getScanNum

        public java.lang.String getScanNum()
        Provides the current scannum string.
        Returns:
        String current scannum string

      • getSessionErr

        public short getSessionErr()
        Provide the value of session err.
        Returns:
        short session_error

      • getSizeOfHeader

        public int getSizeOfHeader()
        Provides the current scannum string.
        Returns:
        String current scannum string

      • getSmax

        public int getSmax()
        Provides current smax value.
        Returns:
        int the smax value

      • getSmin

        public int getSmin()
        Provides current smin value.
        Returns:
        int the smin value

      • getStartField

        public int getStartField()
        Provides the current value for the start_field.
        Returns:
        int the start_field

      • getUnused1

        public short getUnused1()
        provides current unused1 value.
        Returns:
        short unused1 value

      • getUnused2

        public short getUnused2()
        Provides current unused2 value.
        Returns:
        short unused2 value

      • getUnused3

        public short getUnused3()
        Provides current unused3 value.
        Returns:
        short unused3 value

      • getVerified

        public float getVerified()
        Provides the verified value.
        Returns:
        The Analyze verified parameter.

      • getViews

        public int getViews()
        Provides current views value.
        Returns:
        The view parameter.

      • getVolsAdded

        public int getVolsAdded()
        Provides the current vols_added value.
        Returns:
        The vols_added

      • getVoxUnits

        public java.lang.String getVoxUnits()
        Provides the string for vox-units.
        Returns:
        The vox_units parameter

      • setAuxFile

        public void setAuxFile​(java.lang.String auxFile)
        Supplies auxiliary-file string; permits no more than 24 characters.
        Parameters:
        auxFile - T

      • setAxisOrientation

        public void setAxisOrientation​(int axOrient,
                               int axis)
        Sets the image orientation in the specified axis. Creates the axisOrientation if the array has not yet been created.
        Overrides:
        setAxisOrientation in class FileInfoBase
        Parameters:
        axOrient - orientation
        axis - axis of orientation; x is 0, y is 1, z is 2.

      • setBitPix

        public void setBitPix​(short bp)
        Sets bitpix; any value other than 1, 8, 16, 32, 64, or 24 gets set to the dissalowed trap value, -1.
        Parameters:
        bp - DOCUMENT ME!

      • setCalMax

        public void setCalMax​(float cal)
        sets cal-max. if supplied value is less than cal-min, the cal-min gets reset to the supplied value as well, so that cal-min is still no greater than cal-max.
        Parameters:
        cal - DOCUMENT ME!

      • setCalMin

        public void setCalMin​(float cal)
        Sets cal-min. if supplied value is greater than cal-max, the cal-max gets reset to the supplied value as well, so that cal-max is still no less than cal-min.
        Parameters:
        cal - DOCUMENT ME!

      • setCalUnits

        public void setCalUnits​(java.lang.String cal)
        Allows no more than 8 characters for the string describing the cal units.
        Parameters:
        cal - DOCUMENT ME!

      • setCompressed

        public void setCompressed​(float comp)
        sets the compressed variable.
        Parameters:
        comp - DOCUMENT ME!

      • setDataType

        public void setDataType​(java.lang.String dtype)
        Permits 10 charactar large string for data-type.
        Parameters:
        dtype - DOCUMENT ME!

      • setDataType

        public void setDataType​(short dtype)
        Accessor to supply coded datatype.
        Parameters:
        dtype - DOCUMENT ME!

      • setDBname

        public void setDBname​(java.lang.String dbname)
        Set the database name - limit 18 character max to set the DB_NAME value.
        Parameters:
        dbname - DOCUMENT ME!

      • setDescription

        public void setDescription​(java.lang.String description)
        Allows no more than 80 characters to fill in the analyze-image description.
        Parameters:
        description - DOCUMENT ME!

      • setDim

        public void setDim​(short un0)
        DOCUMENT ME!
        Parameters:
        un0 - DOCUMENT ME!

      • setExperimentDate

        public void setExperimentDate​(java.lang.String date)
        Allows a maximum of 10 characters to set the experiment date string.
        Parameters:
        date - DOCUMENT ME!

      • setExperimentTime

        public void setExperimentTime​(java.lang.String time)
        Allows a maximum of 10 characters to set the experiment time string.
        Parameters:
        time - DOCUMENT ME!

      • setFieldSkip

        public void setFieldSkip​(int field)
        Supplies the submitted value to the field_sip variable.
        Parameters:
        field - DOCUMENT ME!

      • setFileExtents

        public void setFileExtents​(int ext)
        DOCUMENT ME!
        Parameters:
        ext - DOCUMENT ME!

      • setFunused1

        public void setFunused1​(float fun)
        Sets the start locations in the x-axis in fileInfoBase. This is a hack into the ANALYZE standard to compensate for start locations not being known. To be Stored in the Funused1 variable.
        Parameters:
        fun - x start location
        See Also:
        FileInfoBase#setStartLocations(float, int)

      • setFunused2

        public void setFunused2​(float fun)
        Sets the start locations in the y-axis in fileInfoBase. This is a hack into the ANALYZE standard to compensate for start locations not being known. To be Stored in the Funused2 variable.
        Parameters:
        fun - y start location
        See Also:
        FileInfoBase#setStartLocations(float, int)

      • setFunused3

        public void setFunused3​(float fun)
        Sets the start locations in the z-axis in fileInfoBase. This is a hack into the ANALYZE standard to compensate for start locations not being known. To be Stored in the Funused3 variable.
        Parameters:
        fun - z start location

      • setGenerated

        public void setGenerated​(java.lang.String gen)
        Allows a maximum of 10 characters to set the generated string.
        Parameters:
        gen - DOCUMENT ME!

      • setGLmax

        public void setGLmax​(int gl)
        Sets glmax. if supplied value is less than glmin, the glmin gets reset to the supplied value as well, so that glmin is still no greater than glmax.
        Parameters:
        gl - DOCUMENT ME!

      • setGLmin

        public void setGLmin​(int gl)
        Sets glmin. if supplied value is greater than glmax, the glmax gets reset to the supplied value as well, so that glmax is still no less than glmin.
        Parameters:
        gl - DOCUMENT ME!

      • setHist

        public void setHist​(java.lang.String hist)
        DOCUMENT ME!
        Parameters:
        hist - DOCUMENT ME!

      • setHkey

        public void setHkey​(char hk)
        DOCUMENT ME!
        Parameters:
        hk - DOCUMENT ME!

      • setOmax

        public void setOmax​(int oMax)
        Sets omax. If supplied value is less than omin, the omin gets reset to the supplied value as well, so that omin is still no greater than omax.
        Parameters:
        oMax - Value that omax is set to.

      • setOmin

        public void setOmin​(int oMin)
        Sets omin. if supplied value is greater than omax, the omax gets reset to the supplied value as well, so that omax is still no less than omin.
        Parameters:
        oMin - Value that omin is set to.

      • setOrientation

        public void setOrientation​(byte orientation)
        Sets the image orientation converting from analyze specific orientation to general orientation. Value may be transverse, coronal, or sagittal.

        see the top of this document for all possible values. supplying a value other than one of these 6 possiblities sets the orientation to an impossible 'flag' value.

        See Also:
        FileInfoBase.setImageOrientation(int)

      • setOrigin

        public void setOrigin​(float[] stlocat)
        Sets start locations of each axis.
        Overrides:
        setOrigin in class FileInfoBase
        Parameters:
        stlocat - axis start location array
        See Also:
        FileInfoBase#getStartLocations()

      • setOrigin

        public void setOrigin​(float fun,
                      int axis)
        Sets the start location of the specified axis.
        Overrides:
        setOrigin in class FileInfoBase
        Parameters:
        fun - origin coord.
        axis - axis of orientation; x is 0, y is 1, z is 2.
        See Also:
        #getStartLocations(int)

      • setOriginator

        public void setOriginator​(java.lang.String originator)
        Allows a maximum of 10 characters to set the originator string.
        Parameters:
        originator - Originator string.

      • setPatientID

        public void setPatientID​(java.lang.String patIDnum)
        Allows a maximum of 10 characters to set the patient ID string.
        Parameters:
        patIDnum - Patient ID string.

      • setRegular

        public void setRegular​(char ch)
        Supply the value of regular character.
        Parameters:
        ch - value of r indicates all images are of the same size which seems to always be the case.

      • setScanNum

        public void setScanNum​(java.lang.String scanNum)
        Allows a maximum of 10 characters to set the scannum string.
        Parameters:
        scanNum - Scan number of the image.

      • setSessionErr

        public void setSessionErr​(short sessionError)
        Supply the value of session error.
        Parameters:
        sessionError - The session error.

      • setSizeOfHeader

        public void setSizeOfHeader​(int size)
        Sets the size of the header which is always 348.
        Parameters:
        size - The size of the header which is always 348 for Analyze images.

      • setSmax

        public void setSmax​(int sMax)
        Sets smax. If supplied value is less than smin, the smin gets reset to the supplied value as well, so that smin is still no greater than smax.
        Parameters:
        sMax - DOCUMENT ME!

      • setSmin

        public void setSmin​(int sMin)
        Sets smin. If supplied value is greater than smax, the smax gets reset to the supplied value as well, so that smax is still no less than smin.
        Parameters:
        sMin - The sMin value.

      • setStartField

        public void setStartField​(int startField)
        Supplies the submitted value to the start_field variable.
        Parameters:
        startField - The start field value.

      • setUnused1

        public void setUnused1​(int unused)
        Sets unused 1.
        Parameters:
        unused - The unused value.

      • setUnused2

        public void setUnused2​(int unused)
        Sets unused 2.
        Parameters:
        unused - The unused value.

      • setUnused3

        public void setUnused3​(int unused)
        Sets unused 3.
        Parameters:
        unused - The unused value.

      • setVerified

        public void setVerified​(float verified)
        Supply the value to verified.
        Parameters:
        verified - The verified value

      • setViews

        public void setViews​(int view)
        Sets the views variable.
        Parameters:
        view - The view value.

      • setVolsAdded

        public void setVolsAdded​(int vols)
        Supplies a value to the vols_added valiable.
        Parameters:
        vols - DOCUMENT ME!

      • setVoxUnits

        public void setVoxUnits​(java.lang.String voxUnits)
        Allows no more than 4 characters for the string describing the vox units.
        Parameters:
        voxUnits - DOCUMENT ME!

      • stateChanged

        public void stateChanged​(java.util.Vector ce)
        .
        ce[0] = table 0 = primary, 1 = secondary, etC
        ce[1] = line of table
        ce[2] = string name eg, "Type"
        ce[3] = Vector codeValue eg, "B"
        ce[4] = string value eg, "Big"

        "ce" comes from ChangeEvent upon which this is based. care to make our own ChangeEvent to store and handle this?

        Parameters:
        ce - DOCUMENT ME!

      • updateFileInfos

        public void updateFileInfos​(FileInfoAnalyze fInfo)
        Propogates the current file info to another FileInfoAnalyze except for the 3 start locations kept in funused1, funused2, funused3.

        It does not copy over the datatypeCode. (though, aside from, "it isn't in the about table", I can't think of a reason why it shouldn't. but it doesn't.) Also, copied over is bitPix, aux_file.

        Some variables, such as the unused1, unused2, unused3, are really taken from unused, rather than from the start locations as we are re-using the funused variables. This means that if the unused variables are not right to begin with, this certainly won't correct them!

        Parameters:
        fInfo - File info. object used to update values in this object.

      • setString

        protected java.lang.String setString​(java.lang.String str,
                                     int length)
        Verifies string is not larger than length; strings larger than length, are clipped before being returned.
        Parameters:
        str - The input string.
        length - The maximum length of the string.
        Returns:
        String new substring

      • selectOrientationText

        private java.lang.String selectOrientationText​(int orientation)
        Selection of text for the table and the editpanel.
        Parameters:
        orientation - value indicating the orientation.
        Returns:
        String the orientation string