Package gov.nih.mipav.model.file

Class FileInfoAnalyze

java.lang.Object
gov.nih.mipav.model.structures.ModelSerialCloneable
gov.nih.mipav.model.file.FileInfoBase
gov.nih.mipav.model.file.FileInfoAnalyze
All Implemented Interfaces:
Serializable, 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:

  • Field Details

    • serialVersionUID

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

    • DT_NONE

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

    • DT_UNKNOWN

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

    • DT_BINARY

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

    • 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:

    • 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:

    • 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:

    • 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:

    • DT_FLOAT

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

    • DT_COMPLEX

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

    • DT_DOUBLE

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

    • DT_RGB

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

    • DT_ALL

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

    • 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:

    • TRANSVERSE_UNFLIPPED

      public static final byte TRANSVERSE_UNFLIPPED
      DOCUMENT ME!
      See Also:

    • CORONAL_UNFLIPPED

      public static final byte CORONAL_UNFLIPPED
      DOCUMENT ME!
      See Also:

    • SAGITTAL_UNFLIPPED

      public static final byte SAGITTAL_UNFLIPPED
      DOCUMENT ME!
      See Also:

    • TRANSVERSE_FLIPPED

      public static final byte TRANSVERSE_FLIPPED
      DOCUMENT ME!
      See Also:

    • CORONAL_FLIPPED

      public static final byte CORONAL_FLIPPED
      DOCUMENT ME!
      See Also:

    • SAGITTAL_FLIPPED

      public static final byte SAGITTAL_FLIPPED
      DOCUMENT ME!
      See Also:

    • aux_file

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

    • descrip

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

    • dim_un0

      private short dim_un0
      Unused.

    • exp_date

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

    • exp_time

      private 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 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 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 String originator
      Unknown use. Length of 10.

    • patient_id

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

    • regular

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

    • scannum

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

  • Constructor Details

    • FileInfoAnalyze

      public FileInfoAnalyze(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

    • getAuxFile

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

    • getDBname

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

    • getDescription

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

    • getExperimentTime

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

    • getPatientID

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

    • setAuxFile

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

    • setAxisOrientation

      public void setAxisOrientation(int[] axOrient)
      Sets orientation of each axis.
      Overrides:
      setAxisOrientation in class FileInfoBase
      Parameters:
      axOrient - axis orientation array
      See Also:

    • 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(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(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(String dbname)
      Set the database name - limit 18 character max to set the DB_NAME value.
      Parameters:
      dbname - DOCUMENT ME!

    • setDescription

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

    • setExperimentTime

      public void setExperimentTime(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:
      • invalid reference 
        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:
      • invalid reference 
        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(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(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:

    • 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:
      • invalid reference 
        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:
      • invalid reference 
        #getStartLocations(int)

    • setOriginator

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

    • setPatientID

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

    • stateChanged

      public void stateChanged(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 String setString(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 String selectOrientationText(int orientation)
      Selection of text for the table and the editpanel.
      Parameters:
      orientation - value indicating the orientation.
      Returns:
      String the orientation string