Package gov.nih.mipav.model.file

Class FileInfoSPM

java.lang.Object
gov.nih.mipav.model.structures.ModelSerialCloneable
gov.nih.mipav.model.file.FileInfoBase
gov.nih.mipav.model.file.FileInfoSPM
All Implemented Interfaces:
Serializable, Cloneable
public class FileInfoSPM extends FileInfoBase
This structures contains the information that describes how an SPM image is stored on disk. We have extended this format to store image orientation and start locations. 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.

Differences between MIPAV ANALYZE and SPM: In MIPAV ANALYZE we have location 60 cal_units 4 unsigned characters location 64 - X-axis orientation @see FileInfoBase for static variables that are set. location 66 - Y-axis orientation // All three unused variables are of short type. location 68 - Z-axis orientation In SPM we have location 60 cal_units 8 unsigned characters location 68 unused1

In MIPAV ANALYZE we have location 112 Funused1 - X-axis starting location (origin from upper left-hand corner) location 116 Funused2 - Y-axis starting location (origin from upper left-hand corner) location 120 Funused3 - Z-axis starting location (origin is the first image slice) In SPM we have location 112 Funused1 scale a floating point scale factor applied during memory mapping location 116 Funused2 location 120 Funused3

In MIPAV ANALYZE we have location 253 originator with 10 characters In SPM we have location 253 origin with 5 shorts. If the first 3 shorts of a 3D image are set to 0, 0, 0, the origin is assumed to be at the center of the volume, since in SPM the corner voxel is at 1, 1, 1. The position(x,y,z) in mm. is determined by the distance(x,y,z) from the origin multiplied by the vox_units(x,y,z).

In SPM the signed byte datatype was added with DT_BYTE = 130. MIPAV ANALYZE uses UNSIGNED_SHORT = 6 while SPM uses DT_UNSIGNED_SHORT = 132. The SPM standard also provides for an unsigned int = 136, but MIPAV does not used the unsigned int data type. Note that in SPM while DATA = datatype * 256 for swapped bytes, only datatype and not DATA is written to the file, so in this program we need never consider the multiplicative factors of 256.

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

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 int DT_NONE
      DOCUMENT ME!
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    • DT_UNKNOWN

      public static final int DT_UNKNOWN
      DOCUMENT ME!
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    • DT_BINARY

      public static final int DT_BINARY
      DOCUMENT ME!
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    • DT_BYTE

      public static final int DT_BYTE
      DOCUMENT ME!
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    • DT_UNSIGNED_CHAR

      public static final int DT_UNSIGNED_CHAR
      DOCUMENT ME!
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    • DT_SIGNED_SHORT

      public static final int DT_SIGNED_SHORT
      DOCUMENT ME!
      See Also:

    • DT_UNSIGNED_SHORT

      public static final int DT_UNSIGNED_SHORT
      DOCUMENT ME!
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    • DT_SIGNED_INT

      public static final int DT_SIGNED_INT
      DOCUMENT ME!
      See Also:

    • DT_UNSIGNED_INT

      public static final int DT_UNSIGNED_INT
      DOCUMENT ME!
      See Also:

    • DT_FLOAT

      public static final int DT_FLOAT
      DOCUMENT ME!
      See Also:

    • DT_COMPLEX

      public static final int DT_COMPLEX
      DOCUMENT ME!
      See Also:

    • DT_DOUBLE

      public static final int DT_DOUBLE
      DOCUMENT ME!
      See Also:

    • DT_RGB

      public static final int DT_RGB
      DOCUMENT ME!
      See Also:

    • DT_ALL

      public static final int DT_ALL
      DOCUMENT ME!
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    • 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 SPM 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
      DOCUMENT ME!

    • cal_max

      private float cal_max
      DOCUMENT ME!

    • cal_min

      private float cal_min
      DOCUMENT ME!

    • cal_units

      private String cal_units
      DOCUMENT ME!

    • compressed

      private float compressed
      DOCUMENT ME!

    • data_type

      private String data_type
      DOCUMENT ME!

    • datatype

      private short datatype
      DOCUMENT ME!

    • db_name

      private String db_name
      DOCUMENT ME!

    • descrip

      private String descrip
      DOCUMENT ME!

    • dim_un0

      private short dim_un0
      DOCUMENT ME!

    • exp_date

      private String exp_date
      DOCUMENT ME!

    • exp_time

      private String exp_time
      DOCUMENT ME!

    • extents

      private int extents
      DOCUMENT ME!

    • field_skip

      private int field_skip
      DOCUMENT ME!

    • generated

      private String generated
      DOCUMENT ME!

    • glmax

      private int glmax
      DOCUMENT ME!

    • glmin

      private int glmin
      DOCUMENT ME!

    • hist_un0

      private String hist_un0
      DOCUMENT ME!

    • hkey_un0

      private char hkey_un0
      DOCUMENT ME!

    • omax

      private int omax
      DOCUMENT ME!

    • omin

      private int omin
      DOCUMENT ME!

    • orient

      private byte orient
      DOCUMENT ME!

    • origin

      private short[] origin
      DOCUMENT ME!

    • patient_id

      private String patient_id
      DOCUMENT ME!

    • regular

      private char regular
      DOCUMENT ME!

    • scale

      private float scale
      a floating point scale factor used during memory mapping.

    • scannum

      private String scannum
      DOCUMENT ME!

    • session_error

      private short session_error
      DOCUMENT ME!

    • sizeof_hdr

      private int sizeof_hdr
      DOCUMENT ME!

    • smax

      private int smax
      DOCUMENT ME!

    • smin

      private int smin
      DOCUMENT ME!

    • start_field

      private int start_field
      DOCUMENT ME!

    • verified

      private float verified
      DOCUMENT ME!

    • views

      private int views
      DOCUMENT ME!

    • vols_added

      private int vols_added
      DOCUMENT ME!

    • vox_offset

      private float vox_offset
      public float pixdim = new float[8]; // image resolutions info mm or ms stored in FileInfoBase pixdim[0] = number of dimensions pixdim[1] = voxel width pixdim[2] = voxel height pixdim[3] = voxel thickness pixdim[4] = time.

    • vox_units

      private String vox_units
      public short dim[] = new short[8]; // image dimension data stored in FileInfoBase dim[0] = number of dimensions; usally 4 dim[1] = image width dim[2] = image height dim[3] = image depth (# of slices) dim[4] = volumes in image --- must be one for 3D image.

  • Constructor Details

    • FileInfoSPM

      public FileInfoSPM(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 SPM-image description.
      Returns:
      String description

    • getDim

      public short getDim()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • 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()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • 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()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getHkey

      public char getHkey()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • 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

    • getOriginLoc

      public short[] getOriginLoc()
      DOCUMENT ME!
      Returns:
      origin

    • 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

    • getScale

      public float getScale()
      DOCUMENT ME!
      Returns:
      float scale

    • 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()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • 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

    • getVerified

      public float getVerified()
      provides the verified value.
      Returns:
      float verified

    • getViews

      public int getViews()
      provides current views value.
      Returns:
      int the view

    • getVolsAdded

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

    • getVoxOffset

      public float getVoxOffset()
      accessor to the vox offset value.
      Returns:
      float vox_offset

    • getVoxUnits

      public String getVoxUnits()
      provides the string for vox-units.
      Returns:
      String string for vox_units

    • setAuxFile

      public void setAuxFile(String aux)
      supplies auxiliary-file string; permits no more than 24 characters.
      Parameters:
      aux - DOCUMENT ME!

    • setAxisOrientation

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

    • 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)
      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 SPM-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!

    • 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 o)
      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:
      o - DOCUMENT ME!

    • setOmin

      public void setOmin(int o)
      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:
      o - DOCUMENT ME!

    • setOrientation

      public void setOrientation(byte orientation)
      Sets the image orientation converting from SPM 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(short[] origin)
      DOCUMENT ME!
      Parameters:
      origin - DOCUMENT ME!

    • setMipavOrigin

      public void setMipavOrigin(float[] mipavOrigin)
      Parameters:
      mipavOrigin -

    • setPatientID

      public void setPatientID(String IDnum)
      allows a maximum of 10 characters to set the patient ID string.
      Parameters:
      IDnum - DOCUMENT ME!

    • setRegular

      public void setRegular(char ch)
      supply the value of regular character.
      Parameters:
      ch - DOCUMENT ME!

    • setScale

      public void setScale(float scale)
      DOCUMENT ME!
      Parameters:
      scale - DOCUMENT ME!

    • setScanNum

      public void setScanNum(String num)
      allows a maximum of 10 characters to set the scannum string.
      Parameters:
      num - DOCUMENT ME!

    • setSessionErr

      public void setSessionErr(short s)
      supply the value of session error.
      Parameters:
      s - DOCUMENT ME!

    • setSizeOfHeader

      public void setSizeOfHeader(int size)
      DOCUMENT ME!
      Parameters:
      size - DOCUMENT ME!

    • setSmax

      public void setSmax(int s)
      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:
      s - DOCUMENT ME!

    • setSmin

      public void setSmin(int s)
      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:
      s - DOCUMENT ME!

    • setStartField

      public void setStartField(int field)
      supplies the submitted value to the start_field variable.
      Parameters:
      field - DOCUMENT ME!

    • setVerified

      public void setVerified(float veri)
      supply the value to verified.
      Parameters:
      veri - DOCUMENT ME!

    • setViews

      public void setViews(int view)
      sets the views variable.
      Parameters:
      view - DOCUMENT ME!

    • setVolsAdded

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

    • setVoxOffset

      public void setVoxOffset(float vox)
      sets vox offset value.
      Parameters:
      vox - DOCUMENT ME!

    • setVoxUnits

      public void setVoxUnits(String vox)
      allows no more than 4 characters for the string describing the vox units.
      Parameters:
      vox - 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(FileInfoSPM fInfo)
      Propogates the current file info to another FileInfoSPM 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 - DOCUMENT ME!

    • setString

      protected String setString(String str, int len)
      verifies string is not larger than len length; strings larger than len, are clipped before being returned.
      Returns:
      String new substring
      See Also:

    • selectOrientationText

      private String selectOrientationText(int or)
      selection of text for the table and the editpanel.
      Parameters:
      or - DOCUMENT ME!
      Returns:
      String the orientation string