java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FileDM3

```
public class FileDM3
extends FileBase
```
Some of this code is derived from DM3_Reader.java in ImageJ.

ImageJ disclaimer:

ImageJ is being developed at the National Institutes of Health by an employee of the Federal Government in the course of his official duties. Pursuant to Title 17, Section 105 of the United States Code, this software is not subject to copyright protection and is in the public domain. ImageJ is an experimental system. NIH assumes no responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic.

Field Summary

Fields
Modifier and Type	Field	Description
`private static int`	`ARRAY`	DOCUMENT ME!
`private long[]`	`arrayLocationArray`	DOCUMENT ME!
`private int[]`	`arraySizeArray`	DOCUMENT ME!
`private static int`	`BOOLEAN`	DOCUMENT ME!
`private int`	`byteOrder`	DOCUMENT ME!
`private static int`	`CHAR`	DOCUMENT ME!
`private boolean`	`dataEndianess`	DOCUMENT ME!
`private int[]`	`dataTypeArray`	DOCUMENT ME!
`private int`	`desiredArraySize`	DOCUMENT ME!
`private int`	`desiredImageNumber`	DOCUMENT ME!
`private java.lang.String[]`	`desiredPixelUnitsArray`	DOCUMENT ME!
`private int[][]`	`dimArray`	DOCUMENT ME!
`private static int`	`DOUBLE`	DOCUMENT ME!
`private boolean`	`endianess`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private int`	`fileBytes`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoDM3`	`fileInfo`	DOCUMENT ME!
`private FileInfoDM3`	`fileInfoCopy`
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private int`	`fileVersion`	DOCUMENT ME!
`private static int`	`FLOAT`	DOCUMENT ME!
`private int`	`identicalDesiredArraySize`	DOCUMENT ME!
`private ModelImage`	`image`	DOCUMENT ME!
`private int`	`imageNum`	DOCUMENT ME!
`private int[]`	`imgExtents`	DOCUMENT ME!
`private boolean`	`isCalibrations`	DOCUMENT ME!
`private boolean`	`isData`	DOCUMENT ME!
`private boolean`	`isDataType`	DOCUMENT ME!
`private boolean`	`isDimension`	DOCUMENT ME!
`private boolean`	`isDimensions`	DOCUMENT ME!
`private boolean`	`isImageData`	DOCUMENT ME!
`private boolean`	`isScale`	DOCUMENT ME!
`private boolean`	`isUnits`	DOCUMENT ME!
`private static int`	`LONG`	DOCUMENT ME!
`private ModelLUT`	`LUT`	DOCUMENT ME!
`private int`	`nDimensions`	DOCUMENT ME!
`private int`	`numberSlices`	DOCUMENT ME!
`private int[]`	`numDimArray`	DOCUMENT ME!
`private static int`	`OCTET`	DOCUMENT ME!
`private float[][]`	`pixelScaleArray`	DOCUMENT ME!
`private java.lang.String[][]`	`pixelUnitsArray`	DOCUMENT ME!
`private int[]`	`pixelUnitsNumber`	DOCUMENT ME!
`private ViewJProgressBar`	`progressBar`	DOCUMENT ME!
`private int`	`routineTagEntry`	DOCUMENT ME!
`private int`	`routineTagGroup`	DOCUMENT ME!
`private int`	`scaleIndex`	DOCUMENT ME!
`private static int`	`SHORT`	Different encoded data types used in DM3 files.
`private int`	`sourceType`	DOCUMENT ME!
`private static int`	`STRING`	DOCUMENT ME!
`private static int`	`STRUCT`	DOCUMENT ME!
`private static int`	`ULONG`	DOCUMENT ME!
`private int`	`unitsIndex`	DOCUMENT ME!
`private static int`	`USHORT`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.file.FileBase
BIG_ENDIAN, bitsPerPixel, fileNames, LITTLE_ENDIAN, pBarVisible, raFile, READ, READ_WRITE

Constructor Summary

Constructors
Constructor Description

FileDM3(java.lang.String fileName, java.lang.String fileDir)
DM3 reader constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`ModelLUT`	`getModelLUT()`	returns LUT if defined.
`private void`	`readArray()`	DOCUMENT ME!
`private int[]`	`readArrayTypes()`	DOCUMENT ME!
`private void`	`readBuffer(int slice, float[] buffer)`	Reads a slice of data at a time and stores the results in the buffer.
`private void`	`readComplexBuffer(int slice, float[] bufferR, float[] bufferI)`	Reads a slice of data at a time and stores the results in the buffer.
`private void`	`readDBuffer(int slice, double[] buffer)`	Reads a slice of data at a time and stores the results in the buffer.
`private void`	`readDComplexBuffer(int slice, double[] bufferR, double[] bufferI)`	Reads a slice of data at a time and stores the results in the buffer.
`ModelImage`	`readImage(boolean one)`	reads the DM3 file header and data.
`private void`	`readLBuffer(int slice, long[] buffer)`	Reads a slice of data at a time and stores the results in the buffer.
`private void`	`readSimpleData(int index, int encodedType)`	DOCUMENT ME!
`private void`	`readString()`	DOCUMENT ME!
`private void`	`readStruct()`	DOCUMENT ME!
`private int[]`	`readStructTypes()`	DOCUMENT ME!
`private void`	`readTagEntry(int index)`	DOCUMENT ME!
`private void`	`readTagGroup()`	DOCUMENT ME!
`private void`	`readTagType(int index)`	DOCUMENT ME!

Methods inherited from class gov.nih.mipav.model.file.FileBase
addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, floatToBytes, getBufferDouble, getBufferFloat, getBufferInt, getBufferLong, getBufferShort, getBufferUShort, getDataType, getDouble, getFloat, getInt, getLong, getProgressChangeListeners, getRaFile, getSignedShort, getString, getUInt, getUnsignedByte, getUnsignedShort, intToBytes, isBigEndian, isProgressBarVisible, linkProgress, longToBytes, readDouble, readFloat, readInt, readLong, readShort, readString, readUnsignedShort, removeProgressChangeListener, setBigEndian, setBufferFloat, setBufferInt, setBufferLong, setBufferShort, setBufferString, setDataType, setEndianess, shortToBytes, writeBytes, writeDouble, writeFloat, writeInt, writeLong, writeShort

Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - SHORT
```
private static final int SHORT
```
    Different encoded data types used in DM3 files.
    
    See Also:
    
    Constant Field Values
  - LONG
```
private static final int LONG
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - USHORT
```
private static final int USHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ULONG
```
private static final int ULONG
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FLOAT
```
private static final int FLOAT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - DOUBLE
```
private static final int DOUBLE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - BOOLEAN
```
private static final int BOOLEAN
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - CHAR
```
private static final int CHAR
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - OCTET
```
private static final int OCTET
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - STRUCT
```
private static final int STRUCT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - STRING
```
private static final int STRING
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ARRAY
```
private static final int ARRAY
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - arrayLocationArray
```
private long[] arrayLocationArray
```
    DOCUMENT ME!
  - arraySizeArray
```
private int[] arraySizeArray
```
    DOCUMENT ME!
  - byteOrder
```
private int byteOrder
```
    DOCUMENT ME!
  - dataEndianess
```
private boolean dataEndianess
```
    DOCUMENT ME!
  - dataTypeArray
```
private int[] dataTypeArray
```
    DOCUMENT ME!
  - desiredArraySize
```
private int desiredArraySize
```
    DOCUMENT ME!
  - desiredImageNumber
```
private int desiredImageNumber
```
    DOCUMENT ME!
  - desiredPixelUnitsArray
```
private java.lang.String[] desiredPixelUnitsArray
```
    DOCUMENT ME!
  - dimArray
```
private int[][] dimArray
```
    DOCUMENT ME!
  - endianess
```
private boolean endianess
```
    DOCUMENT ME!
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileBytes
```
private int fileBytes
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoDM3 fileInfo
```
    DOCUMENT ME!
  - fileInfoCopy
```
private FileInfoDM3 fileInfoCopy
```
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - fileVersion
```
private int fileVersion
```
    DOCUMENT ME!
  - identicalDesiredArraySize
```
private int identicalDesiredArraySize
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - imageNum
```
private int imageNum
```
    DOCUMENT ME!
  - imgExtents
```
private int[] imgExtents
```
    DOCUMENT ME!
  - isCalibrations
```
private boolean isCalibrations
```
    DOCUMENT ME!
  - isData
```
private boolean isData
```
    DOCUMENT ME!
  - isDataType
```
private boolean isDataType
```
    DOCUMENT ME!
  - isDimension
```
private boolean isDimension
```
    DOCUMENT ME!
  - isDimensions
```
private boolean isDimensions
```
    DOCUMENT ME!
  - isImageData
```
private boolean isImageData
```
    DOCUMENT ME!
  - isScale
```
private boolean isScale
```
    DOCUMENT ME!
  - isUnits
```
private boolean isUnits
```
    DOCUMENT ME!
  - LUT
```
private ModelLUT LUT
```
    DOCUMENT ME!
  - nDimensions
```
private int nDimensions
```
    DOCUMENT ME!
  - numberSlices
```
private int numberSlices
```
    DOCUMENT ME!
  - numDimArray
```
private int[] numDimArray
```
    DOCUMENT ME!
  - pixelScaleArray
```
private float[][] pixelScaleArray
```
    DOCUMENT ME!
  - pixelUnitsArray
```
private java.lang.String[][] pixelUnitsArray
```
    DOCUMENT ME!
  - pixelUnitsNumber
```
private int[] pixelUnitsNumber
```
    DOCUMENT ME!
  - progressBar
```
private ViewJProgressBar progressBar
```
    DOCUMENT ME!
  - routineTagEntry
```
private int routineTagEntry
```
    DOCUMENT ME!
  - routineTagGroup
```
private int routineTagGroup
```
    DOCUMENT ME!
  - scaleIndex
```
private int scaleIndex
```
    DOCUMENT ME!
  - sourceType
```
private int sourceType
```
    DOCUMENT ME!
  - unitsIndex
```
private int unitsIndex
```
    DOCUMENT ME!
- Constructor Detail
  - FileDM3
```
public FileDM3(java.lang.String fileName,
               java.lang.String fileDir)
        throws java.io.IOException
```
    DM3 reader 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
  - getModelLUT
```
public ModelLUT getModelLUT()
```
    returns LUT if defined.
    
    Returns:
    
    the LUT if defined else it is null
  - readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException
```
    reads the DM3 file header and data.
    
    Parameters:
    
    one - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readArray
```
private void readArray()
                throws java.io.IOException
```
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readArrayTypes
```
private int[] readArrayTypes()
                      throws java.io.IOException
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readBuffer
```
private void readBuffer(int slice,
                        float[] buffer)
                 throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    buffer - buffer where the info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readComplexBuffer
```
private void readComplexBuffer(int slice,
                               float[] bufferR,
                               float[] bufferI)
                        throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    bufferR - buffer where the real info is stored
    
    bufferI - buffer where the imaginary info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readDBuffer
```
private void readDBuffer(int slice,
                         double[] buffer)
                  throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    buffer - buffer where the info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readDComplexBuffer
```
private void readDComplexBuffer(int slice,
                                double[] bufferR,
                                double[] bufferI)
                         throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    bufferR - buffer where the real info is stored
    
    bufferI - buffer where the imaginary info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readLBuffer
```
private void readLBuffer(int slice,
                         long[] buffer)
                  throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    buffer - buffer where the info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readSimpleData
```
private void readSimpleData(int index,
                            int encodedType)
                     throws java.io.IOException
```
    DOCUMENT ME!
    
    Parameters:
    
    index - DOCUMENT ME!
    
    encodedType - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readString
```
private void readString()
                 throws java.io.IOException
```
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readStruct
```
private void readStruct()
                 throws java.io.IOException
```
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readStructTypes
```
private int[] readStructTypes()
                       throws java.io.IOException
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readTagEntry
```
private void readTagEntry(int index)
                   throws java.io.IOException
```
    DOCUMENT ME!
    
    Parameters:
    
    index - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readTagGroup
```
private void readTagGroup()
                   throws java.io.IOException
```
    DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readTagType
```
private void readTagType(int index)
                  throws java.io.IOException
```
    DOCUMENT ME!
    
    Parameters:
    
    index - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!

Class FileDM3

Field Summary

Fields inherited from class gov.nih.mipav.model.file.FileBase

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.file.FileBase

Methods inherited from class java.lang.Object

Field Detail

SHORT

LONG

USHORT

ULONG

FLOAT

DOUBLE

BOOLEAN

CHAR

OCTET

STRUCT

STRING

ARRAY

arrayLocationArray

arraySizeArray

byteOrder

dataEndianess

dataTypeArray

desiredArraySize

desiredImageNumber

desiredPixelUnitsArray

dimArray

endianess

file

fileBytes

fileDir

fileInfo

fileInfoCopy

fileName

fileVersion

identicalDesiredArraySize

image

imageNum

imgExtents

isCalibrations

isData

isDataType

isDimension

isDimensions

isImageData

isScale

isUnits

LUT

nDimensions

numberSlices

numDimArray

pixelScaleArray

pixelUnitsArray

pixelUnitsNumber

progressBar

routineTagEntry

routineTagGroup

scaleIndex

sourceType

unitsIndex

Constructor Detail

FileDM3

Method Detail

finalize

getModelLUT

readImage

readArray

readArrayTypes

readBuffer

readComplexBuffer

readDBuffer

readDComplexBuffer

readLBuffer

readSimpleData

readString

readStruct

readStructTypes

readTagEntry