java.lang.Object
- gov.nih.mipav.model.file.FileDicomBase

Direct Known Subclasses:

FileDicom
```
public class FileDicomBase
extends java.lang.Object
```
FileDICOMBase is an class that supports the reading/writing of DICOM files. It reads in a buffer of tags that can be parsed more quickly than continued random accesses to the harddrive.

Version:

1.0 June 30, 2005

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`b1`	Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
`private int`	`b2`	Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
`private int`	`b3`	Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
`private int`	`b4`	Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
`private int`	`b5`	Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
`private int`	`b6`	Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
`private int`	`b7`	Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
`private int`	`b8`	Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
`static boolean`	`BIG_ENDIAN`	Byte order.
`private int`	`bPtr`	Buffer pointer (aka file pointer).
`static long`	`BUFFER_SIZE`	The size of the buffer that contains the tags of the DICOM image.
`protected byte[]`	`byteBuffer`	One byte array used to read/write in data so that one doesn't't need to be allocated with each read/write.
`protected byte[]`	`byteBuffer2`	Two byte array used to read/write in data so that one doesn't't need to be allocated with each read/write.
`protected byte[]`	`byteBuffer4`	Four byte array used to read/write in data so that one doesn't need to be allocated with each read/write.
`protected byte[]`	`byteBuffer8`	Eight byte array used to read/write in data so that they don't need to be allocated with each read/write.
`protected long`	`fLength`	Total length of the image file.
`protected int`	`imageElementLength`
`protected int`	`imageElementWord`
`protected int`	`imageGroupWord`
`protected int`	`imageTagLocation`
`protected boolean`	`isDicomRecv`
`static boolean`	`LITTLE_ENDIAN`	Byte order.
`protected boolean`	`notDir`	If file is a DICOMDIR this is false *
`protected int`	`numEmbeddedImages`	The number of images inside of this file which are not the main displayable image (may be icon, RT planning, etc.
`protected boolean`	`pBarVisible`	Flag indicating if the progress bar should be shown.
`protected ProgressBarInterface`	`progressBar`	Progress bar to show when reading in image file.
`protected java.io.RandomAccessFile`	`raFile`	Pointer to file to read or write from.
`static int`	`READ`	Read only access.
`static int`	`READ_WRITE`	Read-write access.
`protected boolean`	`SPECTROSCOPY`
`protected byte[]`	`tagBuffer`	The buffer that holds the tags of the DICOM image.
`protected boolean`	`TAMAR`

Constructor Summary

Constructors
Constructor Description

FileDicomBase()
Empty constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`int`	`getByte()`	Reads unsigned bytes from file.
`double`	`getDouble(boolean endianess)`	Reads eight unsigned bytes from file.
`protected long`	`getFileLength()`
`protected int`	`getFilePointer()`	Gets the file/buffer pointer and returns it.
`float`	`getFloat(boolean endianess)`	Reads four unsigned bytes from file.
`int`	`getInt(boolean endianess)`	Reads four signed bytes from file.
`long`	`getLong(boolean endianess)`	Reads eight unsigned bytes from file.
`int`	`getSignedByte()`	Reads signed bytes from file.
`int`	`getSignedShort(boolean endianess)`	Reads two byte signed short from file.
`java.lang.String`	`getString(int length)`	Reads a string from a file of given `length`.
`java.lang.String`	`getStringFromFile(int length)`	Reads a string from a file of given `length`.
`long`	`getUInt(boolean endianess)`	Reads four unsigned bytes from file.
`int`	`getUnsignedShort(boolean endianess)`	Reads two unsigned bytes from file.
`void`	`initializeFullRead()`	Setups the allocation of memory for the byte buffer to load the entire image.
`boolean`	`isHeaderOnlyRead()`	Returns whether this Dicom read is only interested in the header tags and not the image data (if it exists).
`boolean`	`isProgressBarVisible()`	Returns flag that indicates that the progressBar is visible.
`void`	`loadTagBuffer(int b3)`	Setups the allocation of memory for the byte buffer to load tags.
`int`	`locateImageTag(int offset, int imageNumber, int b3)`	Locates a DICOM image beginning at the given offset.
`protected void`	`read(byte[] byteBuffer)`	Reads into the supplied buffer data from the DICOM tag buffer.
`private boolean`	`searchForImageTag(byte[] tempTagBuffer, byte[] endianBuffer, int bufferIndex)`	Performs internal search for the image tag in a dicom file, given an appropriate endianess.
`protected void`	`seek(int value)`	Seeks to a point in the buffer.
`void`	`setBufferFloat(byte[] buffer, float data, int i, boolean endianess)`	Sets byte buffer with int.
`void`	`setBufferInt(byte[] buffer, int data, int i, boolean endianess)`	Sets byte buffer with int.
`void`	`setBufferLong(byte[] buffer, long data, int i, boolean endianess)`	Sets byte buffer with long.
`void`	`setBufferShort(byte[] buffer, short data, int i, boolean endianess)`	Sets byte buffer with int.
`void`	`setBufferString(byte[] buffer, java.lang.String str, int i)`	Sets byte buffer with int.
`void`	`setHeaderOnlyRead(boolean isHeaderOnly)`	Sets whether this Dicom read is only interested in the header tags and not the image data (if it exists).
`void`	`setProgressBarVisible(boolean flag)`	Sets whether or not the progress bar should be visible.
`void`	`setTagBuffer(byte[] buffer)`	DOCUMENT ME!
`protected void`	`skipBytes(int value)`	Skips to a new point in the buffer.
`void`	`writeByte(byte data)`	Writes a byte to a file.
`void`	`writeDouble(double data, boolean endianess)`	Writes a double as eight bytes to a file.
`void`	`writeFloat(float data, boolean endianess)`	Writes a float as four bytes to a file.
`void`	`writeInt(int data, boolean endianess)`	Writes an int as four bytes to a file.
`void`	`writeLong(long data, boolean endianess)`	Writes a long as eight bytes to a file.
`void`	`writeShort(short data, boolean endianess)`	Writes a short as two bytes to a file.
`void`	`writeUnsignedShort(short data, boolean endianess)`	Writes an unsigned short as two bytes to a file.

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

- Field Detail
  - LITTLE_ENDIAN
```
public static final boolean LITTLE_ENDIAN
```
    Byte order. Rightmost byte is most significant.
    
    See Also:
    
    Constant Field Values
  - BIG_ENDIAN
```
public static final boolean BIG_ENDIAN
```
    Byte order. Leftmost byte is most significant.
    
    See Also:
    
    Constant Field Values
  - READ
```
public static final int READ
```
    Read only access.
    
    See Also:
    
    Constant Field Values
  - READ_WRITE
```
public static final int READ_WRITE
```
    Read-write access.
    
    See Also:
    
    Constant Field Values
  - BUFFER_SIZE
```
public static final long BUFFER_SIZE
```
    The size of the buffer that contains the tags of the DICOM image. Default = 400Thousand.
    
    See Also:
    
    Constant Field Values
  - byteBuffer
```
protected final byte[] byteBuffer
```
    One byte array used to read/write in data so that one doesn't't need to be allocated with each read/write.
  - byteBuffer2
```
protected final byte[] byteBuffer2
```
    Two byte array used to read/write in data so that one doesn't't need to be allocated with each read/write.
  - byteBuffer4
```
protected final byte[] byteBuffer4
```
    Four byte array used to read/write in data so that one doesn't need to be allocated with each read/write.
  - byteBuffer8
```
protected final byte[] byteBuffer8
```
    Eight byte array used to read/write in data so that they don't need to be allocated with each read/write.
  - fLength
```
protected long fLength
```
    Total length of the image file.
  - pBarVisible
```
protected boolean pBarVisible
```
    Flag indicating if the progress bar should be shown.
  - progressBar
```
protected ProgressBarInterface progressBar
```
    Progress bar to show when reading in image file.
  - raFile
```
protected java.io.RandomAccessFile raFile
```
    Pointer to file to read or write from.
  - tagBuffer
```
protected byte[] tagBuffer
```
    The buffer that holds the tags of the DICOM image.
  - b1
```
private int b1
```
    Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
  - b2
```
private int b2
```
    Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
  - b3
```
private int b3
```
    Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
  - b4
```
private int b4
```
    Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
  - b5
```
private int b5
```
    Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
  - b6
```
private int b6
```
    Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
  - b7
```
private int b7
```
    Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
  - b8
```
private int b8
```
    Integer variable used to read/write in data so that they don't need to be allocated with each read/write.
  - bPtr
```
private int bPtr
```
    Buffer pointer (aka file pointer).
  - notDir
```
protected boolean notDir
```
    If file is a DICOMDIR this is false *
  - numEmbeddedImages
```
protected int numEmbeddedImages
```
    The number of images inside of this file which are not the main displayable image (may be icon, RT planning, etc.
  - isDicomRecv
```
protected boolean isDicomRecv
```
  - imageGroupWord
```
protected int imageGroupWord
```
  - imageElementWord
```
protected int imageElementWord
```
  - imageElementLength
```
protected int imageElementLength
```
  - imageTagLocation
```
protected int imageTagLocation
```
  - TAMAR
```
protected boolean TAMAR
```
  - SPECTROSCOPY
```
protected boolean SPECTROSCOPY
```
- Constructor Detail
  - FileDicomBase
```
public FileDicomBase()
```
    Empty constructor.
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for cleanup.
    
    Overrides:
    
    finalize in class java.lang.Object
  - getByte
```
public final int getByte()
                  throws java.io.IOException
```
    Reads unsigned bytes from file.
    
    Returns:
    
    The value of unsigned byte read from the file returned as an int.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getSignedByte
```
public final int getSignedByte()
                        throws java.io.IOException
```
    Reads signed bytes from file.
    
    Returns:
    
    The value of signed byte read from the file returned as an int.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getDouble
```
public final double getDouble(boolean endianess)
                       throws java.io.IOException
```
    Reads eight unsigned bytes from file.
    
    Parameters:
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Returns:
    
    The value of the double read from the file.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getFloat
```
public final float getFloat(boolean endianess)
                     throws java.io.IOException
```
    Reads four unsigned bytes from file.
    
    Parameters:
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Returns:
    
    The value of the float read from the file.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getInt
```
public final int getInt(boolean endianess)
                 throws java.io.IOException
```
    Reads four signed bytes from file.
    
    Parameters:
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Returns:
    
    The value of the integer read from the file.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getLong
```
public final long getLong(boolean endianess)
                   throws java.io.IOException
```
    Reads eight unsigned bytes from file.
    
    Parameters:
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Returns:
    
    The value of the long read from the file.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getSignedShort
```
public final int getSignedShort(boolean endianess)
                         throws java.io.IOException
```
    Reads two byte signed short from file.
    
    Parameters:
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Returns:
    
    The value of signed short read from the file returned as an int.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getString
```
public final java.lang.String getString(int length)
                                 throws java.io.IOException
```
    Reads a string from a file of given length.
    
    Parameters:
    
    length - Number of bytes that form the string.
    
    Returns:
    
    The string read from the file.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getStringFromFile
```
public final java.lang.String getStringFromFile(int length)
                                         throws java.io.IOException
```
    Reads a string from a file of given length.
    
    Parameters:
    
    length - Number of bytes that form the string.
    
    Returns:
    
    The string read from the file.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getUInt
```
public final long getUInt(boolean endianess)
                   throws java.io.IOException
```
    Reads four unsigned bytes from file.
    
    Parameters:
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Returns:
    
    The value of the integer read from the file.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - getUnsignedShort
```
public final int getUnsignedShort(boolean endianess)
                           throws java.io.IOException
```
    Reads two unsigned bytes from file.
    
    Parameters:
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Returns:
    
    The value of unsigned short read from the file returned as an int.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - initializeFullRead
```
public void initializeFullRead()
```
    Setups the allocation of memory for the byte buffer to load the entire image.
  - isProgressBarVisible
```
public boolean isProgressBarVisible()
```
    Returns flag that indicates that the progressBar is visible.
    
    Returns:
    
    true if progress bar is visible, false if not visible.
  - searchForImageTag
```
private boolean searchForImageTag(byte[] tempTagBuffer,
                                  byte[] endianBuffer,
                                  int bufferIndex)
```
    Performs internal search for the image tag in a dicom file, given an appropriate endianess.
  - loadTagBuffer
```
public void loadTagBuffer(int b3)
                   throws java.io.IOException
```
    Setups the allocation of memory for the byte buffer to load tags. This tag buffer is a cache to speed the loading of the images.
    
    Throws:
    
    java.io.IOException
  - locateImageTag
```
public int locateImageTag(int offset,
                          int imageNumber,
                          int b3)
```
    Locates a DICOM image beginning at the given offset. When multiple images after the offset exist, imageNumber can be used to specify the exact image to retrieve.
  - setBufferFloat
```
public final void setBufferFloat(byte[] buffer,
                                 float data,
                                 int i,
                                 boolean endianess)
```
    Sets byte buffer with int.
    
    Parameters:
    
    buffer - Byte buffers where data is to be stored.
    
    data - Float data is broken down in bytes and stored in the byte buffer.
    
    i - Index into byte buffer.
    
    endianess - true indicates big endian byte order, false indicates little endian.
  - setBufferInt
```
public final void setBufferInt(byte[] buffer,
                               int data,
                               int i,
                               boolean endianess)
```
    Sets byte buffer with int.
    
    Parameters:
    
    buffer - Byte buffers where data is to be stored.
    
    data - Integer data is broken down in bytes and stored in the byte buffer.
    
    i - Index into byte buffer.
    
    endianess - true indicates big endian byte order, false indicates little endian.
  - setBufferLong
```
public final void setBufferLong(byte[] buffer,
                                long data,
                                int i,
                                boolean endianess)
```
    Sets byte buffer with long.
    
    Parameters:
    
    buffer - Byte buffers where data is to be stored.
    
    data - Long data is broken down in bytes and stored in the byte buffer.
    
    i - Index into byte buffer.
    
    endianess - true indicates big endian byte order, false indicates little endian.
  - setBufferShort
```
public final void setBufferShort(byte[] buffer,
                                 short data,
                                 int i,
                                 boolean endianess)
```
    Sets byte buffer with int.
    
    Parameters:
    
    buffer - Byte buffers where data is to be stored.
    
    data - Short data is broken down in bytes and stored in the byte buffer.
    
    i - Index into byte buffer.
    
    endianess - true indicates big endian byte order, false indicates little endian.
  - setBufferString
```
public final void setBufferString(byte[] buffer,
                                  java.lang.String str,
                                  int i)
```
    Sets byte buffer with int.
    
    Parameters:
    
    buffer - Byte buffers where data is to be stored.
    
    str - String containing integer data which is broken down in bytes and stored in the byte buffer.
    
    i - Index into byte buffer.
  - setProgressBarVisible
```
public void setProgressBarVisible(boolean flag)
```
    Sets whether or not the progress bar should be visible.
    
    Parameters:
    
    flag - true if should be visible, false if not visible.
  - setTagBuffer
```
public final void setTagBuffer(byte[] buffer)
```
    DOCUMENT ME!
    
    Parameters:
    
    buffer - byte[]
  - writeDouble
```
public final void writeDouble(double data,
                              boolean endianess)
                       throws java.io.IOException
```
    Writes a double as eight bytes to a file.
    
    Parameters:
    
    data - Data to be written to file.
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeFloat
```
public final void writeFloat(float data,
                             boolean endianess)
                      throws java.io.IOException
```
    Writes a float as four bytes to a file.
    
    Parameters:
    
    data - Data to be written to file.
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeInt
```
public final void writeInt(int data,
                           boolean endianess)
                    throws java.io.IOException
```
    Writes an int as four bytes to a file.
    
    Parameters:
    
    data - Data to be written to file.
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeLong
```
public final void writeLong(long data,
                            boolean endianess)
                     throws java.io.IOException
```
    Writes a long as eight bytes to a file.
    
    Parameters:
    
    data - Data to be written to file.
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeShort
```
public final void writeShort(short data,
                             boolean endianess)
                      throws java.io.IOException
```
    Writes a short as two bytes to a file.
    
    Parameters:
    
    data - Data to be written to file.
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeUnsignedShort
```
public final void writeUnsignedShort(short data,
                                     boolean endianess)
                              throws java.io.IOException
```
    Writes an unsigned short as two bytes to a file.
    
    Parameters:
    
    data - Data to be written to file.
    
    endianess - true indicates big endian byte order, false indicates little endian.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeByte
```
public final void writeByte(byte data)
                     throws java.io.IOException
```
    Writes a byte to a file.
    
    Parameters:
    
    data - Data to be written to file.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - getFilePointer
```
protected final int getFilePointer()
```
    Gets the file/buffer pointer and returns it.
    
    Returns:
    
    the file/buffer pointer
  - getFileLength
```
protected final long getFileLength()
```
  - read
```
protected final void read(byte[] byteBuffer)
```
    Reads into the supplied buffer data from the DICOM tag buffer.
    
    Parameters:
    
    byteBuffer - byte[]
  - seek
```
protected final void seek(int value)
```
    Seeks to a point in the buffer.
    
    Parameters:
    
    value - indicates the new buffer pointer value
  - skipBytes
```
protected final void skipBytes(int value)
```
    Skips to a new point in the buffer.
    
    Parameters:
    
    value - number of bytes to skip
  - isHeaderOnlyRead
```
public boolean isHeaderOnlyRead()
```
    Returns whether this Dicom read is only interested in the header tags and not the image data (if it exists). Used by dcm recv and in cases like spectroscopy where there isn't a true image, but some tags may contain data that triggers the image search parameters ("7F" hex value, etc.).
    
    Returns:
    
    Whether the image data should be searched for or otherwise read.
  - setHeaderOnlyRead
```
public void setHeaderOnlyRead(boolean isHeaderOnly)
```
    Sets whether this Dicom read is only interested in the header tags and not the image data (if it exists). Used by dcm recv and in cases like spectroscopy where there isn't a true image, but some tags may contain data that triggers the image search parameters ("7F" hex value, etc.).
    
    Parameters:
    
    isHeaderOnly - Whether we are only interested in reading the tags from the header, not the image data.

Class FileDicomBase

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

LITTLE_ENDIAN

BIG_ENDIAN

READ

READ_WRITE

BUFFER_SIZE

byteBuffer

byteBuffer2

byteBuffer4

byteBuffer8

fLength

pBarVisible

progressBar

raFile

tagBuffer

b1

b2

b3

b4

b5

b6

b7

b8

bPtr

notDir

numEmbeddedImages

isDicomRecv

imageGroupWord

imageElementWord

imageElementLength

imageTagLocation

TAMAR

SPECTROSCOPY

Constructor Detail

FileDicomBase

Method Detail

finalize

getByte

getSignedByte

getDouble

getFloat

getInt

getLong

getSignedShort

getString

getStringFromFile

getUInt

getUnsignedShort

initializeFullRead

isProgressBarVisible

searchForImageTag

loadTagBuffer

locateImageTag

setBufferFloat

setBufferInt

setBufferLong

setBufferShort

setBufferString

setProgressBarVisible

setTagBuffer

writeDouble

writeFloat

writeInt

writeLong

writeShort

writeUnsignedShort

writeByte

getFilePointer

getFileLength

read

seek

skipBytes

isHeaderOnlyRead

setHeaderOnlyRead