loci.formats.in

Class SPEReader.SpeHeader

java.lang.Object

loci.formats.in.SPEReader.SpeHeader

Enclosing class:

SPEReader

private class SPEReader.SpeHeader
extends java.lang.Object

SpeHeader holds a byte array containing the SPE binary data header along with associated methods for reading SPE Header Entry values in various formats

Field Summary

Fields

Modifier and Type	Field and Description
private byte[]	header
private static int	headerSize

Constructor Summary

Constructors

Constructor and Description
SpeHeader(byte[] header) Constructor for SpeHeader

Method Summary

Modifier and Type	Method and Description
private int	getByte(int index) Private method used to retrieve a Byte value from the SPE header
int	getByte(SPEReader.SpeHeaderEntry entry) Method used to retrieve data values for Byte entries into the SPE header table
byte[]	getHeader()
int	getHeaderSize()
private int	getInt(int index) Private method used to retrieve an Integer value from the SPE header
int	getInt(SPEReader.SpeHeaderEntry entry) Method used to retrieve data values for Integer entries into the SPE header table
int[]	getIntArray(SPEReader.SpeHeaderEntry entry) Method used to retrieve data values for Integer Array entries into the SPE header table
private long	getLong(int index) Private method used to retrieve a Long value from the SPE header
long	getLong(SPEReader.SpeHeaderEntry entry) Method used to retrieve data values for Long enteries into the SPE header table
long[]	getLongArray(SPEReader.SpeHeaderEntry entry) Method used to retrieve data values for Long Array entries into the SPE header table
SPEReader.SpeROI[]	getROIs() Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table
private int	getShort(int index) Private method used to retrieve a Short value from the SPE header
int	getShort(SPEReader.SpeHeaderEntry entry) Method used to retrieve data values for Short entries into the SPE header table
int[]	getShortArray(SPEReader.SpeHeaderEntry entry) Method used to retrieve data values for Short Array entries into the SPE header table
int	getStackSize() Method used to determined the stack size of the SPE file.
private java.lang.String	getString(int index, int length) Private method used to retrieve a String value from the SPE header
java.lang.String	getString(SPEReader.SpeHeaderEntry entry) Method used to retrieve data values for String entries into the SPE header table
private boolean	setByte(int index, int value) Private method used to set a Byte value in the SPE header
void	setHeader(byte[] header)
private void	setInt(int index, int value) Private method used to set an Integer value in the SPE header
private void	setLong(int index, int value) Private method used to set a Long value in the SPE header
private boolean	setShort(int index, int value) Private method used to set a Short value in the SPE header
private void	setString(int index, java.lang.String string) Private method used to set a String value in the SPE header

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

headerSize

private static final int headerSize

See Also:

Constant Field Values

header

private byte[] header

Constructor Detail

SpeHeader

public SpeHeader(byte[] header)

Constructor for SpeHeader

Parameters:

header - The binary data header read from the associated SPE file

Method Detail

getHeader

public byte[] getHeader()

Returns:

The raw binary data header

setHeader

public void setHeader(byte[] header)

Parameters:

header - The binary data header to be used

getHeaderSize

public int getHeaderSize()

Returns:

The expected size of the SPE data header

getByte

public int getByte(SPEReader.SpeHeaderEntry entry)
            throws FormatException

Method used to retrieve data values for Byte entries into the SPE header table

Parameters:

entry - The header entry to read

Returns:

The value read at the given header entry location

Throws:

FormatException - Thrown if the value at the given header entry location is not of type Byte

getByte

private int getByte(int index)

Private method used to retrieve a Byte value from the SPE header

Parameters:

index - The index of the expected value in the header array

Returns:

The value read at the given header entry location

setByte

private boolean setByte(int index,
                        int value)

Private method used to set a Byte value in the SPE header

Parameters:

index - The starting index in the header array in which to write the value

value - The Byte value to be written to the SPE header

getShort

public int getShort(SPEReader.SpeHeaderEntry entry)
             throws FormatException

Method used to retrieve data values for Short entries into the SPE header table

Parameters:

entry - The header entry to read

Returns:

The value read at the given header entry location

Throws:

FormatException - Thrown if the value at the given header entry location is not of type Short

getShort

private int getShort(int index)

Private method used to retrieve a Short value from the SPE header

Parameters:

index - The index of the expected value in the header array

Returns:

The value read at the given header entry location

setShort

private boolean setShort(int index,
                         int value)

Private method used to set a Short value in the SPE header

Parameters:

index - The starting index in the header array in which to write the value

value - The Short value to be written to the SPE header

getInt

public int getInt(SPEReader.SpeHeaderEntry entry)
           throws FormatException

Method used to retrieve data values for Integer entries into the SPE header table

Parameters:

entry - The header entry to read

Returns:

The value read at the given header entry location

Throws:

FormatException - Thrown if the value at the given header entry location is not of type Integer

getInt

private int getInt(int index)

Private method used to retrieve an Integer value from the SPE header

Parameters:

index - The index of the expected value in the header array

Returns:

The value read at the given header entry location

setInt

private void setInt(int index,
                    int value)

Private method used to set an Integer value in the SPE header

Parameters:

index - The starting index in the header array in which to write the value

value - The Integer value to be written to the SPE header

getLong

public long getLong(SPEReader.SpeHeaderEntry entry)
             throws FormatException

Method used to retrieve data values for Long enteries into the SPE header table

Parameters:

entry - The header entry to read

Returns:

The value read at the given header entry location

Throws:

FormatException - Thrown if the value at the given header entry location is not of type Long

getLong

private long getLong(int index)

Private method used to retrieve a Long value from the SPE header

Parameters:

index - The index of the expected value in the header array

Returns:

The value read at the given header entry location

setLong

private void setLong(int index,
                     int value)

Private method used to set a Long value in the SPE header

Parameters:

index - The starting index in the header array in which to write the value

value - The Long value to be written to the SPE header

getString

public java.lang.String getString(SPEReader.SpeHeaderEntry entry)
                           throws FormatException,
                                  java.io.UnsupportedEncodingException

Method used to retrieve data values for String entries into the SPE header table

Parameters:

entry - The header entry to read

Returns:

The value read at the given header entry location

Throws:

FormatException - Thrown if the value at the given header entry location is not of type String or if the length of the String cannot be determined

java.io.UnsupportedEncodingException - Thrown if the String value found in the header location is not in UTF-8 encoding

getString

private java.lang.String getString(int index,
                                   int length)
                            throws java.io.UnsupportedEncodingException

Private method used to retrieve a String value from the SPE header

Parameters:

index - The starting index of the expected value in the header array

length - The length of the String to be read from the array

Returns:

The String value read at the given header entry location

Throws:

java.io.UnsupportedEncodingException - Thrown if the String read at the given location is not in UTF-8 encoding

setString

private void setString(int index,
                       java.lang.String string)

Private method used to set a String value in the SPE header

Parameters:

index - The starting index in the header array in which to write the String

string - The String to be written to the SPE header

getIntArray

public int[] getIntArray(SPEReader.SpeHeaderEntry entry)
                  throws FormatException

Method used to retrieve data values for Integer Array entries into the SPE header table

Parameters:

entry - The header entry to read

Returns:

The array of Integer values read at the given header entry location. Returns null if all values read are 0.

Throws:

FormatException - Thrown if the value at the given header entry location is not of type Integer Array

getShortArray

public int[] getShortArray(SPEReader.SpeHeaderEntry entry)
                    throws FormatException

Method used to retrieve data values for Short Array entries into the SPE header table

Parameters:

entry - The header entry to read

Returns:

The array of Short values read at the given header entry location. Returns null if all values read are 0.

Throws:

FormatException - Thrown if the value at the given header entry location is not of type Short Array

getLongArray

public long[] getLongArray(SPEReader.SpeHeaderEntry entry)
                    throws FormatException

Method used to retrieve data values for Long Array entries into the SPE header table

Parameters:

entry - The header entry to read

Returns:

The array of Long values read at the given header entry location. Returns null if all values read are 0.

Throws:

FormatException - Thrown if the value at the given header entry location is not of type Long Array

getROIs

public SPEReader.SpeROI[] getROIs()
                           throws FormatException

Method used to read and return meta data for upto 10 rectangular ROI's stored in the SPE header table

Returns:

An array of SpeROI objects, each containing meta data for a single ROI

Throws:

FormatException - Thrown if any of the values read during the call are not in the correct format

getStackSize

public int getStackSize()
                 throws FormatException

Method used to determined the stack size of the SPE file. This should usually be the value in the Number of Frames header entry, but other older entry values are also still supported if still in use.

Returns:

The stack size of the SPE file

Throws:

FormatException - Thrown if any of the values read during the call are not in the correct format