JPEG2000MetadataParser (Bio-Formats API)

java.lang.Object
- loci.formats.in.JPEG2000MetadataParser

public class JPEG2000MetadataParser
extends Object

A parser for JPEG 2000 metadata.

Field Summary

Fields
Modifier and Type	Field and Description
`private long`	`codestreamOffset` Offset to first contiguous codestream.
`private Integer`	`codestreamPixelType` Pixel type as specified in the JPEG 2000 codestream..
`private Short`	`codestreamSizeC` Number of channels the image as specified in the JPEG 2000 codestream.
`private Integer`	`codestreamSizeX` Width of the image as specified in the JPEG 2000 codestream.
`private Integer`	`codestreamSizeY` Height of the image as specified in the JPEG 2000 codestream.
`private ArrayList<String>`	`comments` List of comments stored in the file.
`private Integer`	`headerPixelType` Pixel type as specified in the header.
`private Short`	`headerSizeC` Number of channels the image has as specified in the header.
`private Integer`	`headerSizeX` Width of the image as specified in the header.
`private Integer`	`headerSizeY` Height of the image as specified in the header.
`private loci.common.RandomAccessInputStream`	`in` Stream that we're parsing metadata from.
`private boolean`	`isRawCodestream` Whether or not the codestream is raw and not JP2 boxed.
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`private int[][]`	`lut` Color lookup table stored in the file.
`private long`	`maximumReadOffset` Maximum read offset within in the stream.
`private Integer`	`resolutionLevels` Number of JPEG 2000 resolution levels the file has.

Constructor Summary

Constructors
Constructor and Description
`JPEG2000MetadataParser(loci.common.RandomAccessInputStream in)` Constructs a new JPEG2000MetadataParser.
`JPEG2000MetadataParser(loci.common.RandomAccessInputStream in, long maximumReadOffset)` Constructs a new JPEG2000MetadataParser.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private int`	`convertPixelType(int type)`
`long`	`getCodestreamOffset()` Retrieves the offset to the first contiguous codestream.
`Integer`	`getCodestreamPixelType()` Returns the pixel type as specified in the header.
`Short`	`getCodestreamSizeC()` Returns the number of channels the image has as specified in the header.
`Integer`	`getCodestreamSizeX()` Returns the width of the image as specified in the header.
`Integer`	`getCodestreamSizeY()` Returns the height of the image as specified in the header.
`ArrayList<String>`	`getComments()` Retrieves the list of comments stored in the file.
`Integer`	`getHeaderPixelType()` Returns the pixel type as specified in the header.
`Short`	`getHeaderSizeC()` Returns the number of channels the image has as specified in the header.
`Integer`	`getHeaderSizeX()` Returns the width of the image as specified in the header.
`Integer`	`getHeaderSizeY()` Returns the height of the image as specified in the header.
`int[][]`	`getLookupTable()` Returns the color lookup table stored in the file, or null if a lookup table is not present.
`Integer`	`getResolutionLevels()` Returns the number of resolution levels the file JPEG 2000 data has.
`boolean`	`isRawCodestream()` Whether or not the codestream is raw and not JP2 boxed.
`private void`	`parseBoxes()` Parses the JPEG 2000 JP2 metadata boxes.
`private void`	`parseContiguousCodestream(long length)` Parses the JPEG 2000 codestream metadata.

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

- Field Detail
  - LOGGER
```
private static final org.slf4j.Logger LOGGER
```
    Logger for this class.
  - in
```
private loci.common.RandomAccessInputStream in
```
    Stream that we're parsing metadata from.
  - codestreamOffset
```
private long codestreamOffset
```
    Offset to first contiguous codestream.
  - maximumReadOffset
```
private long maximumReadOffset
```
    Maximum read offset within in the stream.
  - headerSizeX
```
private Integer headerSizeX
```
    Width of the image as specified in the header.
  - headerSizeY
```
private Integer headerSizeY
```
    Height of the image as specified in the header.
  - headerSizeC
```
private Short headerSizeC
```
    Number of channels the image has as specified in the header.
  - headerPixelType
```
private Integer headerPixelType
```
    Pixel type as specified in the header.
  - codestreamSizeX
```
private Integer codestreamSizeX
```
    Width of the image as specified in the JPEG 2000 codestream.
  - codestreamSizeY
```
private Integer codestreamSizeY
```
    Height of the image as specified in the JPEG 2000 codestream.
  - codestreamSizeC
```
private Short codestreamSizeC
```
    Number of channels the image as specified in the JPEG 2000 codestream.
  - codestreamPixelType
```
private Integer codestreamPixelType
```
    Pixel type as specified in the JPEG 2000 codestream..
  - isRawCodestream
```
private boolean isRawCodestream
```
    Whether or not the codestream is raw and not JP2 boxed.
  - resolutionLevels
```
private Integer resolutionLevels
```
    Number of JPEG 2000 resolution levels the file has.
  - lut
```
private int[][] lut
```
    Color lookup table stored in the file.
  - comments
```
private ArrayList<String> comments
```
    List of comments stored in the file.
- Constructor Detail
  - JPEG2000MetadataParser
```
public JPEG2000MetadataParser(loci.common.RandomAccessInputStream in)
                       throws IOException
```
    Constructs a new JPEG2000MetadataParser.
    
    Parameters:
    
    in - Stream to parse JPEG 2000 metadata from.
    
    Throws:
    
    IOException - Thrown if there is an error reading from the file.
  - JPEG2000MetadataParser
```
public JPEG2000MetadataParser(loci.common.RandomAccessInputStream in,
                              long maximumReadOffset)
                       throws IOException
```
    Constructs a new JPEG2000MetadataParser.
    
    Parameters:
    
    in - Stream to parse JPEG 2000 metadata from.
    
    maximumReadOffset - Maximum read offset within the stream when parsing.
    
    Throws:
    
    IOException - Thrown if there is an error reading from the file.
- Method Detail
  - getCodestreamOffset
```
public long getCodestreamOffset()
```
    Retrieves the offset to the first contiguous codestream.
  - getComments
```
public ArrayList<String> getComments()
```
    Retrieves the list of comments stored in the file.
  - parseBoxes
```
private void parseBoxes()
                 throws IOException
```
    Parses the JPEG 2000 JP2 metadata boxes.
    
    Throws:
    
    IOException - Thrown if there is an error reading from the file.
  - parseContiguousCodestream
```
private void parseContiguousCodestream(long length)
                                throws IOException
```
    Parses the JPEG 2000 codestream metadata.
    
    Parameters:
    
    length - Total length of the codestream block.
    
    Throws:
    
    IOException - Thrown if there is an error reading from the file.
  - isRawCodestream
```
public boolean isRawCodestream()
```
    Whether or not the codestream is raw and not JP2 boxed.
    
    Returns:
    
    true if the codestream is raw and false otherwise.
  - getResolutionLevels
```
public Integer getResolutionLevels()
```
    Returns the number of resolution levels the file JPEG 2000 data has.
    
    Returns:
    
    The number of resolution levels or null if the number cannot be parsed.
  - getHeaderSizeX
```
public Integer getHeaderSizeX()
```
    Returns the width of the image as specified in the header.
    
    Returns:
    
    See above.
  - getHeaderSizeY
```
public Integer getHeaderSizeY()
```
    Returns the height of the image as specified in the header.
    
    Returns:
    
    See above.
  - getHeaderSizeC
```
public Short getHeaderSizeC()
```
    Returns the number of channels the image has as specified in the header.
    
    Returns:
    
    See above.
  - getHeaderPixelType
```
public Integer getHeaderPixelType()
```
    Returns the pixel type as specified in the header.
    
    Returns:
    
    See above.
  - getCodestreamSizeX
```
public Integer getCodestreamSizeX()
```
    Returns the width of the image as specified in the header.
    
    Returns:
    
    See above.
  - getCodestreamSizeY
```
public Integer getCodestreamSizeY()
```
    Returns the height of the image as specified in the header.
    
    Returns:
    
    See above.
  - getCodestreamSizeC
```
public Short getCodestreamSizeC()
```
    Returns the number of channels the image has as specified in the header.
    
    Returns:
    
    See above.
  - getCodestreamPixelType
```
public Integer getCodestreamPixelType()
```
    Returns the pixel type as specified in the header.
    
    Returns:
    
    See above.
  - getLookupTable
```
public int[][] getLookupTable()
```
    Returns the color lookup table stored in the file, or null if a lookup table is not present.
    
    Returns:
    
    See above.
  - convertPixelType
```
private int convertPixelType(int type)
```

Class JPEG2000MetadataParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

LOGGER

in

codestreamOffset

maximumReadOffset

headerSizeX

headerSizeY

headerSizeC

headerPixelType

codestreamSizeX

codestreamSizeY

codestreamSizeC

codestreamPixelType

isRawCodestream

resolutionLevels

lut

comments

Constructor Detail

JPEG2000MetadataParser

JPEG2000MetadataParser

Method Detail

getCodestreamOffset

getComments

parseBoxes

parseContiguousCodestream

isRawCodestream

getResolutionLevels

getHeaderSizeX

getHeaderSizeY

getHeaderSizeC

getHeaderPixelType

getCodestreamSizeX

getCodestreamSizeY

getCodestreamSizeC

getCodestreamPixelType

getLookupTable

convertPixelType