loci.formats
Class GatanReader

java.lang.Object
  loci.formats.FormatHandler
      loci.formats.FormatReader
          loci.formats.GatanReader

public class GatanReader

extends FormatReader

GatanReader is the file format reader for Gatan files.

Field Summary

protected int[]	dims Dimensions -- width, height, bytes per pixel
protected RandomAccessFile	in Current file.
protected boolean	littleEndian Flag indicating whether current file is little endian.
protected byte[]	pixelData Array of pixel bytes.
protected int	pixelDataNum

Fields inherited from class loci.formats.FormatReader

DEBUG, DEBUG_LEVEL, metadata, ome

Fields inherited from class loci.formats.FormatHandler

chooser, currentId, filters, format, suffixes

Constructor Summary

GatanReader()
Constructs a new Gatan reader.

Method Summary

void	close() Closes any open files.
int	getImageCount(String id) Determines the number of images in the given Gatan file.
protected void	initFile(String id) Initializes the given Gatan file.
boolean	isThisType(byte[] block) Checks if the given block is a valid header for a Gatan file.
static void	main(String[] args)
BufferedImage	open(String id, int no) Obtains the specified image from the given Gatan file.
void	parseTags(int numTags, String parent) Parses Gatan DM3 tags.

Methods inherited from class loci.formats.FormatReader

createFilters, getMetadata, getMetadataValue, getOMENode, open, testRead

Methods inherited from class loci.formats.FormatHandler

getFileChooser, getFileFilters, getFormat, getSuffixes, isThisType

Methods inherited from class java.lang.Object

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

Field Detail

in

protected RandomAccessFile in

Current file.

littleEndian

protected boolean littleEndian

Flag indicating whether current file is little endian.

pixelData

protected byte[] pixelData

Array of pixel bytes.

dims

protected int[] dims

Dimensions -- width, height, bytes per pixel

pixelDataNum

protected int pixelDataNum

Constructor Detail

GatanReader

public GatanReader()

Constructs a new Gatan reader.

Method Detail

isThisType

public boolean isThisType(byte[] block)

Checks if the given block is a valid header for a Gatan file.

Specified by:

isThisType in class FormatReader

getImageCount

public int getImageCount(String id)
                  throws FormatException,
                         IOException

Determines the number of images in the given Gatan file.

Specified by:

getImageCount in class FormatReader

Throws:

FormatException

IOException

open

public BufferedImage open(String id,
                          int no)
                   throws FormatException,
                          IOException

Obtains the specified image from the given Gatan file.

Specified by:

open in class FormatReader

Throws:

FormatException

IOException

close

public void close()
           throws FormatException,
                  IOException

Closes any open files.

Specified by:

close in class FormatReader

Throws:

FormatException

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
                        IOException

Initializes the given Gatan file.

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

parseTags

public void parseTags(int numTags,
                      String parent)
               throws IOException

Parses Gatan DM3 tags. Information on the DM3 structure found at: http://rsb.info.nih.gov/ij/plugins/DM3Format.gj.html and http://www-hrem.msm.cam.ac.uk/~cbb/info/dmformat/

Throws:

IOException

main

public static void main(String[] args)
                 throws FormatException,
                        IOException

Throws:

FormatException

IOException