ome.io.nio
Class DeltaVisionHeader

java.lang.Object
  extended by ome.io.nio.DeltaVisionHeader

public class DeltaVisionHeader
extends Object

Temporary class implementation of an image file header for the server-side import of a DeltaVision file.

Copyright 2007 Glencoe Software Inc. All rights reserved. Use is subject to license terms supplied in LICENSE.txt

Since:
3.0
Version:
$Revision$
Author:
David L. Whitehurst      david@glencoesoftware.com
See Also:
DeltaVision

Field Summary
static int PIXEL_TYPE_2BYTE_COMPLEX
          Pixels are of type 4 byte, complex, composed of two 2 byte signed integers.
static int PIXEL_TYPE_4BYTE_COMPLEX
          Pixels are of type 8 byte, complex, composed of two 4 byte floating-point numbers.
static int PIXEL_TYPE_BYTE
          Pixels are of type 1 byte, unsigned integer.
static int PIXEL_TYPE_FLOAT
          Pixels are of type 4 byte, floating-point.
static int PIXEL_TYPE_SIGNED_SHORT
          Pixels are of type 2 byte, unsigned integer.
static int PIXEL_TYPE_UNSIGNED_SHORT
          Pixels are of type 2 byte, signed integer.
static short WZT_SEQUENCE
          The most common sequence of images acquired from a microscope.
static short ZTW_SEQUENCE
          A common sequence of processed images.
static short ZWT_SEQUENCE
          A new image sequence, as of DeltaVision version 2.10.
 
Constructor Summary
DeltaVisionHeader(ByteBuffer data, boolean endian)
          Constructor
 
Method Summary
 int getBytesPerPixel()
          Returns the number of bytes per pixel.
 int getExtendedHeaderSize()
          Returns the size in bytes of the extended header
 int getImageCount()
          Returns the number of plane images
 int getImageTypeCode()
          Returns the numeric image type
 ome.model.enums.PixelsType getOmeroPixelType()
          Returns a new OMERO pixels type object which corresponds to the DeltaVision pixels type.
 int getPixelBeginOffset()
          Returns the number of bytes to the beginning of the Pixels
 int getPixelType()
          Returns a numeric value for the pixel type
 short getSequence()
          Returns a numeric value that represents the Z,C, and T ordering
 int getSizeC()
          Returns the number of channels
 int getSizeT()
          Returns the number of timepoints taken
 int getSizeX()
          Returns the width (no. of X pixels) of a single plane image
 int getSizeY()
          Returns the height (no. of Y pixels) of a single plane image
 int getSizeZ()
          Returns the number of focal points (Z-dimension) taken
 boolean isNative()
          Returns true if the DeltaVision file is of native endianness.
 void setSequence(short sequence)
          Sets the sequence of the file.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

ZTW_SEQUENCE

public static final short ZTW_SEQUENCE
A common sequence of processed images. Sometimes referred to as "interleaved".

See Also:
Constant Field Values

WZT_SEQUENCE

public static final short WZT_SEQUENCE
The most common sequence of images acquired from a microscope. Sometimes referred to as "non-interleaved" since the wavelengths are interleaved with the Z sections.

See Also:
Constant Field Values

ZWT_SEQUENCE

public static final short ZWT_SEQUENCE
A new image sequence, as of DeltaVision version 2.10. Although not widely used, ZWT will find uses with certain processing algorithms and data collection schemes.

See Also:
Constant Field Values

PIXEL_TYPE_BYTE

public static final int PIXEL_TYPE_BYTE
Pixels are of type 1 byte, unsigned integer.

See Also:
Constant Field Values

PIXEL_TYPE_SIGNED_SHORT

public static final int PIXEL_TYPE_SIGNED_SHORT
Pixels are of type 2 byte, unsigned integer.

See Also:
Constant Field Values

PIXEL_TYPE_FLOAT

public static final int PIXEL_TYPE_FLOAT
Pixels are of type 4 byte, floating-point.

See Also:
Constant Field Values

PIXEL_TYPE_2BYTE_COMPLEX

public static final int PIXEL_TYPE_2BYTE_COMPLEX
Pixels are of type 4 byte, complex, composed of two 2 byte signed integers.

See Also:
Constant Field Values

PIXEL_TYPE_4BYTE_COMPLEX

public static final int PIXEL_TYPE_4BYTE_COMPLEX
Pixels are of type 8 byte, complex, composed of two 4 byte floating-point numbers.

See Also:
Constant Field Values

PIXEL_TYPE_UNSIGNED_SHORT

public static final int PIXEL_TYPE_UNSIGNED_SHORT
Pixels are of type 2 byte, signed integer.

See Also:
Constant Field Values
Constructor Detail

DeltaVisionHeader

public DeltaVisionHeader(ByteBuffer data,
                         boolean endian)
Constructor

Parameters:
data -
endian -
Method Detail

getSizeC

public int getSizeC()
Returns the number of channels

Returns:

getImageCount

public int getImageCount()
Returns the number of plane images

Returns:
int

getImageTypeCode

public int getImageTypeCode()
Returns the numeric image type

Returns:

getPixelBeginOffset

public int getPixelBeginOffset()
Returns the number of bytes to the beginning of the Pixels

Returns:

getExtendedHeaderSize

public int getExtendedHeaderSize()
Returns the size in bytes of the extended header

Returns:

getPixelType

public int getPixelType()
Returns a numeric value for the pixel type

Returns:

setSequence

public void setSequence(short sequence)
Sets the sequence of the file. Should be used for testing ONLY.

Parameters:
sequence -

getSequence

public short getSequence()
Returns a numeric value that represents the Z,C, and T ordering

Returns:

getSizeT

public int getSizeT()
Returns the number of timepoints taken

Returns:

getSizeX

public int getSizeX()
Returns the width (no. of X pixels) of a single plane image

Returns:

getSizeY

public int getSizeY()
Returns the height (no. of Y pixels) of a single plane image

Returns:

getSizeZ

public int getSizeZ()
Returns the number of focal points (Z-dimension) taken

Returns:

getBytesPerPixel

public int getBytesPerPixel()
Returns the number of bytes per pixel.

Returns:
See above.

getOmeroPixelType

public ome.model.enums.PixelsType getOmeroPixelType()
Returns a new OMERO pixels type object which corresponds to the DeltaVision pixels type.

Returns:

isNative

public boolean isNative()
Returns true if the DeltaVision file is of native endianness.

Returns:
See above.
Throws:
RuntimeException - if there is an error with the DeltaVision file's DVID.


OmeroJava Api

Version: Beta4.2.1-r8614-Beta4.2-b41

Copyright © 2009 The University of Dundee. All Rights Reserved.