fr.igred.omero.core

Class PixelsWrapper

java.lang.Object

fr.igred.omero.ObjectWrapper<PixelsData>

fr.igred.omero.core.PixelsWrapper

All Implemented Interfaces:

Pixels, RemoteObject

public class PixelsWrapper
extends ObjectWrapper<PixelsData>
implements Pixels

Class containing a PixelData object.

Wraps function calls to the PixelData contained.

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_DIST Size of tiles when retrieving pixels

Fields inherited from class fr.igred.omero.ObjectWrapper

data

Constructor Summary

Constructors

Constructor and Description
PixelsWrapper(PixelsData pixels) Constructor of the PixelsWrapper class

Method Summary

Modifier and Type	Method and Description
double[][][][][]	getAllPixels(ConnectionHandler client, int[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds) Returns an array containing the value for each voxel corresponding to the bounds
Time	getMeanExposureTime(int channel) Computes the mean exposure time for a given channel from the planes exposureTime.
Time	getMeanTimeInterval() Computes the mean time interval from the planes deltaTs.
Length	getPixelSizeX() Gets the size of a single image pixel on the X axis.
Length	getPixelSizeY() Gets the size of a single image pixel on the Y axis.
Length	getPixelSizeZ() Gets the size of a single image pixel on the Z axis.
String	getPixelType() Gets the pixel type.
List<PlaneInfo>	getPlanesInfo() Retrieves the planes information (which need to be loaded first).
Length	getPositionX() Retrieves the X stage position.
Length	getPositionY() Retrieves the Y stage position.
Length	getPositionZ() Retrieves the Z stage position.
byte[][][][]	getRawPixels(ConnectionHandler client, int[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds, int bpp) Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
int	getSizeC() Gets the size of the image on the C axis
int	getSizeT() Gets the size of the image on the T axis
int	getSizeX() Gets the size of the image on the X axis
int	getSizeY() Gets the size of the image on the Y axis
int	getSizeZ() Gets the size of the image on the Z axis
Time	getTimeIncrement() Gets the time increment between time points.
void	loadPlanesInfo(Browser browser) Loads the planes information.

Methods inherited from class fr.igred.omero.ObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, getCreated, getGroupId, getId, getOwner, getUpdated, saveAndUpdate, toString, wrap, wrap

Methods inherited from class java.lang.Object

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

Methods inherited from interface fr.igred.omero.core.Pixels

asDataObject, getAllPixels, getRawPixels

Methods inherited from interface fr.igred.omero.RemoteObject

canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, distinct, flatten, getCreated, getElementsOf, getGroupId, getId, getOwner, getUpdated, saveAndUpdate

Field Detail

MAX_DIST

public static final int MAX_DIST

Size of tiles when retrieving pixels

See Also:

Constant Field Values

Constructor Detail

PixelsWrapper

public PixelsWrapper(PixelsData pixels)

Constructor of the PixelsWrapper class

Parameters:

pixels - The PixelData to be wrap.

Method Detail

loadPlanesInfo

public void loadPlanesInfo(Browser browser)
                    throws ServiceException,
                           AccessException,
                           ExecutionException

Loads the planes information.

Specified by:

loadPlanesInfo in interface Pixels

Parameters:

browser - The data browser.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getPlanesInfo

public List<PlaneInfo> getPlanesInfo()

Retrieves the planes information (which need to be loaded first).

Specified by:

getPlanesInfo in interface Pixels

Returns:

See above.

getPixelType

public String getPixelType()

Gets the pixel type.

Specified by:

getPixelType in interface Pixels

Returns:

the pixel type.

getPixelSizeX

public Length getPixelSizeX()

Gets the size of a single image pixel on the X axis.

Specified by:

getPixelSizeX in interface Pixels

Returns:

Size of a pixel on the X axis.

getPixelSizeY

public Length getPixelSizeY()

Gets the size of a single image pixel on the Y axis.

Specified by:

getPixelSizeY in interface Pixels

Returns:

Size of a pixel on the Y axis.

getPixelSizeZ

public Length getPixelSizeZ()

Gets the size of a single image pixel on the Z axis.

Specified by:

getPixelSizeZ in interface Pixels

Returns:

Size of a pixel on the Z axis.

getTimeIncrement

public Time getTimeIncrement()

Gets the time increment between time points.

Specified by:

getTimeIncrement in interface Pixels

Returns:

Time increment between time points.

getMeanTimeInterval

public Time getMeanTimeInterval()

Computes the mean time interval from the planes deltaTs.

Planes information needs to be loaded first.

Specified by:

getMeanTimeInterval in interface Pixels

Returns:

See above.

getMeanExposureTime

public Time getMeanExposureTime(int channel)

Computes the mean exposure time for a given channel from the planes exposureTime.

Planes information needs to be loaded first.

Specified by:

getMeanExposureTime in interface Pixels

Parameters:

channel - The channel index.

Returns:

See above.

getPositionX

public Length getPositionX()

Retrieves the X stage position.

Planes information needs to be loaded first.

Specified by:

getPositionX in interface Pixels

Returns:

See above.

getPositionY

public Length getPositionY()

Retrieves the Y stage position.

Planes information needs to be loaded first.

Specified by:

getPositionY in interface Pixels

Returns:

See above.

getPositionZ

public Length getPositionZ()

Retrieves the Z stage position.

Planes information needs to be loaded first.

Specified by:

getPositionZ in interface Pixels

Returns:

See above.

getSizeX

public int getSizeX()

Gets the size of the image on the X axis

Specified by:

getSizeX in interface Pixels

Returns:

Size of the image on the X axis.

getSizeY

public int getSizeY()

Gets the size of the image on the Y axis

Specified by:

getSizeY in interface Pixels

Returns:

Size of the image on the Y axis.

getSizeZ

public int getSizeZ()

Gets the size of the image on the Z axis

Specified by:

getSizeZ in interface Pixels

Returns:

Size of the image on the Z axis.

getSizeC

public int getSizeC()

Gets the size of the image on the C axis

Specified by:

getSizeC in interface Pixels

Returns:

Size of the image on the C axis.

getSizeT

public int getSizeT()

Gets the size of the image on the T axis

Specified by:

getSizeT in interface Pixels

Returns:

Size of the image on the T axis.

getAllPixels

public double[][][][][] getAllPixels(ConnectionHandler client,
                                     int[] xBounds,
                                     int[] yBounds,
                                     int[] cBounds,
                                     int[] zBounds,
                                     int[] tBounds)
                              throws AccessException,
                                     ExecutionException

Returns an array containing the value for each voxel corresponding to the bounds

Specified by:

getAllPixels in interface Pixels

Parameters:

client - The client handling the connection.

xBounds - Array containing the X bounds from which the pixels should be retrieved.

yBounds - Array containing the Y bounds from which the pixels should be retrieved.

cBounds - Array containing the C bounds from which the pixels should be retrieved.

zBounds - Array containing the Z bounds from which the pixels should be retrieved.

tBounds - Array containing the T bounds from which the pixels should be retrieved.

Returns:

Array containing the value for each voxel of the image.

Throws:

AccessException - If an error occurs while retrieving the plane data from the pixels source.

ExecutionException - A Facility can't be retrieved or instantiated.

getRawPixels

public byte[][][][] getRawPixels(ConnectionHandler client,
                                 int[] xBounds,
                                 int[] yBounds,
                                 int[] cBounds,
                                 int[] zBounds,
                                 int[] tBounds,
                                 int bpp)
                          throws ExecutionException,
                                 AccessException

Returns an array containing the raw values for each voxel for each plane corresponding to the bounds

Specified by:

getRawPixels in interface Pixels

Parameters:

client - The client handling the connection.

xBounds - Array containing the X bounds from which the pixels should be retrieved.

yBounds - Array containing the Y bounds from which the pixels should be retrieved.

cBounds - Array containing the C bounds from which the pixels should be retrieved.

zBounds - Array containing the Z bounds from which the pixels should be retrieved.

tBounds - Array containing the T bounds from which the pixels should be retrieved.

bpp - Bytes per pixels of the image.

Returns:

a table of bytes containing the pixel values

Throws:

AccessException - If an error occurs while retrieving the plane data from the pixels source.

ExecutionException - A Facility can't be retrieved or instantiated.