Package fr.igred.omero.repository

Class PixelsWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<PixelsData>

fr.igred.omero.repository.PixelsWrapper

public class PixelsWrapper
extends GenericObjectWrapper<PixelsData>

Class containing a PixelData object.

Wraps function calls to the PixelData contained.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PixelsWrapper.Bounds	Class containing 5D bounds coordinates
static class	PixelsWrapper.Coordinates	Class containing 5D pixel coordinates

Field Summary

Fields

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

Fields inherited from class fr.igred.omero.GenericObjectWrapper

data

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
double[][][][][]	getAllPixels(Client client)	Returns an array containing the value for each voxel
double[][][][][]	getAllPixels(Client 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<PlaneInfoWrapper>	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(Client client, int bpp)	Returns an array containing the raw values for each voxel for each planes
byte[][][][]	getRawPixels(Client 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(Client client)	Loads the planes information.

Methods inherited from class fr.igred.omero.GenericObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, delete, distinct, flatten, 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

Field Details

MAX_DIST

public static final int MAX_DIST

Size of tiles when retrieving pixels

See Also:

• Constant Field Values

Constructor Details

PixelsWrapper

public PixelsWrapper(PixelsData pixels)

Constructor of the PixelsWrapper class

Parameters:

pixels - The PixelData to be wrap.

Method Details

loadPlanesInfo

public void loadPlanesInfo(Client client)
                    throws ServiceException,
AccessException,
ExecutionException

Loads the planes information.

Parameters:

client - The client handling the connection.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getPlanesInfo

public List<PlaneInfoWrapper> getPlanesInfo()

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

Returns:

See above.

getPixelType

public String getPixelType()

Gets the pixel type.

Returns:

the pixel type.

getPixelSizeX

public Length getPixelSizeX()

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

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.

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.

Returns:

Size of a pixel on the Z axis.

getTimeIncrement

public Time getTimeIncrement()

Gets the time increment between time points.

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.

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.

Parameters:

channel - The channel index.

Returns:

See above.

getPositionX

public Length getPositionX()

Retrieves the X stage position.

Planes information needs to be loaded first.

Returns:

See above.

getPositionY

public Length getPositionY()

Retrieves the Y stage position.

Planes information needs to be loaded first.

Returns:

See above.

getPositionZ

public Length getPositionZ()

Retrieves the Z stage position.

Planes information needs to be loaded first.

Returns:

See above.

getSizeX

public int getSizeX()

Gets the size of the image on the X axis

Returns:

Size of the image on the X axis.

getSizeY

public int getSizeY()

Gets the size of the image on the Y axis

Returns:

Size of the image on the Y axis.

getSizeZ

public int getSizeZ()

Gets the size of the image on the Z axis

Returns:

Size of the image on the Z axis.

getSizeC

public int getSizeC()

Gets the size of the image on the C axis

Returns:

Size of the image on the C axis.

getSizeT

public int getSizeT()

Gets the size of the image on the T axis

Returns:

Size of the image on the T axis.

getAllPixels

public double[][][][][] getAllPixels(Client client)
                              throws AccessException,
ExecutionException

Returns an array containing the value for each voxel

Parameters:

client - The client handling the connection.

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.

getAllPixels

public double[][][][][] getAllPixels(Client 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

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(Client client,
 int bpp)
                          throws AccessException,
ExecutionException

Returns an array containing the raw values for each voxel for each planes

Parameters:

client - The client handling the connection.

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.

getRawPixels

public byte[][][][] getRawPixels(Client 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

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.