fr.igred.omero.core

Interface Pixels

All Superinterfaces:

RemoteObject

All Known Implementing Classes:

PixelsWrapper

public interface Pixels
extends RemoteObject

Interface to handle Pixels on OMERO.

Method Summary

Modifier and Type	Method and Description
PixelsData	asDataObject() Returns a PixelsData corresponding to the handled object.
default double[][][][][]	getAllPixels(ConnectionHandler client) Returns an array containing the value for each voxel
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.
default byte[][][][]	getRawPixels(ConnectionHandler client, int bpp) Returns an array containing the raw values for each voxel of each plane.
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 interface fr.igred.omero.RemoteObject

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

Method Detail

asDataObject

PixelsData asDataObject()

Returns a PixelsData corresponding to the handled object.

Specified by:

asDataObject in interface RemoteObject

Returns:

See above.

loadPlanesInfo

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

Loads the planes information.

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

List<PlaneInfo> getPlanesInfo()

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

Returns:

See above.

getPixelType

String getPixelType()

Gets the pixel type.

Returns:

the pixel type.

getPixelSizeX

Length getPixelSizeX()

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

Returns:

Size of a pixel on the X axis.

getPixelSizeY

Length getPixelSizeY()

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

Returns:

Size of a pixel on the Y axis.

getPixelSizeZ

Length getPixelSizeZ()

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

Returns:

Size of a pixel on the Z axis.

getTimeIncrement

Time getTimeIncrement()

Gets the time increment between time points.

Returns:

Time increment between time points.

getMeanTimeInterval

Time getMeanTimeInterval()

Computes the mean time interval from the planes deltaTs.

Planes information needs to be loaded first.

Returns:

See above.

getMeanExposureTime

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

Length getPositionX()

Retrieves the X stage position.

Planes information needs to be loaded first.

Returns:

See above.

getPositionY

Length getPositionY()

Retrieves the Y stage position.

Planes information needs to be loaded first.

Returns:

See above.

getPositionZ

Length getPositionZ()

Retrieves the Z stage position.

Planes information needs to be loaded first.

Returns:

See above.

getSizeX

int getSizeX()

Gets the size of the image on the X axis

Returns:

Size of the image on the X axis.

getSizeY

int getSizeY()

Gets the size of the image on the Y axis

Returns:

Size of the image on the Y axis.

getSizeZ

int getSizeZ()

Gets the size of the image on the Z axis

Returns:

Size of the image on the Z axis.

getSizeC

int getSizeC()

Gets the size of the image on the C axis

Returns:

Size of the image on the C axis.

getSizeT

int getSizeT()

Gets the size of the image on the T axis

Returns:

Size of the image on the T axis.

getAllPixels

default double[][][][][] getAllPixels(ConnectionHandler 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

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

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

default byte[][][][] getRawPixels(ConnectionHandler client,
                                  int bpp)
                           throws AccessException,
                                  ExecutionException

Returns an array containing the raw values for each voxel of each plane.

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

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

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.