omero.gateway.facility

Class ROIFacility

java.lang.Object

omero.gateway.facility.Facility

omero.gateway.facility.ROIFacility

public class ROIFacility
extends Facility

A Facility for ROI.

Since:

5.1

Method Summary

Modifier and Type	Method and Description
java.util.Map<FolderData,java.util.Collection<ROIData>>	addRoisToFolders(SecurityContext ctx, long imageID, java.util.Collection<ROIData> roiList, java.util.Collection<FolderData> folders) Adds ROIs to Folders
java.util.Map<FolderData,java.util.Collection<ROIData>>	addRoisToFolders(SecurityContext ctx, long imageID, java.util.Collection<ROIData> roiList, java.util.Collection<FolderData> folders, boolean removeFromOtherFolders) Adds ROIs to Folders
int	getROICount(SecurityContext ctx, long imageId) Get the number of ROIs for an image (-1 in case of error)
java.util.Collection<FolderData>	getROIFolders(SecurityContext ctx, long imageId) Get all ROI folders for a certain image
ROIResult	loadROI(SecurityContext ctx, long roiId) Loads the ROI
java.util.List<ROIResult>	loadROIs(SecurityContext ctx, long imageID) Loads the ROI related to the specified image.
java.util.List<ROIResult>	loadROIs(SecurityContext ctx, long imageID, java.util.List<java.lang.Long> measurements) Loads the ROI related to the specified image.
java.util.List<ROIResult>	loadROIs(SecurityContext ctx, long imageID, java.util.List<java.lang.Long> measurements, long userID) Loads the ROI related to the specified image.
java.util.List<ROIResult>	loadROIsByPlane(SecurityContext ctx, long imageID, int z, int t) Loads the ROI related to the specified image.
java.util.Collection<ROIResult>	loadROIsForFolder(SecurityContext ctx, long imageId, long folderId) Get all ROIs which are part of a certain folder
void	removeRoisFromFolders(SecurityContext ctx, long imageID, java.util.Collection<ROIData> roiList, java.util.Collection<FolderData> folders) Remove the ROIs from the folders
java.util.Collection<ROIData>	saveROIs(SecurityContext ctx, long imageID, java.util.Collection<ROIData> roiList) Save the ROI for the image to the server.
java.util.Collection<ROIData>	saveROIs(SecurityContext ctx, long imageID, long userID, java.util.Collection<ROIData> roiList) Save the ROI for the image to the server.

Methods inherited from class omero.gateway.facility.Facility

addPropertyChangeListener, clear, firePropertyChanged, firePropertyChanged, getFacility, logDebug, logError, logInfo, logWarn, removePropertyChangeListener

Methods inherited from class java.lang.Object

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

Method Detail

getROICount

public int getROICount(SecurityContext ctx,
                       long imageId)
                throws DSOutOfServiceException,
                       DSAccessException

Get the number of ROIs for an image (-1 in case of error)

Parameters:

ctx - The SecurityContext

imageId - The image Id

Returns:

See above

Throws:

DSOutOfServiceException

DSAccessException

loadROI

public ROIResult loadROI(SecurityContext ctx,
                         long roiId)
                  throws DSOutOfServiceException,
                         DSAccessException

Loads the ROI

Parameters:

ctx - The security context.

roiId - The ROI's id.

Returns:

See above.

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

loadROIsByPlane

public java.util.List<ROIResult> loadROIsByPlane(SecurityContext ctx,
                                                 long imageID,
                                                 int z,
                                                 int t)
                                          throws DSOutOfServiceException,
                                                 DSAccessException

Loads the ROI related to the specified image.

Parameters:

ctx - The security context.

imageID - The image's ID.

z - The selection z-section.

t - The selection timepoint.

Returns:

See above.

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

loadROIs

public java.util.List<ROIResult> loadROIs(SecurityContext ctx,
                                          long imageID)
                                   throws DSOutOfServiceException,
                                          DSAccessException

Loads the ROI related to the specified image.

Parameters:

ctx - The security context.

imageID - The image's ID.

Returns:

See above.

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

loadROIs

public java.util.List<ROIResult> loadROIs(SecurityContext ctx,
                                          long imageID,
                                          java.util.List<java.lang.Long> measurements)
                                   throws DSOutOfServiceException,
                                          DSAccessException

Loads the ROI related to the specified image.

Parameters:

ctx - The security context.

imageID - The image's ID.

measurements - The measurements IDs linked to the image if any.

Returns:

See above.

Throws:

DSOutOfServiceException - If the connection is broken, or logged in.

DSAccessException - If an error occurred while trying to retrieve data from OMEDS service.

loadROIs

public java.util.List<ROIResult> loadROIs(SecurityContext ctx,
                                          long imageID,
                                          java.util.List<java.lang.Long> measurements,
                                          long userID)
                                   throws DSOutOfServiceException,
                                          DSAccessException

Loads the ROI related to the specified image.

Parameters:

ctx - The security context.

imageID - The image's ID.

measurements - The measurements IDs linked to the image if any.

userID - The user's ID.

Returns:

See above.

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

saveROIs

public java.util.Collection<ROIData> saveROIs(SecurityContext ctx,
                                              long imageID,
                                              java.util.Collection<ROIData> roiList)
                                       throws DSOutOfServiceException,
                                              DSAccessException

Save the ROI for the image to the server.

Parameters:

ctx - The security context.

imageID - The image's ID.

roiList - The list of ROI to save.

Returns:

updated list of ROIData objects.

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

addRoisToFolders

public java.util.Map<FolderData,java.util.Collection<ROIData>> addRoisToFolders(SecurityContext ctx,
                                                                                long imageID,
                                                                                java.util.Collection<ROIData> roiList,
                                                                                java.util.Collection<FolderData> folders)
                                                                         throws DSOutOfServiceException,
                                                                                DSAccessException

Adds ROIs to Folders

Parameters:

ctx - The SecurityContext

imageID - The image id

roiList - The ROIs to add to the Folders

folders - The Folders to add the ROIs to

Returns:

The updated Folders and ROIs

Throws:

DSOutOfServiceException

DSAccessException

addRoisToFolders

public java.util.Map<FolderData,java.util.Collection<ROIData>> addRoisToFolders(SecurityContext ctx,
                                                                                long imageID,
                                                                                java.util.Collection<ROIData> roiList,
                                                                                java.util.Collection<FolderData> folders,
                                                                                boolean removeFromOtherFolders)
                                                                         throws DSOutOfServiceException,
                                                                                DSAccessException

Adds ROIs to Folders

Parameters:

ctx - The SecurityContext

imageID - The image id

roiList - The ROIs to add to the Folders

folders - The Folders to add the ROIs to

removeFromOtherFolders - Pass true if the ROIs should only be linked to the specified folders, others will be unlinked.

Returns:

The updated Folders and ROIs

Throws:

DSOutOfServiceException

DSAccessException

removeRoisFromFolders

public void removeRoisFromFolders(SecurityContext ctx,
                                  long imageID,
                                  java.util.Collection<ROIData> roiList,
                                  java.util.Collection<FolderData> folders)
                           throws DSOutOfServiceException,
                                  DSAccessException

Remove the ROIs from the folders

Parameters:

ctx - The SecurityContext

imageID - The image id

roiList - The ROIs to remove from the folders

folders - The Folders to remove the ROIs from

Throws:

DSOutOfServiceException

DSAccessException

saveROIs

public java.util.Collection<ROIData> saveROIs(SecurityContext ctx,
                                              long imageID,
                                              long userID,
                                              java.util.Collection<ROIData> roiList)
                                       throws DSOutOfServiceException,
                                              DSAccessException

Save the ROI for the image to the server.

Parameters:

ctx - The security context.

imageID - The image's ID (can be -1 for ROIs not attached to an image)

userID - The user's ID.

roiList - The list of ROI to save.

Returns:

updated list of ROIData objects.

Throws:

DSOutOfServiceException - If the connection is broken, or not logged in

DSAccessException - If an error occurred while trying to retrieve data from OMERO service.

getROIFolders

public java.util.Collection<FolderData> getROIFolders(SecurityContext ctx,
                                                      long imageId)
                                               throws DSOutOfServiceException,
                                                      DSAccessException

Get all ROI folders for a certain image

Parameters:

ctx - The SecurityContext

imageId - The image id

Returns:

See above

Throws:

DSOutOfServiceException - If the connection is broken, or logged in.

DSAccessException - If an error occurred while trying to retrieve data from OMEDS service.

loadROIsForFolder

public java.util.Collection<ROIResult> loadROIsForFolder(SecurityContext ctx,
                                                         long imageId,
                                                         long folderId)
                                                  throws DSOutOfServiceException,
                                                         DSAccessException

Get all ROIs which are part of a certain folder

Parameters:

ctx - The SecurityContext

imageId - The image id

folderId - The folder id

Returns:

See above

Throws:

DSOutOfServiceException - If the connection is broken, or logged in.

DSAccessException - If an error occurred while trying to retrieve data from OMEDS service.