Index (qupath-extension-biop-omero 1.0.0-SNAPSHOT API)

A B C D E F G H I K L N O P Q R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values

A

addAndDeleteMetadata(Map<String, String>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addKeyValuesToQuPath(ProjectImageEntry, Map, Utils.UpdatePolicy, boolean) instead
addAndUpdateMetadata(Map<String, String>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addKeyValuesToQuPath(ProjectImageEntry, Map, Utils.UpdatePolicy, boolean) instead
addAttachmentToOmero(File, OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead
addAttachmentToOmero(File, OmeroRawClient, long, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead
addAttachmentToOmero(File, OmeroRawClient, long, String, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead
addAttachmentToOmero(File, OmeroRawClient, DataObject) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead
addAttachmentToOmero(File, OmeroRawClient, DataObject, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead
addAttachmentToOmero(File, OmeroRawClient, DataObject, String, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead
addClient(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClients: Add a server (with an empty list of clients) to the client list.
addContainersAsMetadataFields(ProjectImageEntry<BufferedImage>, OmeroRawObjects.OmeroRawObject) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Adds the OMERO object hierarchy as QuPath metadata fields
addKeyValuesOnOmero(MapAnnotationData, OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper) instead
addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Read and add OMERO Key-Value pairs as QuPath metadata to the current image in the QuPath project.
addKeyValuesToQuPath(ProjectImageEntry<BufferedImage>, Map<String, String>, Utils.UpdatePolicy, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: add Key-Value pairs as QuPath metadata to the image in the QuPath project.
addMeasurementsToParentTable(LinkedHashMap<String, List<String>>, Collection<PathObject>, OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Populate a map "header, List_of_measurements" with new measurements coming from a measurement table of new pathObjects.
addMetadata(Map<String, String>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addKeyValuesToQuPath(ProjectImageEntry, Map, Utils.UpdatePolicy, boolean) instead
addOmeroKeyValues(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
addOmeroKeyValuesAndDeleteMetadata(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
addOmeroKeyValuesAndUpdateMetadata(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
addParentHierarchyToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: add the parent containers of the current image as QuPath metadata fields
addROIsToQuPath(OmeroRawImageServer, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: get and add to QuPath all ROIs owned by the specified owner and linked to the current image from OMERO to QuPath
addTableToOmero(TableData, String, OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.addTable(Client, TableWrapper) instead
addTableToOmero(TableData, String, OmeroRawClient, DataObject) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.addTable(Client, TableWrapper) instead
addTagsOnOmero(TagAnnotationData, OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper) instead
addTagsToQuPath(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Read, from OMERO, tags attached to the current image and add them as QuPath metadata fields
addTagsToQuPath(ProjectImageEntry<BufferedImage>, List<String>, Utils.UpdatePolicy, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Add a list of tags (string) as QuPath metadata fields
addURI(URI) - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: Add a URI to the list of this client's URIs.
ALL_USERS - Static variable in class qupath.ext.biop.servers.omero.raw.utils.Utils

B

buildCSVFileFromListsOfStrings(LinkedHashMap<String, List<String>>, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Convert a map into a CSV file
buildCSVFileFromMeasurementTable(Collection<PathObject>, ObservableMeasurementTableData, long, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Convert a QuPath measurement table into a CSV file, including the OMERO image ID on which the measurements are referring to.
buildCSVFileFromMeasurementTable(Collection<PathObject>, ObservableMeasurementTableData, long, String, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Method moved to a non-public class
buildListsOfStringsFromMeasurementTable(LinkedHashMap<String, List<String>>, ObservableMeasurementTableData, Collection<PathObject>, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Populate a map with new measurements coming from a measurement table of new pathObjects.
buildMetadata() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: read image metadata and build a QuPath ImageServerMetadata object.
buildOmeroTableFromListsOfStrings(LinkedHashMap<String, List<String>>, OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Convert a map into an OMERO.table
buildOmeroTableFromMeasurementTable(Collection<PathObject>, ObservableMeasurementTableData, ImageWrapper) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Convert a QuPath measurement table to an OMERO table
buildServer(URI, String...) - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServerBuilder

C

checkIfLoggedIn() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: check if the current client is connected to the server
checkImageSupport(URI, String...) - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServerBuilder
checkUniqueKeyInAnnotationMap(List<NamedValue>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
method moved with a non-public access
checkUniqueKeyInAnnotationMap(List<NamedValue>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Try to solve an error in OMERO regarding the keys creation.
close() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
convertMapAnnotationWrapperToMap(MapAnnotationWrapper) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Utils to convert the MapAnnotationWrapper object into a map of the OMERO key-values
convertMeasurementTableToOmeroTable(Collection<PathObject>, ObservableMeasurementTableData, OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Method moved with a non-public access
convertOmeroROIsToQuPathROIs(ROIWrapper) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Convert OMERO ROIs To QuPath ROIs.
convertQuPathRoiToOmeroRoi(PathObject, String, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Convert a PathObject into OMERO-readable objects.
copyOmeroChannelsColorToQuPath(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Set the color of each channel on QuPath, based on OMERO settings.
QuPath image and thumbnail are updated accordingly.
Channel indices are taken as reference.
copyOmeroChannelsDisplayRangeToQuPath(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Set the minimum and maximum display range value of each channel on QuPath, based on OMERO settings.
QuPath image and thumbnail are updated accordingly.
Channel indices are taken as reference.
copyOmeroChannelsNameToQuPath(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Set the name of each channel on QuPath, based on OMERO settings.
create(URI) - Static method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient
createAndSaveFile(String, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Create a file in the given path, with the given content, and save it
createClientAndLogin(URI) - Static method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClients: Create client from the server URI provided.
createID() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
createNewDataset(OmeroRawClient, long, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ProjectWrapper.addDataset(Client, String, String) instead
createNewDataset(OmeroRawClient, long, String, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ProjectWrapper.addDataset(Client, String, String) instead
createNewDataset(OmeroRawClient, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use DatasetWrapper(String, String) instead followed by GenericObjectWrapper.saveAndUpdate(Client)
createNewDataset(OmeroRawClient, String, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use DatasetWrapper(String, String) instead followed by GenericObjectWrapper.saveAndUpdate(Client)
createOmeroROIsFromPathObjects(Collection<PathObject>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Convert QuPath pathObjects into OMERO ROIs.
createOmeroROIsFromPathObjects(Collection<PathObject>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Method moved with a non-public access
createPathObjectFromQuPathRoi(ROI, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Create a PathObject of type annotation or detection from a QuPath ROI object without any class and with the default red color.
createPathObjectFromQuPathRoi(ROI, String, Color) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Create a PathObject of type annotation or detection from a QuPath ROI object, with a certain color.
createPathObjectFromQuPathRoi(ROI, String, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Create a PathObject of type annotation or detection from a QuPath ROI object.
createPathObjectsFromOmeroROIs(List<ROIWrapper>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Convert OMERO ROIs into QuPath pathObjects
createPathObjectsFromOmeroROIs(List<ROIWrapper>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Method moved with a non-public access
createServerBuilder() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
createStateNode(boolean) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Build a colored-coded disk indicating the status of the server connection
createStateNode(boolean) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawImageServerBrowserCommand: Deprecated.
use OmeroRawBrowserTools.createStateNode(boolean) instead

D

DELETE_KEYS - Enum constant in enum class qupath.ext.biop.servers.omero.raw.utils.Utils.UpdatePolicy: Delete all existing keys
deleteAllOmeroROIs(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Client.delete(Collection) instead
deleteAnnotationFiles(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.deleteAnnotationMeasurements(OmeroRawImageServer, String, boolean) instead
deleteAnnotationFiles(OmeroRawImageServer, Collection<FileAnnotationData>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.deleteAnnotationMeasurements(OmeroRawImageServer, String, boolean) instead
deleteAnnotationFiles(OmeroRawImageServer, Collection<FileAnnotationData>, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
OmeroRawScripting.deleteAnnotationMeasurements(OmeroRawImageServer, String, boolean) instead
deleteAnnotationMeasurements(OmeroRawImageServer, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Delete all previous version of annotation tables (OMERO and csv files) related to the current QuPath project.
deleteDetectionFiles(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.deleteDetectionMeasurements(OmeroRawImageServer, String, boolean) instead
deleteDetectionFiles(OmeroRawImageServer, Collection<FileAnnotationData>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.deleteDetectionMeasurements(OmeroRawImageServer, String, boolean) instead
deleteDetectionFiles(OmeroRawImageServer, Collection<FileAnnotationData>, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.deleteDetectionMeasurements(OmeroRawImageServer, String, boolean) instead
deleteDetectionMeasurements(OmeroRawImageServer, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Delete all previous version of detection tables (OMERO and csv files) related to the current QuPath project.
deleteFiles(OmeroRawClient, List<FileAnnotationData>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Client.delete(Collection) instead
deleteFiles(OmeroRawImageServer, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use Client.delete(Collection) instead
deleteKeyValuesOnOmero(List<MapAnnotationData>, OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Client.delete(Collection) instead
deleteOmeroROIs(OmeroRawClient, Collection<ROIData>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Client.delete(Collection)} instead
downloadImage(OmeroRawClient, long, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ImageWrapper.download(Client, String) instead

E

equals(Object) - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient
equals(Object) - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
errorLog(Logger, String, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Error Logger to inform in QuPath GUI and / or in the logger window
errorLog(Logger, String, String, Exception, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Error Logger to inform in QuPath GUI and / or in the logger window
EXISTING_KVP - Static variable in class qupath.ext.biop.servers.omero.raw.utils.Utils

F

filterByOwner(OmeroRawClient, List<ROIWrapper>, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes
flattenMapAnnotationWrapperList(List<MapAnnotationWrapper>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Create one single MapAnnotationWrapper object from a list of them

G

getAllClients() - Static method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClients: Return the observable list of all clients.
getAllOmeroGroups(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Client.getGroups() if the user is admin. Otherwise, use ExperimenterWrapper.getGroups()
getAvailableGroupUsersMap(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Return a map of available groups with its attached users.
getClient() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Return the raw client used for this image server.
getClientFromServerURI(URI) - Static method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClients: Return the client associated with the specified server URI.
getCurrentDateAndHour() - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Utils.getCurrentDateAndHour() instead
getCurrentDateAndHour() - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils
getDefaultGroupItem(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Method removed
getDefaultOmeroGroup(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ExperimenterWrapper.getDefaultGroup() instead and Client.getUser(long) to get the ExperimenterWrapper object.
getDefaultOwnerItem(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Method removed
getDefaultThumbnail(int, int) - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Overridden method to generate a thumbnail even if it cannot be read from OMERO Code adapted from AbstractImageServer
getDescription() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawExtension
getDescription() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServerBuilder
getErrorStackTraceAsString(Exception) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Utils.getErrorStackTraceAsString(Exception) instead
getErrorStackTraceAsString(Exception) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils
getGroupIdFromImageId(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: get the group of which an image is part of.
getGroupUsersMapAvailableForCurrentUser(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
use OmeroRawBrowserTools.getAvailableGroupUsersMap(OmeroRawClient) instead
getHost() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Return the URI host used by this image server
getId() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Return the OMERO ID of the image
getImageType() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServerBuilder
getImageWrapper() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
getLoggedInUser() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient
getName() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawExtension
getName() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServerBuilder
getOmeroGroup(OmeroRawClient, long, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Client.getGroup(long) or Client.getGroup(String)instead
getOmeroIcons() - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Load container / image icons for the nice browser interface
getOmeroUser(OmeroRawClient, long, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Client.getUser(long) or Client.getUser(String) instead
getOmeroUsersInGroup(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use GroupWrapper.getExperimenters() instead and Client.getGroup(long) to get the GroupWrapper object
getOpenedRawBrowsers() - Static method in class qupath.ext.biop.servers.omero.raw.OmeroRawExtension: Return map of currently opened browsers.
getOriginalMetadata() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
getOrphanedFolderItem(OmeroRawClient, OmeroRawObjects.Group, OmeroRawObjects.Owner) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Internal method ; not public anymore
getOwnerItem(Experimenter) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Method removed
getOwnerStringConverter(Collection<OmeroRawObjects.Owner>) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools
getParent(OmeroRawClient, String, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use OmeroRawTools.getParentContainer(OmeroRawClient, GenericRepositoryObjectWrapper, boolean) instead
getParentContainer(OmeroRawClient, GenericRepositoryObjectWrapper<?>, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: fetch parents container of OMERO containers
getParentHierarchy(OmeroRawImageServer, GenericRepositoryObjectWrapper<?>, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: get the parents of an OMERO object (from dataset/well to screen/project)
getPort() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient
getPort() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Return the URI port used by this image server
getPreferredTileHeight() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Return the preferred tile height of this ImageServer.
getPreferredTileWidth() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Return the preferred tile width of this ImageServer.
getQuPathVersion() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawExtension
getRepository() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawExtension
getROIComment(ROIWrapper) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Read the comments attach to an OMERO ROI (i.e.
getROIComment(ROIData) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Method moved with a non-public access
getROIComment(Shape) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Read the comment attached to one shape of an OMERO ROI.
getROIComment(Shape) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Method moved with a non-public access
getROIs(OmeroRawClient, long, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: get ROIs owned by the specified owner and linked to the current image from OMERO to QuPath
getROIs(OmeroRawImageServer, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: get ROIs owned by the specified owner and linked to the current image from OMERO to QuPath
getScheme() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Return the URI scheme used by this image server
getServerType() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
getServerURI() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: Return the server URI ('clean' URI) of this OmeroRawClient.
getServerURI(URI) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Return a clean URI of the server from which the given URI is specified.
getSimpleClient() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient
getSimpleOmeroClientInstance(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawClient.getSimpleClient() instead (accessible from OmeroRawImageServer.getClient())
getStage() - Method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawImageServerBrowserCommand
getStandardURI(URI, OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Method removed
getThumbnail(OmeroRawClient, long, int) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ImageWrapper.getThumbnail(Client, int) instead
getURIs() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: Return an unmodifiable list of all URIs using this OmeroRawClient.
getURIs() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
getURIs(URI, OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Method removed
getUsername() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: Gets the value of the property username.
getUserOmeroGroups(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ExperimenterWrapper.getGroups() instead and Client.getUser(long) to get ExperimenterWrapper object.

H

hashCode() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient
hashCode() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer

I

importOmeroKeyValues(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
importOmeroROIsToQuPath(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addROIsToQuPath(OmeroRawImageServer, boolean, String, boolean) instead
importOmeroROIsToQuPath(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addROIsToQuPath(OmeroRawImageServer, boolean, String, boolean) instead
importOmeroROIsToQuPath(OmeroRawImageServer, boolean, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addROIsToQuPath(OmeroRawImageServer, boolean, String, boolean) instead
importOmeroTags(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
infoLog(Logger, String, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Info Logger to inform in QuPath GUI and / or in the logger window
infoLog(Logger, String, String, Exception, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Info Logger to inform in QuPath GUI and / or in the logger window
installExtension(QuPathGUI) - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawExtension
isAdmin() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient
isLoggedIn() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: Return whether the client is logged in to its server (not necessarily with access to all its images).

K

KEEP_KEYS - Enum constant in enum class qupath.ext.biop.servers.omero.raw.utils.Utils.UpdatePolicy: Keep all existing keys without updating
KVP_KEY - Static variable in class qupath.ext.biop.servers.omero.raw.utils.Utils

L

linkFile(OmeroRawClient, FileAnnotationData, DataObject) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead
logIn(String...) - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: Log in to the client's server with optional args.
logOut() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: Log out this client from the server.
logOut(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClients: Log the specified client out.
logProperty() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient

N

NEW_KVP - Static variable in class qupath.ext.biop.servers.omero.raw.utils.Utils
NO_IMAGE_THUMBNAIL - Static variable in class qupath.ext.biop.servers.omero.raw.utils.Utils
NO_UPDATE - Enum constant in enum class qupath.ext.biop.servers.omero.raw.utils.Utils.UpdatePolicy: Do not modify the target neither add new stuff

O

OmeroRawBrowserTools - Class in qupath.ext.biop.servers.omero.raw.browser: Utility class grouping static methods in relation to the browser command
OmeroRawBrowserTools() - Constructor for class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools
OmeroRawClient - Class in qupath.ext.biop.servers.omero.raw.client: Class representing an OMERO Raw Client.
OmeroRawClients - Class in qupath.ext.biop.servers.omero.raw.client: Class to keep track of active OMERO clients.
OmeroRawClientsCommand - Class in qupath.ext.biop.servers.omero.raw.client: Command to manually manage OMERO web clients.
OmeroRawClientsCommand(QuPathGUI) - Constructor for class qupath.ext.biop.servers.omero.raw.client.OmeroRawClientsCommand
OmeroRawExtension - Class in qupath.ext.biop.servers.omero.raw: Extension to access images hosted on OMERO.
OmeroRawExtension() - Constructor for class qupath.ext.biop.servers.omero.raw.OmeroRawExtension
OmeroRawImageServer - Class in qupath.ext.biop.servers.omero.raw: ImageServer that reads pixels using the OMERO-JAVA gateway
OmeroRawImageServerBrowserCommand - Class in qupath.ext.biop.servers.omero.raw.browser: Command to browse a specified OMERO server and import images from that server
OmeroRawImageServerBrowserCommand(QuPathGUI, OmeroRawClient) - Constructor for class qupath.ext.biop.servers.omero.raw.browser.OmeroRawImageServerBrowserCommand
OmeroRawImageServerBuilder - Class in qupath.ext.biop.servers.omero.raw: Builder for ImageServers that make use of the OMERO-java library.
OmeroRawImageServerBuilder() - Constructor for class qupath.ext.biop.servers.omero.raw.OmeroRawImageServerBuilder
OmeroRawImportAnnotationObjectsCommand - Class in qupath.ext.biop.servers.omero.raw.command: Import ROIs from OMERO for the current open image.
OmeroRawImportAnnotationObjectsCommand(QuPathGUI) - Constructor for class qupath.ext.biop.servers.omero.raw.command.OmeroRawImportAnnotationObjectsCommand
OmeroRawImportChannelSettingsCommand - Class in qupath.ext.biop.servers.omero.raw.command: Import channel rendering settings from OMERO.
OmeroRawImportChannelSettingsCommand(QuPathGUI) - Constructor for class qupath.ext.biop.servers.omero.raw.command.OmeroRawImportChannelSettingsCommand
OmeroRawImportMetadataCommand - Class in qupath.ext.biop.servers.omero.raw.command: Import key-values and tags from OMERO with a certain rule - Keep existing and add new => only add in QuPath the new keys (if the key already exists, it is not imported) - Replace existing and add new => add news keys and update those which already exist (i.e.replace the old value) - Delete all and add new => delete all keys in QuPath and all those coming from OMERO.
OmeroRawImportMetadataCommand(QuPathGUI) - Constructor for class qupath.ext.biop.servers.omero.raw.command.OmeroRawImportMetadataCommand
OmeroRawScripting - Class in qupath.ext.biop.servers.omero.raw.utils: Static class which groups the methods of the scripting API for an OMERORawImageServer
OmeroRawScripting() - Constructor for class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting
OmeroRawShapes - Class in qupath.ext.biop.servers.omero.raw.utils: Handles the conversion between PathObjects and OMERO-ROIs
OmeroRawShapes() - Constructor for class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes
OmeroRawTools - Class in qupath.ext.biop.servers.omero.raw.utils: Static helper methods related to OMERORawImageServer.
OmeroRawWriteAnnotationObjectsCommand - Class in qupath.ext.biop.servers.omero.raw.command: Command to write path objects back to the OMERO server where the current image is hosted.
OmeroRawWriteAnnotationObjectsCommand(QuPathGUI) - Constructor for class qupath.ext.biop.servers.omero.raw.command.OmeroRawWriteAnnotationObjectsCommand
OmeroRawWriteChannelSettingsCommand - Class in qupath.ext.biop.servers.omero.raw.command: Command to send QuPath channel settings (display range, colors and name) to the corresponding image on OMERO
OmeroRawWriteChannelSettingsCommand(QuPathGUI) - Constructor for class qupath.ext.biop.servers.omero.raw.command.OmeroRawWriteChannelSettingsCommand
OmeroRawWriteMetadataCommand - Class in qupath.ext.biop.servers.omero.raw.command: Command to import QuPath metadata to OMERO server where the current image is hosted.
OmeroRawWriteMetadataCommand(QuPathGUI) - Constructor for class qupath.ext.biop.servers.omero.raw.command.OmeroRawWriteMetadataCommand

P

paintBufferedImageOnCanvas(BufferedImage, Canvas, int) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawImageServerBrowserCommand: Paint the specified image onto the specified canvas (of the preferred size).
parseOmeroRawObjectId(URI, OmeroRawObjects.OmeroRawObjectType) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Method removed
parseOmeroRawObjectType(URI) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Method removed
parseROIComment(String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawShapes: Parse the comment based on the format introduced in {OmeroRawShapes.setRoiComment(PathObject src, String objectID, String parentID)}
parseROIComment(String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Method moved with a non-public access
promptToImportOmeroImages(QuPathGUI, String...) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Prompt to import images, specifying the OmeroRawImageServerBuilder if possible.

Q

qupath.ext.biop.servers.omero.raw - package qupath.ext.biop.servers.omero.raw: Read images from OMERO (https://www.openmicroscopy.org/omero/).
qupath.ext.biop.servers.omero.raw.browser - package qupath.ext.biop.servers.omero.raw.browser
qupath.ext.biop.servers.omero.raw.client - package qupath.ext.biop.servers.omero.raw.client
qupath.ext.biop.servers.omero.raw.command - package qupath.ext.biop.servers.omero.raw.command
qupath.ext.biop.servers.omero.raw.utils - package qupath.ext.biop.servers.omero.raw.utils

R

readAnnotationsItems(OmeroRawClient, OmeroRawObjects.OmeroRawObject, OmeroRawAnnotations.OmeroRawAnnotationType) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Deprecated.
Internal method ; not public anymore
readAttachments(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.getFileAnnotations(Client) instead
readAttachments(OmeroRawClient, DataObject) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.getFileAnnotations(Client) instead
readFilesAttachedToCurrentImageOnOmero(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use AnnotatableWrapper.getFileAnnotations(Client) instead
readImageFileType(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ImageWrapper.getFormat() instead
readKeyValues(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.getMapAnnotations(Client) instead
readKeyValuesAsNamedValue(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use MapAnnotationWrapper.getContent() instead
readLocalImage(String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: read an image stored in the resource folder of the main class
readOmeroAnnotations(OmeroRawClient, DataObject) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.getAnnotations(Client) instead
readOmeroChannels(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ImageWrapper.getChannels(Client) instead
readOmeroDataset(OmeroRawClient, Long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Browser.getDataset(Long) instead
readOmeroDatasets(OmeroRawClient, List<Long>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Browser.getDatasets(Long...)
readOmeroImage(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Browser.getImage(Long) instead
readOmeroObjectsItems(OmeroRawObjects.OmeroRawObject, OmeroRawClient, OmeroRawObjects.Group, OmeroRawObjects.Owner) - Static method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools: Get all the child OMERO objects present in the OMERO server with the specified parent.
readOmeroOrphanedDatasets(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
user Browser.getOrphanedDatasets(ExperimenterWrapper)} instead
readOmeroPlates(OmeroRawClient, List<Long>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use OmeroRawTools.readPlates(OmeroRawClient, List) instead
readOmeroProjects(OmeroRawClient, List<Long>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Browser.getProjects(Long...) instead
readOmeroProjectsByUser(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Use Browser.getProjects(ExperimenterWrapper) instead
readOmeroRenderingSettings(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: read the rendering settings object linked to the specified pixels Code partially copied ImageWrapper.getChannelColor(Client, int)
readOmeroScreensByUser(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Use Browser.getScreens(ExperimenterWrapper) instead
readOmeroWells(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use PlateWrapper.getWells(Client)
readOrphanedDatasets(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
user Browser.getOrphanedDatasets(ExperimenterWrapper) instead
readOrphanedImages(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Browser.getOrphanedImages(ExperimenterWrapper) instead
readPathObjects() - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: See below
readPathObjects(String) - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer: Deprecated.
use OmeroRawScripting.getROIs(OmeroRawImageServer, String, boolean) instead
readPlates(OmeroRawClient, List<Long>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: fetch all OMERO plates corresponding to the list of ids.
readTables(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.getTables(Client) instead
readTags(OmeroRawClient, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use AnnotatableWrapper.getTags(Client) instead
readTile(TileRequest) - Method in class qupath.ext.biop.servers.omero.raw.OmeroRawImageServer
readUserTags(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Browser.getTags() instead
removeClient(OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClients: Remove the client from the clients list (losing all info about its URIs).
requestClose() - Method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawImageServerBrowserCommand: Request closure of the dialog
run() - Method in class qupath.ext.biop.servers.omero.raw.browser.OmeroRawImageServerBrowserCommand
run() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClientsCommand
run() - Method in class qupath.ext.biop.servers.omero.raw.command.OmeroRawImportAnnotationObjectsCommand
run() - Method in class qupath.ext.biop.servers.omero.raw.command.OmeroRawImportChannelSettingsCommand
run() - Method in class qupath.ext.biop.servers.omero.raw.command.OmeroRawImportMetadataCommand
run() - Method in class qupath.ext.biop.servers.omero.raw.command.OmeroRawWriteAnnotationObjectsCommand
run() - Method in class qupath.ext.biop.servers.omero.raw.command.OmeroRawWriteChannelSettingsCommand
run() - Method in class qupath.ext.biop.servers.omero.raw.command.OmeroRawWriteMetadataCommand

S

sendAnnotationMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection<PathObject>, ImageData<BufferedImage>, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send pathObjects' measurements to OMERO as a CSV file with a default table name referring to annotation
sendAnnotationMeasurementsToOmero(OmeroRawImageServer, Collection<PathObject>, ImageData<BufferedImage>, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send pathObjects' measurements to OMERO as an OMERO.table with a default table name referring to annotations
sendAnnotationMeasurementTable(Collection<PathObject>, OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
sendAnnotationMeasurementTable(OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
sendAnnotationMeasurementTableAsCSV(Collection<PathObject>, OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
sendAnnotationMeasurementTableAsCSV(OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
sendAnnotationsToOmero(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead
sendAnnotationsToOmero(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead.
sendAnnotationsToOmero(OmeroRawImageServer, boolean, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead
sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send a collection of QuPath objects (annotations and/or detections) to OMERO, without deleting existing ROIs
sendChannelsColorToOmero(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendQuPathChannelsColorToOmero(OmeroRawImageServer, boolean) instead
sendChannelsDisplayRangeToOmero(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendQuPathChannelsDisplayRangeToOmero(OmeroRawImageServer, boolean) instead
sendChannelsNameToOmero(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendQuPathChannelsNameToOmero(OmeroRawImageServer, boolean) instead
sendDetectionMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection<PathObject>, ImageData<BufferedImage>, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send pathObjects' measurements to OMERO as a CSV file with a default table name referring to annotation
sendDetectionMeasurementsToOmero(OmeroRawImageServer, Collection<PathObject>, ImageData<BufferedImage>, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send pathObjects' measurements to OMERO as an OMERO.table with a default table name referring to detections
sendDetectionMeasurementTable(Collection<PathObject>, OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendDetectionMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
sendDetectionMeasurementTable(OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendDetectionMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
sendDetectionMeasurementTableAsCSV(Collection<PathObject>, OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendDetectionMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
sendDetectionMeasurementTableAsCSV(OmeroRawImageServer, ImageData<BufferedImage>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendDetectionMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
sendDetectionsToOmero(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
method removed
sendDetectionsToOmero(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
method removed
sendDetectionsToOmero(OmeroRawImageServer, boolean, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
method removed
sendImageNameToOmero(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendQuPathImageNameToOmero(OmeroRawImageServer, boolean) instead
sendKeyValuesToOmero(Map<String, String>, OmeroRawImageServer, Utils.UpdatePolicy, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send a map to OMERO as Key-Value pairs.
sendMeasurementTableAsCSVToOmero(Collection<PathObject>, OmeroRawImageServer, ImageData<BufferedImage>, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendMeasurementAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, String, boolean, String, boolean) instead
sendMeasurementTableToOmero(Collection<PathObject>, OmeroRawImageServer, ImageData<BufferedImage>, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, String, boolean, String, boolean) instead
sendMetadataOnOmero(Map<String, String>, OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendQPMetadataToOmero(Map, OmeroRawImageServer, Utils.UpdatePolicy, Utils.UpdatePolicy, boolean) instead
sendMetadataOnOmeroAndDeleteKeyValues(Map<String, String>, OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendQPMetadataToOmero(Map, OmeroRawImageServer, Utils.UpdatePolicy, Utils.UpdatePolicy, boolean) instead
sendMetadataOnOmeroAndUpdateKeyValues(Map<String, String>, OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendQPMetadataToOmero(Map, OmeroRawImageServer, Utils.UpdatePolicy, Utils.UpdatePolicy, boolean) instead
sendParentMeasurementsAsCSVToOmero(LinkedHashMap<String, List<String>>, OmeroRawClient, Collection<GenericRepositoryObjectWrapper<?>>, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send the summary map "header, List_of_measurements" to OMERO as an CSV file attached to the parent containers.
sendParentMeasurementsToOmero(LinkedHashMap<String, List<String>>, OmeroRawClient, Collection<GenericRepositoryObjectWrapper<?>>, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send the summary map "header, List_of_measurements" to OMERO as an OMERO.table attached to the parent container
sendParentMeasurementTableAsCSV(LinkedHashMap<String, List<String>>, OmeroRawClient, Collection<DataObject>, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendParentMeasurementsAsCSVToOmero(LinkedHashMap, OmeroRawClient, Collection, boolean, String, boolean) instead
sendParentMeasurementTableAsCSV(LinkedHashMap<String, List<String>>, OmeroRawClient, Collection<DataObject>, boolean, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendParentMeasurementsAsCSVToOmero(LinkedHashMap, OmeroRawClient, Collection, boolean, String, boolean) instead
sendParentMeasurementTableAsOmeroTable(LinkedHashMap<String, List<String>>, OmeroRawClient, Collection<DataObject>, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendParentMeasurementsToOmero(LinkedHashMap, OmeroRawClient, Collection, boolean, String, boolean) instead
sendParentMeasurementTableAsOmeroTable(LinkedHashMap<String, List<String>>, OmeroRawClient, Collection<DataObject>, boolean, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendParentMeasurementsToOmero(LinkedHashMap, OmeroRawClient, Collection, boolean, String, boolean) instead
sendPathObjectsToOmero(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead
sendPathObjectsToOmero(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead.
sendPathObjectsToOmero(OmeroRawImageServer, boolean, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead
sendPathObjectsToOmero(OmeroRawImageServer, Collection<PathObject>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendPathObjectsToOmero(OmeroRawImageServer, Collection, boolean, String, boolean) instead
sendPathObjectsToOmero(OmeroRawImageServer, Collection<PathObject>, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendPathObjectsToOmero(OmeroRawImageServer, Collection, boolean, String, boolean) instead.
sendPathObjectsToOmero(OmeroRawImageServer, Collection<PathObject>, boolean, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendPathObjectsToOmero(OmeroRawImageServer, Collection, boolean, String, boolean) instead
sendPathObjectsToOmero(OmeroRawImageServer, Collection<PathObject>, boolean, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send a collection of pathObjects to OMERO.
sendQPMetadataToOmero(Map<String, String>, OmeroRawImageServer, Utils.UpdatePolicy, Utils.UpdatePolicy, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send QuPath metadata to OMERO.
sendQuPathChannelsColorToOmero(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Set the color of each channel on OMERO, based on QuPath settings.
sendQuPathChannelsDisplayRangeToOmero(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Set the minimum and maximum display range value of each channel on OMERO, based on QuPath settings.
OMERO image and thumbnail are updated accordingly.
sendQuPathChannelsNameToOmero(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Set the name of each channel on OMERO, based on QuPath settings.
sendQuPathImageNameToOmero(OmeroRawImageServer, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Set the name the image on OMERO, based on QuPath settings.
sendTagsToOmero(List<String>, OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.sendTagsToOmero(List, OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
sendTagsToOmero(List<String>, OmeroRawImageServer, Utils.UpdatePolicy, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Send a list of tags to OMERO.
setChannelsColorFromOmeroChannel(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.copyOmeroChannelsColorToQuPath(OmeroRawImageServer, boolean) instead
setChannelsDisplayRangeFromOmeroChannel(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.copyOmeroChannelsDisplayRangeToQuPath(OmeroRawImageServer, boolean) instead
setChannelsNameFromOmeroChannel(OmeroRawImageServer) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting: Deprecated.
use OmeroRawScripting.copyOmeroChannelsNameToQuPath(OmeroRawImageServer, boolean) instead
splitNewAndExistingKeyValues(Map<String, String>, Map<String, String>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use Utils.splitNewAndExistingKeyValues(Map, Map) instead
splitNewAndExistingKeyValues(Map<String, String>, Map<String, String>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Splits the "target" map into two parts : one part containing key/values that are referenced in the "reference" map and the other containing remaining key/values that are not referenced in the "reference".
switchGroup(long) - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: switch the current group to another group where the user is also part of

T

TAG_KEY - Static variable in class qupath.ext.biop.servers.omero.raw.utils.Utils

U

UPDATE_KEYS - Enum constant in enum class qupath.ext.biop.servers.omero.raw.utils.Utils.UpdatePolicy: Update all existing key with new values
updateKeyValuesOnOmero(List<MapAnnotationData>, OmeroRawClient) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
method removed
updateObjectOnOmero(OmeroRawClient, IObject) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
updateObjectsOnOmero(OmeroRawClient, List<IObject>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
Method removed ; use the official API
updateOmeroThumbnail(OmeroRawClient, long, long) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Update the thumbnail of an OMERO image.
uploadImage(OmeroRawClient, long, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use DatasetWrapper.importImage(Client, String) instead
uploadImage(OmeroRawClient, DatasetWrapper, String) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use DatasetWrapper.importImage(Client, String) instead
usernameProperty() - Method in class qupath.ext.biop.servers.omero.raw.client.OmeroRawClient: The username might be empty (public), and might also change (user switching account)
Utils - Class in qupath.ext.biop.servers.omero.raw.utils: Utils class regrouping tools that are not restricted to OMERO.
Utils() - Constructor for class qupath.ext.biop.servers.omero.raw.utils.Utils
Utils.UpdatePolicy - Enum Class in qupath.ext.biop.servers.omero.raw.utils

V

valueOf(String) - Static method in enum class qupath.ext.biop.servers.omero.raw.utils.Utils.UpdatePolicy: Returns the enum constant of this class with the specified name.
values() - Static method in enum class qupath.ext.biop.servers.omero.raw.utils.Utils.UpdatePolicy: Returns an array containing the constants of this enum class, in the order they are declared.

W

warnLog(Logger, String, String, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Warning Logger to inform in QuPath GUI and / or in the logger window
warnLog(Logger, String, String, Exception, boolean) - Static method in class qupath.ext.biop.servers.omero.raw.utils.Utils: Warning Logger to inform in QuPath GUI and / or in the logger window
writeOmeroROIs(OmeroRawClient, long, List<ROIData>) - Static method in class qupath.ext.biop.servers.omero.raw.utils.OmeroRawTools: Deprecated.
use ImageWrapper.saveROIs(Client, ROIWrapper...) instead

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