Package qupath.ext.biop.servers.omero.raw.browser

Class OmeroRawBrowserTools

java.lang.Object
qupath.ext.biop.servers.omero.raw.browser.OmeroRawBrowserTools
public class OmeroRawBrowserTools extends Object
Utility class grouping static methods in relation to the browser command

  • Constructor Summary

    Constructors
    Constructor
    Description
    OmeroRawBrowserTools()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    addContainersAsMetadataFields(qupath.lib.projects.ProjectImageEntry<BufferedImage> entry, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject obj)
    Adds the OMERO object hierarchy as QuPath metadata fields
    static javafx.scene.Node
    createStateNode(boolean loggedIn)
    Build a colored-coded disk indicating the status of the server connection
    static Map<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group,List<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner>>
    getAvailableGroupUsersMap(OmeroRawClient client)
    Return a map of available groups with its attached users.
    static qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group
    getDefaultGroupItem(OmeroRawClient client)
    Deprecated.
    Method removed
    static qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner
    getDefaultOwnerItem(OmeroRawClient client)
    Deprecated.
    Method removed
    static Map<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group,List<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner>>
    getGroupUsersMapAvailableForCurrentUser(OmeroRawClient client)
    Deprecated.
    use getAvailableGroupUsersMap(OmeroRawClient) instead
    protected static Map<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObjectType,BufferedImage>
    getOmeroIcons()
    Load container / image icons for the nice browser interface
    static List<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject>
    getOrphanedFolderItem(OmeroRawClient client, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group group, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner owner)
    Deprecated.
    Internal method ; not public anymore
    static qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner
    getOwnerItem(omero.model.Experimenter user)
    Deprecated.
    Method removed
    protected static javafx.util.StringConverter<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner>
    getOwnerStringConverter(Collection<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner> owners)
     
    static URI
    getStandardURI(URI uri, OmeroRawClient client)
    Deprecated.
    Method removed
    static List<URI>
    getURIs(URI uri, OmeroRawClient client)
    Deprecated.
    Method removed
    static int
    parseOmeroRawObjectId(URI uri, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObjectType type)
    Deprecated.
    Method removed
    static qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObjectType
    parseOmeroRawObjectType(URI uri)
    Deprecated.
    Method removed
    protected static List<qupath.lib.projects.ProjectImageEntry<BufferedImage>>
    promptToImportOmeroImages(qupath.lib.gui.QuPathGUI qupath, String... validUris)
    Prompt to import images, specifying the OmeroRawImageServerBuilder if possible.
    static qupath.ext.biop.servers.omero.raw.browser.OmeroRawAnnotations
    readAnnotationsItems(OmeroRawClient client, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject obj, qupath.ext.biop.servers.omero.raw.browser.OmeroRawAnnotations.OmeroRawAnnotationType category)
    Deprecated.
    Internal method ; not public anymore
    static List<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject>
    readOmeroObjectsItems(qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject parent, OmeroRawClient client, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group group, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner owner)
    Get all the child OMERO objects present in the OMERO server with the specified parent.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • OmeroRawBrowserTools

      public OmeroRawBrowserTools()

  • Method Details

    • readOmeroObjectsItems

      public static List<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject> readOmeroObjectsItems(qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject parent, OmeroRawClient client, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group group, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner owner)
      Get all the child OMERO objects present in the OMERO server with the specified parent.
      Parameters:
      client -
      parent -
      group -
      owner -
      Returns:
      list of OmeroRawObjects

    • getAvailableGroupUsersMap

      public static Map<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group,List<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner>> getAvailableGroupUsersMap(OmeroRawClient client)
      Return a map of available groups with its attached users.
      Parameters:
      client -
      Returns:
      available groups for the current user

    • addContainersAsMetadataFields

      public static void addContainersAsMetadataFields(qupath.lib.projects.ProjectImageEntry<BufferedImage> entry, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject obj)
      Adds the OMERO object hierarchy as QuPath metadata fields
      Parameters:
      entry - current QuPath entry
      obj - OMERO object to read the hierarchy from

    • getOmeroIcons

      protected static Map<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObjectType,BufferedImage> getOmeroIcons()
      Load container / image icons for the nice browser interface
      Returns:

    • getOwnerStringConverter

      protected static javafx.util.StringConverter<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner> getOwnerStringConverter(Collection<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner> owners)

    • promptToImportOmeroImages

      protected static List<qupath.lib.projects.ProjectImageEntry<BufferedImage>> promptToImportOmeroImages(qupath.lib.gui.QuPathGUI qupath, String... validUris)
      Prompt to import images, specifying the OmeroRawImageServerBuilder if possible.
      Parameters:
      validUris -
      Returns:

    • createStateNode

      public static javafx.scene.Node createStateNode(boolean loggedIn)
      Build a colored-coded disk indicating the status of the server connection
      Parameters:
      loggedIn -
      Returns:

    • getURIs

      @Deprecated public static List<URI> getURIs(URI uri, OmeroRawClient client) throws IOException, omero.gateway.exception.DSOutOfServiceException, ExecutionException, omero.gateway.exception.DSAccessException
      Deprecated.
      Method removed
      Return a list of valid URIs from the given URI. If no valid URI can be parsed from it, an IOException is thrown.

      E.g. "/host/webclient/?show=image=4|image=5" returns a list containing: "/host/webclient/?show=image=4" and "/host/webclient/?show=image=5".

      Parameters:
      uri -
      client -
      Returns:
      list
      Throws:
      IOException
      omero.gateway.exception.DSOutOfServiceException
      ExecutionException
      omero.gateway.exception.DSAccessException

    • getStandardURI

      @Deprecated public static URI getStandardURI(URI uri, OmeroRawClient client) throws IOException, ExecutionException, omero.gateway.exception.DSOutOfServiceException, omero.gateway.exception.DSAccessException
      Deprecated.
      Method removed
      Parameters:
      uri -
      client -
      Returns:
      Throws:
      IOException
      ExecutionException
      omero.gateway.exception.DSOutOfServiceException
      omero.gateway.exception.DSAccessException

    • parseOmeroRawObjectId

      @Deprecated public static int parseOmeroRawObjectId(URI uri, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObjectType type)
      Deprecated.
      Method removed
      Return the Id associated with the URI provided. If multiple Ids are present, only the first one will be retrieved. If no Id could be found, return -1.
      Parameters:
      uri -
      type -
      Returns:
      Id

    • parseOmeroRawObjectType

      @Deprecated public static qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObjectType parseOmeroRawObjectType(URI uri)
      Deprecated.
      Method removed
      Return the type associated with the URI provided. If multiple types are present, only the first one will be retrieved. If no type is found, return UNKNOWN.

      Accepts the same formats as the OmeroRawImageServer constructor.
      E.g., https://{server}/webclient/?show=dataset-{datasetId}

      Parameters:
      uri -
      Returns:
      omeroRawObjectType

    • readAnnotationsItems

      @Deprecated public static qupath.ext.biop.servers.omero.raw.browser.OmeroRawAnnotations readAnnotationsItems(OmeroRawClient client, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject obj, qupath.ext.biop.servers.omero.raw.browser.OmeroRawAnnotations.OmeroRawAnnotationType category)
      Deprecated.
      Internal method ; not public anymore
      Request the OmeroRawAnnotations object of type category associated with the OmeroRawObject specified.
      Parameters:
      client -
      obj -
      category -
      Returns:
      omeroRawAnnotations object

    • getOrphanedFolderItem

      @Deprecated public static List<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.OmeroRawObject> getOrphanedFolderItem(OmeroRawClient client, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group group, qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner owner)
      Deprecated.
      Internal method ; not public anymore
      Get all the orphaned images from the server for a certain user as list of OmeroRawObjects.OmeroRawObject
      Parameters:
      client -
      group -
      owner -
      Returns:

    • getOwnerItem

      @Deprecated public static qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner getOwnerItem(omero.model.Experimenter user)
      Deprecated.
      Method removed
      Build an OmeroRawObjects.Owner object based on the OMERO ExperimenterData user
      Parameters:
      user -
      Returns:

    • getDefaultOwnerItem

      @Deprecated public static qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner getDefaultOwnerItem(OmeroRawClient client)
      Deprecated.
      Method removed
      Return the OmeroRawObjects.Owner object corresponding to the logged-in user on the current OMERO session
      Parameters:
      client -
      Returns:

    • getDefaultGroupItem

      @Deprecated public static qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group getDefaultGroupItem(OmeroRawClient client)
      Deprecated.
      Method removed
      Return the group object corresponding to the default group attributed to the logged in user
      Parameters:
      client -
      Returns:

    • getGroupUsersMapAvailableForCurrentUser

      @Deprecated public static Map<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Group,List<qupath.ext.biop.servers.omero.raw.browser.OmeroRawObjects.Owner>> getGroupUsersMapAvailableForCurrentUser(OmeroRawClient client)
      Deprecated.
      use getAvailableGroupUsersMap(OmeroRawClient) instead
      Return a map of available groups with its attached users.
      Parameters:
      client -
      Returns:
      available groups for the current user