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

Class OmeroRawScripting

java.lang.Object
qupath.ext.biop.servers.omero.raw.utils.OmeroRawScripting
public class OmeroRawScripting extends Object
Static class which groups the methods of the scripting API for an OMERORawImageServer

  • Constructor Details

    • OmeroRawScripting

      public OmeroRawScripting()

  • Method Details

    • getROIs

      public static Collection<qupath.lib.objects.PathObject> getROIs(OmeroRawImageServer imageServer, String owner, boolean qpNotif)
      get ROIs owned by the specified owner and linked to the current image from OMERO to QuPath
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      owner - owner of the ROis to filter
      qpNotif - true to display a QuPath notification
      Returns:
      The list of OMERO rois converted into pathObjects

    • getROIs

      public static Collection<qupath.lib.objects.PathObject> getROIs(OmeroRawClient client, long imageId, String owner, boolean qpNotif)
      get ROIs owned by the specified owner and linked to the current image from OMERO to QuPath
      Parameters:
      client - Omero client that handles the connection
      imageId - OMERO image ID
      owner - owner of the ROis to filter
      qpNotif - true to display a QuPath notification
      Returns:
      The list of OMERO rois converted into pathObjects

    • addROIsToQuPath

      public static Collection<qupath.lib.objects.PathObject> addROIsToQuPath(OmeroRawImageServer imageServer, boolean removePathObjects, String owner, boolean qpNotif)
      get and add to QuPath all ROIs owned by the specified owner and linked to the current image from OMERO to QuPath
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      owner - owner of the ROis to filter
      qpNotif - true to display a QuPath notification
      Returns:
      The list of OMERO rois converted into pathObjects

    • sendAnnotationsToOmero

      public static List<fr.igred.omero.roi.ROIWrapper> sendAnnotationsToOmero(OmeroRawImageServer imageServer, boolean deleteROIs, String owner, boolean qpNotif)
      Send a collection of QuPath objects (annotations and/or detections) to OMERO, without deleting existing ROIs
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      deleteROIs - Boolean to keep or delete ROIs on the current image on OMERO
      owner - the owner of the ROIs to delete. If null, then all ROIs are deleted whatever the owner
      qpNotif - true to display a QuPath notification
      Returns:
      the list of sent ROIWrappers or null if nothing can be sent to OMERO

    • sendPathObjectsToOmero

      public static List<fr.igred.omero.roi.ROIWrapper> sendPathObjectsToOmero(OmeroRawImageServer imageServer, Collection<qupath.lib.objects.PathObject> pathObjects, boolean deleteROIsOnOMERO, String owner, boolean qpNotif)
      Send a collection of pathObjects to OMERO.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      pathObjects - QuPath annotations or detections objects
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      owner - the owner of the ROIs to delete. If null, then all ROIs are deleted whatever the owner
      qpNotif - true to display a QuPath notification
      Returns:
      the list of sent ROIWrappers or null if nothing can be sent to OMERO

    • sendQPMetadataToOmero

      public static Map<String,Map<String,String>> sendQPMetadataToOmero(Map<String,String> qpMetadata, OmeroRawImageServer imageServer, Utils.UpdatePolicy kvpPolicy, Utils.UpdatePolicy tagPolicy, boolean qpNotif)
      Send QuPath metadata to OMERO.

      • If the QuPath metadata key and value are identical, then a tag is created on OMERO
      • If the QuPath metadata key and value are different, then a key-value pair is created on OMERO

      Parameters:
      qpMetadata - Map of key-value
      imageServer - ImageServer of an image loaded from OMERO
      kvpPolicy - replacement policy you choose to replace key-value pairs on OMERO
      tagPolicy - replacement policy you choose to replace tags on OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      a map containing the key-values / tags sent. Use Utils.KVP_KEY and Utils.TAG_KEY to access the corresponding map. For tag, the returned map has identical key:value

    • sendKeyValuesToOmero

      public static boolean sendKeyValuesToOmero(Map<String,String> qpMetadataKVP, OmeroRawImageServer imageServer, Utils.UpdatePolicy policy, boolean qpNotif)
      Send a map to OMERO as Key-Value pairs. Check if OMERO keys are unique. If they are not, metadata are not sent
      Parameters:
      qpMetadataKVP - Map of key-value
      imageServer - ImageServer of an image loaded from OMERO
      policy - replacement policy you choose to replace annotations on OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      Sending status (true if key-value pairs have been sent ; false if there were troubles during the sending process)

    • sendTagsToOmero

      public static boolean sendTagsToOmero(List<String> tags, OmeroRawImageServer imageServer, Utils.UpdatePolicy policy, boolean qpNotif)
      Send a list of tags to OMERO. If tags are already attached to the image, these tags are not sent.
      Parameters:
      tags - List of tags to add to the image
      imageServer - ImageServer of an image loaded from OMERO
      policy - replacement policy you choose to replace annotations on OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      Sending status (true if tags have been sent ; false if there were troubles during the sending process)

    • addKeyValuesToQuPath

      public static Map<String,String> addKeyValuesToQuPath(OmeroRawImageServer imageServer, Utils.UpdatePolicy policy, boolean qpNotif)
      Read and add OMERO Key-Value pairs as QuPath metadata to the current image in the QuPath project.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      policy - replacement policy you choose to replace annotations on OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      a map of OMERO key-value pairs

    • addKeyValuesToQuPath

      public static void addKeyValuesToQuPath(qupath.lib.projects.ProjectImageEntry<BufferedImage> entry, Map<String,String> kvps, Utils.UpdatePolicy policy, boolean qpNotif)
      add Key-Value pairs as QuPath metadata to the image in the QuPath project.

      WARNING : If you run addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) and / or addParentHierarchyToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) before addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) and if you would like to use the policy Utils.UpdatePolicy.DELETE_KEYS, then you should apply this policy to the first method but NOT to the second ones (use Utils.UpdatePolicy.KEEP_KEYS instead)

      Parameters:
      entry - the project entry to link the key-values to
      kvps - map containing the key-value to add
      policy - replacement policy you choose to replace annotations on OMERO
      qpNotif - true to display a QuPath notification

    • addTagsToQuPath

      public static List<String> addTagsToQuPath(OmeroRawImageServer imageServer, Utils.UpdatePolicy policy, boolean qpNotif)
      Read, from OMERO, tags attached to the current image and add them as QuPath metadata fields

      WARNING : If you run addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) and / or addParentHierarchyToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) before addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) and if you would like to use the policy Utils.UpdatePolicy.DELETE_KEYS, then you should apply this policy to the first method but NOT to the second ones (use Utils.UpdatePolicy.KEEP_KEYS instead)

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      policy - replacement policy you choose to replace annotations on OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      list of OMERO tags.

    • addTagsToQuPath

      public static List<String> addTagsToQuPath(qupath.lib.projects.ProjectImageEntry<BufferedImage> entry, List<String> tags, Utils.UpdatePolicy policy, boolean qpNotif)
      Add a list of tags (string) as QuPath metadata fields

      WARNING : If you run addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) and / or addParentHierarchyToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) before addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) and if you would like to use the policy Utils.UpdatePolicy.DELETE_KEYS, then you should apply this policy to the first method but NOT to the second ones (use Utils.UpdatePolicy.KEEP_KEYS instead)

      Parameters:
      entry - the project entry to link the tags to
      tags - List of strings
      policy - replacement policy you choose to replace annotations on OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      list of OMERO tags.

    • addParentHierarchyToQuPath

      public static Map<String,String> addParentHierarchyToQuPath(OmeroRawImageServer imageServer, Utils.UpdatePolicy policy, boolean qpNotif)
      add the parent containers of the current image as QuPath metadata fields

      WARNING : If you run addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) and / or addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) before addParentHierarchyToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) and if you would like to use the policy Utils.UpdatePolicy.DELETE_KEYS, then you should apply this policy to the first method but NOT to the second ones (use Utils.UpdatePolicy.KEEP_KEYS instead)

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      policy - replacement policy you choose to replace annotations on OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      a map of the parent containers name % id

    • sendAnnotationMeasurementsToOmero

      public static long sendAnnotationMeasurementsToOmero(OmeroRawImageServer imageServer, Collection<qupath.lib.objects.PathObject> annotationObjects, qupath.lib.images.ImageData<BufferedImage> imageData, boolean deleteOlderVersions, String owner, boolean qpNotif)
      Send pathObjects' measurements to OMERO as an OMERO.table with a default table name referring to annotations
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      annotationObjects - QuPath annotations objects
      imageData - QuPath image
      deleteOlderVersions - Delete of not all previous OMERO measurement tables
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      qpNotif - true to display a QuPath notification
      Returns:
      the ID of the new table ; -1 if sending failed

    • sendDetectionMeasurementsToOmero

      public static long sendDetectionMeasurementsToOmero(OmeroRawImageServer imageServer, Collection<qupath.lib.objects.PathObject> detectionObjects, qupath.lib.images.ImageData<BufferedImage> imageData, boolean deletePrevious, String owner, boolean qpNotif)
      Send pathObjects' measurements to OMERO as an OMERO.table with a default table name referring to detections
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      detectionObjects - QuPath annotations or detections objects
      imageData - QuPath image
      deletePrevious - Delete of not all previous OMERO measurement tables
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      qpNotif - true to display a QuPath notification
      Returns:
      the ID of the new table ; -1 if sending failed

    • sendAnnotationMeasurementsAsCSVToOmero

      public static long sendAnnotationMeasurementsAsCSVToOmero(OmeroRawImageServer imageServer, Collection<qupath.lib.objects.PathObject> annotationObjects, qupath.lib.images.ImageData<BufferedImage> imageData, boolean deletePrevious, String owner, boolean qpNotif)
      Send pathObjects' measurements to OMERO as a CSV file with a default table name referring to annotation
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      annotationObjects - QuPath annotations objects
      imageData - QuPath image
      deletePrevious - Delete of not all previous OMERO measurement tables
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      qpNotif - true to display a QuPath notification
      Returns:
      the ID of the new CSV file ; -1 if sending failed

    • sendDetectionMeasurementsAsCSVToOmero

      public static long sendDetectionMeasurementsAsCSVToOmero(OmeroRawImageServer imageServer, Collection<qupath.lib.objects.PathObject> detectionObjects, qupath.lib.images.ImageData<BufferedImage> imageData, boolean deletePrevious, String owner, boolean qpNotif)
      Send pathObjects' measurements to OMERO as a CSV file with a default table name referring to annotation
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      detectionObjects - QuPath annotations objects
      imageData - QuPath image
      deletePrevious - Delete of not all previous OMERO measurement tables
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      qpNotif - true to display a QuPath notification
      Returns:
      the ID of the new CSV file ; -1 if sending failed

    • addMeasurementsToParentTable

      public static void addMeasurementsToParentTable(LinkedHashMap<String,List<String>> parentTable, Collection<qupath.lib.objects.PathObject> pathObjects, OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Populate a map "header, List_of_measurements" with new measurements coming from a measurement table of new pathObjects.
      Parameters:
      parentTable - LinkedHashMap "header, List_of_measurements" to populate. Other type of maps will not work
      pathObjects - QuPath annotations or detections objects
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image

    • sendParentMeasurementsAsCSVToOmero

      public static long sendParentMeasurementsAsCSVToOmero(LinkedHashMap<String,List<String>> parentTable, OmeroRawClient client, Collection<fr.igred.omero.repository.GenericRepositoryObjectWrapper<?>> parents, boolean deleteOlderVersions, String owner, boolean qpNotif)
      Send the summary map "header, List_of_measurements" to OMERO as an CSV file attached to the parent containers.

      • IMPORTANT : The attached file is uploaded ONCE on the OMERO database. The same file is then linked to the multiple parent containers. If one deletes the file, all the links will also be deleted

      Parameters:
      parentTable - LinkedHashMap "header, List_of_measurements" to populate. Other type of maps will not work
      client - OMERO Client Object to handle OMERO connection
      parents - Collection of parent container on OMERO to link the file to
      deleteOlderVersions - True if you want to delete previous CSV files on the parent container, linked to the current QuPath project
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      qpNotif - true to display a QuPath notification
      Returns:
      the ID of the new csv file ; -1 if sending failed

    • sendParentMeasurementsToOmero

      public static long sendParentMeasurementsToOmero(LinkedHashMap<String,List<String>> parentTable, OmeroRawClient client, Collection<fr.igred.omero.repository.GenericRepositoryObjectWrapper<?>> parents, boolean deleteOlderVersions, String owner, boolean qpNotif)
      Send the summary map "header, List_of_measurements" to OMERO as an OMERO.table attached to the parent container

      • IMPORTANT : The attached file is uploaded ONCE on the OMERO database. The same file is then linked to the multiple parent containers. If one deletes the file, all the links will also be deleted

      Parameters:
      parentTable - LinkedHashMap "header, List_of_measurements" to populate. Other type of maps will not work
      client - OMERO Client Object to handle OMERO connection
      parents - Collection of parent containers on OMERO to link the file to
      deleteOlderVersions - True if you want to delete previous CSV files on the parent container, linked to the current QuPath project
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      qpNotif - true to display a QuPath notification
      Returns:
      the ID of the new table ; -1 if sending failed

    • deleteAnnotationMeasurements

      public static boolean deleteAnnotationMeasurements(OmeroRawImageServer imageServer, String owner, boolean qpNotif)
      Delete all previous version of annotation tables (OMERO and csv files) related to the current QuPath project. Files to delete are filtered according to the current QuPath project.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      qpNotif - true to display a QuPath notification

    • deleteDetectionMeasurements

      public static boolean deleteDetectionMeasurements(OmeroRawImageServer imageServer, String owner, boolean qpNotif)
      Delete all previous version of detection tables (OMERO and csv files) related to the current QuPath project. Files to delete are filtered according to the current QuPath project.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      qpNotif - true to display a QuPath notification

    • copyOmeroChannelsDisplayRangeToQuPath

      public static void copyOmeroChannelsDisplayRangeToQuPath(OmeroRawImageServer imageServer, boolean qpNotif)
      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.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      qpNotif - true to display a QuPath notification

    • copyOmeroChannelsColorToQuPath

      public static void copyOmeroChannelsColorToQuPath(OmeroRawImageServer imageServer, boolean qpNotif)
      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.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      qpNotif - true to display a QuPath notification

    • copyOmeroChannelsNameToQuPath

      public static void copyOmeroChannelsNameToQuPath(OmeroRawImageServer imageServer, boolean qpNotif)
      Set the name of each channel on QuPath, based on OMERO settings. Channel indices are taken as reference.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      qpNotif - true to display a QuPath notification

    • sendQuPathChannelsDisplayRangeToOmero

      public static boolean sendQuPathChannelsDisplayRangeToOmero(OmeroRawImageServer imageServer, boolean qpNotif)
      Set the minimum and maximum display range value of each channel on OMERO, based on QuPath settings.
      OMERO image and thumbnail are updated accordingly.
      Channel indices are taken as reference.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      Sending status (true if the image and thumbnail on OMERO has been updated ; false if there were troubles during the sending process)

    • sendQuPathChannelsNameToOmero

      public static boolean sendQuPathChannelsNameToOmero(OmeroRawImageServer imageServer, boolean qpNotif)
      Set the name of each channel on OMERO, based on QuPath settings. Channel indices are taken as reference.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      Sending status (true if the image and thumbnail on OMERO has been updated ; false if there were troubles during the sending process)

    • sendQuPathChannelsColorToOmero

      public static boolean sendQuPathChannelsColorToOmero(OmeroRawImageServer imageServer, boolean qpNotif)
      Set the color of each channel on OMERO, based on QuPath settings. OMERO image and thumbnail are updated accordingly.
      Channel indices are taken as reference.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      Sending status (true if the image and thumbnail on OMERO has been updated ; false if there were troubles during the sending process)

    • sendQuPathImageNameToOmero

      public static boolean sendQuPathImageNameToOmero(OmeroRawImageServer imageServer, boolean qpNotif)
      Set the name the image on OMERO, based on QuPath settings.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      qpNotif - true to display a QuPath notification
      Returns:
      Sending status (true if the image name on OMERO has been updated ; false if there were troubles during the sending process)

    • importOmeroROIsToQuPath

      @Deprecated public static Collection<qupath.lib.objects.PathObject> importOmeroROIsToQuPath(OmeroRawImageServer imageServer)
      Deprecated.
      use addROIsToQuPath(OmeroRawImageServer, boolean, String, boolean) instead
      Import all ROIs, whatever the owner, from OMERO to QuPath, for the current image and remove all current annotations/detections in QuPath.
      Parameters:
      imageServer - : ImageServer of an image loaded from OMERO
      Returns:
      The list of OMERO rois converted into pathObjects.

    • importOmeroTags

      @Deprecated public static List<String> importOmeroTags(OmeroRawImageServer imageServer)
      Deprecated.
      use addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
      Read, from OMERO, tags attached to the current image.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      list of OMERO tags.

    • sendPathObjectsToOmero

      @Deprecated public static boolean sendPathObjectsToOmero(OmeroRawImageServer imageServer, Collection<qupath.lib.objects.PathObject> pathObjects, boolean deleteROIsOnOMERO)
      Deprecated.
      use sendPathObjectsToOmero(OmeroRawImageServer, Collection, boolean, String, boolean) instead.
      Send a collection of pathObjects to OMERO.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      pathObjects - QuPath annotations or detections objects
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendDetectionsToOmero

      @Deprecated public static boolean sendDetectionsToOmero(OmeroRawImageServer imageServer, boolean deleteROIsOnOMERO)
      Deprecated.
      method removed
      Send all QuPath detections to OMERO and delete existing ROIs is specified.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendPathObjectsToOmero

      @Deprecated public static boolean sendPathObjectsToOmero(OmeroRawImageServer imageServer)
      Deprecated.
      use sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead
      Send all QuPath objects (annotations and detections) to OMERO and deletes ROIs already stored on OMERO Be careful : the number of ROIs that can be displayed at the same time on OMERO is 500.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendPathObjectsToOmero

      @Deprecated public static boolean sendPathObjectsToOmero(OmeroRawImageServer imageServer, boolean deleteROIsOnOMERO, String owner)
      Deprecated.
      use sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead
      Send all QuPath objects (annotations and detections) to OMERO. Be careful : the number of ROIs that can be displayed at the same time on OMERO is 500.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      owner - the owner of the ROIs to delete. If null, then all ROIs are deleted whatever the owner
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendAnnotationsToOmero

      @Deprecated public static boolean sendAnnotationsToOmero(OmeroRawImageServer imageServer)
      Deprecated.
      use sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead
      Send all QuPath annotation objects to OMERO, without deleting current ROIs on OMERO.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendAnnotationsToOmero

      @Deprecated public static boolean sendAnnotationsToOmero(OmeroRawImageServer imageServer, boolean deleteROIsOnOMERO, String owner)
      Deprecated.
      use sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead
      Send all QuPath annotation objects to OMERO.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      owner - the owner of the ROIs to delete. If null, then all ROIs are deleted whatever the owner
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendDetectionsToOmero

      @Deprecated public static boolean sendDetectionsToOmero(OmeroRawImageServer imageServer)
      Deprecated.
      method removed
      Send all QuPath detection objects to OMERO without deleting existing ROIs.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendDetectionsToOmero

      @Deprecated public static boolean sendDetectionsToOmero(OmeroRawImageServer imageServer, boolean deleteROIsOnOMERO, String owner)
      Deprecated.
      method removed
      Send all QuPath detections to OMERO and delete existing ROIs is specified.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      owner - the owner of the ROIs to delete. If null, then all ROIs are deleted whatever the owner
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendPathObjectsToOmero

      @Deprecated public static boolean sendPathObjectsToOmero(OmeroRawImageServer imageServer, Collection<qupath.lib.objects.PathObject> pathObjects, boolean deleteROIsOnOMERO, String owner)
      Deprecated.
      use sendPathObjectsToOmero(OmeroRawImageServer, Collection, boolean, String, boolean) instead
      Send a collection of pathObjects to OMERO.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      pathObjects - QuPath annotations or detections objects
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      owner - the owner of the ROIs to delete. If null, then all ROIs are deleted whatever the owner
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendPathObjectsToOmero

      @Deprecated public static boolean sendPathObjectsToOmero(OmeroRawImageServer imageServer, Collection<qupath.lib.objects.PathObject> pathObjects)
      Deprecated.
      use sendPathObjectsToOmero(OmeroRawImageServer, Collection, boolean, String, boolean) instead
      Send a collection of QuPath objects (annotations and/or detections) to OMERO, without deleting existing ROIs
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      pathObjects - QuPath annotations or detections objects
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendAnnotationsToOmero

      @Deprecated public static boolean sendAnnotationsToOmero(OmeroRawImageServer imageServer, boolean deleteROIsOnOMERO)
      Deprecated.
      use sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead.
      Send all QuPath annotation objects to OMERO.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • sendPathObjectsToOmero

      @Deprecated public static boolean sendPathObjectsToOmero(OmeroRawImageServer imageServer, boolean deleteROIsOnOMERO)
      Deprecated.
      use sendAnnotationsToOmero(OmeroRawImageServer, boolean, String, boolean) instead.
      Send all QuPath objects (annotations and detections) to OMERO. Be careful : the number of ROIs that can be displayed at the same time on OMERO is 500.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      deleteROIsOnOMERO - Boolean to keep or delete ROIs on the current image on OMERO
      Returns:
      Sending status (true if ROIs have been sent ; false if there were troubles during the sending process)

    • getSimpleOmeroClientInstance

      @Deprecated public static fr.igred.omero.Client getSimpleOmeroClientInstance(OmeroRawImageServer imageServer)
      Deprecated.
      use OmeroRawClient.getSimpleClient() instead (accessible from OmeroRawImageServer.getClient())
      This method creates an instance of simple-omero-client object to get access to the full simple-omero-client API, developed by Pierre Pouchin (...).
      Parameters:
      imageServer - : ImageServer of an image loaded from OMERO
      Returns:
      fr.igred.omero.Client object

    • importOmeroROIsToQuPath

      @Deprecated public static Collection<qupath.lib.objects.PathObject> importOmeroROIsToQuPath(OmeroRawImageServer imageServer, boolean removePathObjects)
      Deprecated.
      use addROIsToQuPath(OmeroRawImageServer, boolean, String, boolean) instead
      Import all ROIs linked to the current image from OMERO to QuPath.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      removePathObjects - Boolean to delete or keep pathObjects (annotations, detections) on the current image.
      Returns:
      The list of OMERO rois converted into pathObjects

    • importOmeroROIsToQuPath

      @Deprecated public static Collection<qupath.lib.objects.PathObject> importOmeroROIsToQuPath(OmeroRawImageServer imageServer, boolean removePathObjects, String owner)
      Deprecated.
      use addROIsToQuPath(OmeroRawImageServer, boolean, String, boolean) instead
      Import ROIs owned by the specified owner and linked to the current image from OMERO to QuPath
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      removePathObjects - Boolean to delete or keep pathObjects (annotations, detections) on the current image.
      owner - owner of the ROis to filter
      Returns:
      The list of OMERO rois converted into pathObjects

    • sendMetadataOnOmero

      @Deprecated public static boolean sendMetadataOnOmero(Map<String,String> qpMetadata, OmeroRawImageServer imageServer)
      Deprecated.
      use sendQPMetadataToOmero(Map, OmeroRawImageServer, Utils.UpdatePolicy, Utils.UpdatePolicy, boolean) instead
      Send QuPath metadata to OMERO as Key-Value pairs. Check if OMERO keys are unique. If they are not, metadata are not sent
      Existing keys on OMERO are :

      • deleted : NO
      • updated : NO

      Parameters:
      qpMetadata - Map of key-value
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if key-value pairs have been sent ; false if there were troubles during the sending process)

    • sendMetadataOnOmeroAndDeleteKeyValues

      @Deprecated public static boolean sendMetadataOnOmeroAndDeleteKeyValues(Map<String,String> qpMetadata, OmeroRawImageServer imageServer)
      Deprecated.
      use sendQPMetadataToOmero(Map, OmeroRawImageServer, Utils.UpdatePolicy, Utils.UpdatePolicy, boolean) instead
      Send QuPath metadata to OMERO as Key-Value pairs. Check if OMERO keys are unique. If they are not, metadata are not sent
      Existing keys on OMERO are :

      • deleted : YES
      • updated : NO

      Parameters:
      qpMetadata - Map of key-value
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if key-value pairs have been sent ; false if there were troubles during the sending process)

    • sendMetadataOnOmeroAndUpdateKeyValues

      @Deprecated public static boolean sendMetadataOnOmeroAndUpdateKeyValues(Map<String,String> qpMetadata, OmeroRawImageServer imageServer)
      Deprecated.
      use sendQPMetadataToOmero(Map, OmeroRawImageServer, Utils.UpdatePolicy, Utils.UpdatePolicy, boolean) instead
      Send QuPath metadata to OMERO as Key-Value pairs. Check if OMERO keys are unique. If they are not, metadata are not sent.
      Existing keys on OMERO are :

      • deleted : NO
      • updated : YES

      Parameters:
      qpMetadata - Map of key-value
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if key-value pairs have been sent ; false if there were troubles during the sending process)

    • importOmeroKeyValues

      @Deprecated public static Map<String,String> importOmeroKeyValues(OmeroRawImageServer imageServer)
      Deprecated.
      use addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
      Read, from OMERO, Key-Value pairs attached to the current image and check if all keys are unique. If they are not unique, no Key-Values are returned.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      map of OMERO Key-Value pairs

    • sendTagsToOmero

      @Deprecated public static boolean sendTagsToOmero(List<String> tags, OmeroRawImageServer imageServer)
      Deprecated.
      use sendTagsToOmero(List, OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
      Send a list of tags to OMERO. If tags are already attached to the image, these tags are not sent.
      Parameters:
      tags - List of tags to add to the image
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if tags have been sent ; false if there were troubles during the sending process)

    • addMetadata

      @Deprecated public static void addMetadata(Map<String,String> keyValues)
      Deprecated.
      use addKeyValuesToQuPath(ProjectImageEntry, Map, Utils.UpdatePolicy, boolean) instead
      Add new QuPath metadata to the current image in the QuPath project.
      Existing keys in QuPath are :

      • deleted : NO
      • updated : NO

      Parameters:
      keyValues - map of key-values

    • addOmeroKeyValues

      @Deprecated public static void addOmeroKeyValues(OmeroRawImageServer imageServer)
      Deprecated.
      use addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
      Read and add OMERO Key-Value pairs as QuPath metadata to the current image in the QuPath project.
      Existing keys in QuPath are :

      • deleted : NO
      • updated : NO

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO

    • addAndUpdateMetadata

      @Deprecated public static void addAndUpdateMetadata(Map<String,String> keyValues)
      Deprecated.
      use addKeyValuesToQuPath(ProjectImageEntry, Map, Utils.UpdatePolicy, boolean) instead
      Add new QuPath metadata to the current image in the QuPath project.
      Existing keys in QuPath are :

      • deleted : NO
      • updated : YES

      Parameters:
      keyValues - map of key-values

    • addOmeroKeyValuesAndUpdateMetadata

      @Deprecated public static void addOmeroKeyValuesAndUpdateMetadata(OmeroRawImageServer imageServer)
      Deprecated.
      use addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
      Read and add OMERO Key-Value pairs as QuPath metadata to the current image in the QuPath project.
      Existing keys in QuPath are :

      • deleted : NO
      • updated : YES

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO

    • addOmeroKeyValuesAndDeleteMetadata

      @Deprecated public static void addOmeroKeyValuesAndDeleteMetadata(OmeroRawImageServer imageServer)
      Deprecated.
      use addKeyValuesToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
      Read and add OMERO Key-Value pairs as QuPath metadata to the current image in the QuPath project.
      Existing keys in QuPath are :

      • deleted : YES
      • updated : NO

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO

    • addAndDeleteMetadata

      @Deprecated public static void addAndDeleteMetadata(Map<String,String> keyValues)
      Deprecated.
      use addKeyValuesToQuPath(ProjectImageEntry, Map, Utils.UpdatePolicy, boolean) instead
      Add new QuPath metadata to the current image in the QuPath project.
      Existing keys in QuPath are :

      • deleted : YES
      • updated : NO

      Parameters:
      keyValues - map of key-values

    • addTagsToQuPath

      @Deprecated public static List<String> addTagsToQuPath(OmeroRawImageServer imageServer)
      Deprecated.
      use addTagsToQuPath(OmeroRawImageServer, Utils.UpdatePolicy, boolean) instead
      Read, from OMERO, tags attached to the current image and add them as QuPath metadata fields
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      list of OMERO tags.

    • sendDetectionMeasurementTable

      @Deprecated public static boolean sendDetectionMeasurementTable(OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Deprecated.
      use sendDetectionMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
      Send all detections measurements to OMERO as an OMERO.table
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      Returns:
      Sending status (true if the OMERO.table has been sent ; false if there were troubles during the sending process)

    • sendDetectionMeasurementTable

      @Deprecated public static boolean sendDetectionMeasurementTable(Collection<qupath.lib.objects.PathObject> detectionObjects, OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Deprecated.
      use sendDetectionMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
      Send pathObjects' measurements to OMERO as an OMERO.table with a default table name referring to detections
      Parameters:
      detectionObjects - QuPath detection objects
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      Returns:
      Sending status (true if the OMERO.table has been sent ; false if there were troubles during the sending process)

    • sendMeasurementTableToOmero

      @Deprecated public static boolean sendMeasurementTableToOmero(Collection<qupath.lib.objects.PathObject> annotationObjects, OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData, String tableName)
      Deprecated.
      use sendMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, String, boolean, String, boolean) instead
      Send pathObjects' measurements to OMERO as an OMERO.table with a default table name referring to annotations
      Parameters:
      annotationObjects - QuPath annotations objects
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      tableName - Name of the table to upload
      Returns:
      Sending status (true if the OMERO.table has been sent ; false if there were troubles during the sending process)

    • sendAnnotationMeasurementTable

      @Deprecated public static boolean sendAnnotationMeasurementTable(OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Deprecated.
      use sendAnnotationMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
      Send all annotations measurements to OMERO as an OMERO.table
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      Returns:
      Sending status (true if the OMERO.table has been sent ; false if there were troubles during the sending process)

    • sendAnnotationMeasurementTable

      @Deprecated public static boolean sendAnnotationMeasurementTable(Collection<qupath.lib.objects.PathObject> annotationObjects, OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Deprecated.
      use sendAnnotationMeasurementsToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
      Send pathObjects' measurements to OMERO as an OMERO.table with a default table name referring to annotations
      Parameters:
      annotationObjects - QuPath annotations objects
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      Returns:
      Sending status (true if the OMERO.table has been sent ; false if there were troubles during the sending process)

    • sendDetectionMeasurementTableAsCSV

      @Deprecated public static boolean sendDetectionMeasurementTableAsCSV(OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Deprecated.
      use sendDetectionMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
      Send all detections measurements to OMERO as a CSV file
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • sendDetectionMeasurementTableAsCSV

      @Deprecated public static boolean sendDetectionMeasurementTableAsCSV(Collection<qupath.lib.objects.PathObject> detectionObjects, OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Deprecated.
      use sendDetectionMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
      Send pathObjects' measurements to OMERO as a CSV file with a default table name referring to annotation
      Parameters:
      detectionObjects - QuPath detection objects
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • sendAnnotationMeasurementTableAsCSV

      @Deprecated public static boolean sendAnnotationMeasurementTableAsCSV(OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Deprecated.
      use sendAnnotationMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
      Send all annotations measurements to OMERO as a CSV file
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • sendAnnotationMeasurementTableAsCSV

      @Deprecated public static boolean sendAnnotationMeasurementTableAsCSV(Collection<qupath.lib.objects.PathObject> annotationObjects, OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData)
      Deprecated.
      use sendAnnotationMeasurementsAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, boolean, String, boolean) instead
      Send pathObjects' measurements to OMERO as a CSV file with a default table name referring to annotation
      Parameters:
      annotationObjects - QuPath annotation objects
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • sendMeasurementTableAsCSVToOmero

      @Deprecated public static boolean sendMeasurementTableAsCSVToOmero(Collection<qupath.lib.objects.PathObject> pathObjects, OmeroRawImageServer imageServer, qupath.lib.images.ImageData<BufferedImage> imageData, String filename)
      Deprecated.
      use sendMeasurementAsCSVToOmero(OmeroRawImageServer, Collection, ImageData, String, boolean, String, boolean) instead
      Send pathObjects' measurements to OMERO as a CSV file with a default table name referring to annotation
      Parameters:
      pathObjects - QuPath detection objects
      imageServer - ImageServer of an image loaded from OMERO
      imageData - QuPath image
      filename - Name of the file to upload
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • deleteDetectionFiles

      @Deprecated public static void deleteDetectionFiles(OmeroRawImageServer imageServer)
      Deprecated.
      use deleteDetectionMeasurements(OmeroRawImageServer, String, boolean) instead
      Delete all previous version of detection tables (OMERO and csv files) related to the current QuPath project. Files to delete are retrieved from the corresponding image on OMERO and filtered according to the current QuPath project
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO

    • deleteDetectionFiles

      @Deprecated public static void deleteDetectionFiles(OmeroRawImageServer imageServer, Collection<omero.gateway.model.FileAnnotationData> files)
      Deprecated.
      use deleteDetectionMeasurements(OmeroRawImageServer, String, boolean) instead
      Delete all previous version of detection tables (OMERO and csv files) related to the current QuPath project. Files to delete are filtered according to the current QuPath project.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      files - List of files to browse

    • deleteDetectionFiles

      @Deprecated public static void deleteDetectionFiles(OmeroRawImageServer imageServer, Collection<omero.gateway.model.FileAnnotationData> files, String owner)
      Deprecated.
      use deleteDetectionMeasurements(OmeroRawImageServer, String, boolean) instead
      Delete all previous version of detection tables (OMERO and csv files) related to the current QuPath project. Files to delete are filtered according to the current QuPath project.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      files - List of files to browse
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner

    • deleteFiles

      @Deprecated public static void deleteFiles(OmeroRawImageServer imageServer, String name)
      Deprecated.
      use Client.delete(Collection) instead
      Delete all previous version of a file, identified by the name given in parameters. This name may or may not be the full name of the files to delete.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      name - contained in the table/file name to delete (i.e. filtering item). It may be a part of the full table/file name

    • readFilesAttachedToCurrentImageOnOmero

      @Deprecated public static List<omero.gateway.model.FileAnnotationData> readFilesAttachedToCurrentImageOnOmero(OmeroRawImageServer imageServer)
      Deprecated.
      use AnnotatableWrapper.getFileAnnotations(Client) instead
      Return the files as FileAnnotationData attached to the current image from OMERO.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      a list of read FileAnnotationData

    • linkFile

      @Deprecated protected static omero.gateway.model.FileAnnotationData linkFile(OmeroRawClient client, omero.gateway.model.FileAnnotationData fileAnnotationData, omero.gateway.model.DataObject container)
      Deprecated.
      use AnnotatableWrapper.link(Client, GenericAnnotationWrapper[]) instead
      Link a FileAnnotationData to an OMERO container The FileAnnotationData must already have a valid ID on OMERO (i.e. already existing in the OMERO database)
      Parameters:
      client - OmeroRawClient object to handle OMERO connection
      fileAnnotationData - annotation to link
      container - on OMERO
      Returns:
      the linked FileAnnotationData

    • deleteAnnotationFiles

      @Deprecated public static void deleteAnnotationFiles(OmeroRawImageServer imageServer)
      Deprecated.
      use deleteAnnotationMeasurements(OmeroRawImageServer, String, boolean) instead
      Delete all previous version of annotation tables (OMERO and csv files) related to the current QuPath project. Files to delete are retrieved from the corresponding image on OMERO and filtered according to the current QuPath project
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO

    • deleteAnnotationFiles

      @Deprecated public static void deleteAnnotationFiles(OmeroRawImageServer imageServer, Collection<omero.gateway.model.FileAnnotationData> files)
      Deprecated.
      use deleteAnnotationMeasurements(OmeroRawImageServer, String, boolean) instead
      Delete all previous version of annotation tables (OMERO and csv files) related to the current QuPath project. Files to delete are filtered according to the current QuPath project.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      files - List of files to browse

    • deleteAnnotationFiles

      @Deprecated public static void deleteAnnotationFiles(OmeroRawImageServer imageServer, Collection<omero.gateway.model.FileAnnotationData> files, String owner)
      Deprecated.
      deleteAnnotationMeasurements(OmeroRawImageServer, String, boolean) instead
      Delete all previous version of annotation tables (OMERO and csv files) related to the current QuPath project. Files to delete are filtered according to the current QuPath project.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      files - List of files to browse
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner

    • sendParentMeasurementTableAsOmeroTable

      @Deprecated public static boolean sendParentMeasurementTableAsOmeroTable(LinkedHashMap<String,List<String>> parentTable, OmeroRawClient client, Collection<omero.gateway.model.DataObject> parents, boolean deletePreviousTable)
      Deprecated.
      use sendParentMeasurementsToOmero(LinkedHashMap, OmeroRawClient, Collection, boolean, String, boolean) instead
      Send the summary map "header, List_of_measurements" to OMERO as an OMERO.table attached to the parent container

      • IMPORTANT : The attached file is uploaded ONCE on the OMERO database. The same file is then linked to the multiple parent containers. If one deletes the file, all the links will also be deleted

      Parameters:
      parentTable - LinkedHashMap "header, List_of_measurements" to populate. Other type of maps will not work
      client - OMERO Client Object to handle OMERO connection
      parents - Collection of parent containers on OMERO to link the file to
      deletePreviousTable - True if you want to delete previous CSV files on the parent container, linked to the current QuPath project
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • sendParentMeasurementTableAsOmeroTable

      @Deprecated public static boolean sendParentMeasurementTableAsOmeroTable(LinkedHashMap<String,List<String>> parentTable, OmeroRawClient client, Collection<omero.gateway.model.DataObject> parents, boolean deletePreviousTable, String owner)
      Deprecated.
      use sendParentMeasurementsToOmero(LinkedHashMap, OmeroRawClient, Collection, boolean, String, boolean) instead
      Send the summary map "header, List_of_measurements" to OMERO as an OMERO.table attached to the parent container

      • IMPORTANT : The attached file is uploaded ONCE on the OMERO database. The same file is then linked to the multiple parent containers. If one deletes the file, all the links will also be deleted

      Parameters:
      parentTable - LinkedHashMap "header, List_of_measurements" to populate. Other type of maps will not work
      client - OMERO Client Object to handle OMERO connection
      parents - Collection of parent containers on OMERO to link the file to
      deletePreviousTable - True if you want to delete previous CSV files on the parent container, linked to the current QuPath project
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • sendParentMeasurementTableAsCSV

      @Deprecated public static boolean sendParentMeasurementTableAsCSV(LinkedHashMap<String,List<String>> parentTable, OmeroRawClient client, Collection<omero.gateway.model.DataObject> parents, boolean deletePreviousTable)
      Deprecated.
      use sendParentMeasurementsAsCSVToOmero(LinkedHashMap, OmeroRawClient, Collection, boolean, String, boolean) instead
      Send the summary map "header, List_of_measurements" to OMERO as an CSV file attached to the parent containers.

      • IMPORTANT : The attached file is uploaded ONCE on the OMERO database. The same file is then linked to the multiple parent containers. If one deletes the file, all the links will also be deleted

      Parameters:
      parentTable - LinkedHashMap "header, List_of_measurements" to populate. Other type of maps will not work
      client - OMERO Client Object to handle OMERO connection
      parents - Collection of parent container on OMERO to link the file to
      deletePreviousTable - True if you want to delete previous CSV files on the parent container, linked to the current QuPath project
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • sendParentMeasurementTableAsCSV

      @Deprecated public static boolean sendParentMeasurementTableAsCSV(LinkedHashMap<String,List<String>> parentTable, OmeroRawClient client, Collection<omero.gateway.model.DataObject> parents, boolean deletePreviousTable, String owner)
      Deprecated.
      use sendParentMeasurementsAsCSVToOmero(LinkedHashMap, OmeroRawClient, Collection, boolean, String, boolean) instead
      Send the summary map "header, List_of_measurements" to OMERO as an CSV file attached to the parent containers.

      • IMPORTANT : The attached file is uploaded ONCE on the OMERO database. The same file is then linked to the multiple parent containers. If one deletes the file, all the links will also be deleted

      Parameters:
      parentTable - LinkedHashMap "header, List_of_measurements" to populate. Other type of maps will not work
      client - OMERO Client Object to handle OMERO connection
      parents - Collection of parent container on OMERO to link the file to
      deletePreviousTable - True if you want to delete previous CSV files on the parent container, linked to the current QuPath project
      owner - the owner of the files to delete. If null, then all tables are deleted whatever the owner
      Returns:
      Sending status (true if the CSV file has been sent ; false if there were troubles during the sending process)

    • setChannelsDisplayRangeFromOmeroChannel

      @Deprecated public static void setChannelsDisplayRangeFromOmeroChannel(OmeroRawImageServer imageServer)
      Deprecated.
      use copyOmeroChannelsDisplayRangeToQuPath(OmeroRawImageServer, boolean) instead
      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.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO

    • setChannelsColorFromOmeroChannel

      @Deprecated public static void setChannelsColorFromOmeroChannel(OmeroRawImageServer imageServer)
      Deprecated.
      use copyOmeroChannelsColorToQuPath(OmeroRawImageServer, boolean) instead
      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.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO

    • setChannelsNameFromOmeroChannel

      @Deprecated public static void setChannelsNameFromOmeroChannel(OmeroRawImageServer imageServer)
      Deprecated.
      use copyOmeroChannelsNameToQuPath(OmeroRawImageServer, boolean) instead
      Set the name of each channel on QuPath, based on OMERO settings. Channel indices are taken as reference.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO

    • sendChannelsDisplayRangeToOmero

      @Deprecated public static boolean sendChannelsDisplayRangeToOmero(OmeroRawImageServer imageServer)
      Deprecated.
      use sendQuPathChannelsDisplayRangeToOmero(OmeroRawImageServer, boolean) instead
      Set the minimum and maximum display range value of each channel on OMERO, based on QuPath settings.
      OMERO image and thumbnail are updated accordingly.
      Channel indices are taken as reference.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if the image and thumbnail on OMERO has been updated ; false if there were troubles during the sending process)

    • sendChannelsNameToOmero

      @Deprecated public static boolean sendChannelsNameToOmero(OmeroRawImageServer imageServer)
      Deprecated.
      use sendQuPathChannelsNameToOmero(OmeroRawImageServer, boolean) instead
      Set the name of each channel on OMERO, based on QuPath settings. Channel indices are taken as reference.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if the image and thumbnail on OMERO has been updated ; false if there were troubles during the sending process)

    • sendChannelsColorToOmero

      @Deprecated public static boolean sendChannelsColorToOmero(OmeroRawImageServer imageServer)
      Deprecated.
      use sendQuPathChannelsColorToOmero(OmeroRawImageServer, boolean) instead
      Set the color of each channel on OMERO, based on QuPath settings. OMERO image and thumbnail are updated accordingly.
      Channel indices are taken as reference.

      • Only works for fluorescence images

      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if the image and thumbnail on OMERO has been updated ; false if there were troubles during the sending process)

    • sendImageNameToOmero

      @Deprecated public static boolean sendImageNameToOmero(OmeroRawImageServer imageServer)
      Deprecated.
      use sendQuPathImageNameToOmero(OmeroRawImageServer, boolean) instead
      Set the name the image on OMERO, based on QuPath settings.
      Parameters:
      imageServer - ImageServer of an image loaded from OMERO
      Returns:
      Sending status (true if the image name on OMERO has been updated ; false if there were troubles during the sending process)