| Package | Description |
|---|---|
| fr.igred.omero |
This package contains the main interfaces and abstract classes to handle OME Remote Objects.
|
| fr.igred.omero.annotations |
This package contains interfaces and classes for handling annotations.
|
| fr.igred.omero.client |
This package contains the client interfaces used to interact with an OMERO server and a class implementing them.
|
| fr.igred.omero.containers |
This package contains interfaces and classes related to the hierarchical organization for images,
e.g. containers (projects, datasets and folders).
|
| fr.igred.omero.core |
This package contains interfaces and classes to handle images and their content, such as pixels, channels or planes.
|
| fr.igred.omero.exception |
This package contains wrapper classes for OMERO exceptions and an exception handler.
|
| fr.igred.omero.roi |
This package contains wrapper classes for OMERO shapes and ROIs.
|
| fr.igred.omero.screen |
This package contains interfaces and classes related to the HCS organization, such as screens, plates or wells.
|
| Modifier and Type | Method and Description |
|---|---|
default long |
Annotatable.addAndReplaceFile(Client client,
File file)
Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're
orphaned.
|
default long |
Annotatable.addAndReplaceFile(Client client,
File file)
Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're
orphaned.
|
long |
Annotatable.addAndReplaceFile(Client client,
File file,
ReplacePolicy policy)
Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
|
long |
AnnotatableWrapper.addAndReplaceFile(Client client,
File file,
ReplacePolicy policy)
Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
|
long |
AnnotatableWrapper.addAndReplaceFile(Client client,
File file,
ReplacePolicy policy)
Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
|
long |
Annotatable.addAndReplaceFile(Client client,
File file,
ReplacePolicy policy)
Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
|
default void |
Annotatable.addAndReplaceTable(Client client,
Table table)
Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're
orphaned.
|
default void |
Annotatable.addAndReplaceTable(Client client,
Table table)
Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're
orphaned.
|
void |
Annotatable.addAndReplaceTable(Client client,
Table table,
ReplacePolicy policy)
Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
|
void |
AnnotatableWrapper.addAndReplaceTable(Client client,
Table table,
ReplacePolicy policy)
Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
|
void |
AnnotatableWrapper.addAndReplaceTable(Client client,
Table table,
ReplacePolicy policy)
Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
|
void |
Annotatable.addAndReplaceTable(Client client,
Table table,
ReplacePolicy policy)
Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
|
void |
Annotatable.addKeyValuePair(DataManager dm,
String key,
String value)
Adds a single Key-Value pair to the object.
|
void |
AnnotatableWrapper.addKeyValuePair(DataManager dm,
String key,
String value)
Adds a single Key-Value pair to the object.
|
void |
AnnotatableWrapper.addKeyValuePair(DataManager dm,
String key,
String value)
Adds a single Key-Value pair to the object.
|
void |
Annotatable.addKeyValuePair(DataManager dm,
String key,
String value)
Adds a single Key-Value pair to the object.
|
default void |
Annotatable.addTable(DataManager dm,
Table table)
Adds a table to the object in OMERO.
|
default void |
Annotatable.addTable(DataManager dm,
Table table)
Adds a table to the object in OMERO.
|
void |
Annotatable.addTag(DataManager dm,
Long id)
Adds a tag to the object in OMERO, if possible.
|
void |
AnnotatableWrapper.addTag(DataManager dm,
Long id)
Adds a tag to the object in OMERO, if possible.
|
void |
AnnotatableWrapper.addTag(DataManager dm,
Long id)
Adds a tag to the object in OMERO, if possible.
|
void |
Annotatable.addTag(DataManager dm,
Long id)
Adds a tag to the object in OMERO, if possible.
|
void |
Annotatable.addTag(DataManager dm,
String name,
String description)
Adds a newly created tag to the object in OMERO, if possible.
|
void |
AnnotatableWrapper.addTag(DataManager dm,
String name,
String description)
Adds a newly created tag to the object in OMERO, if possible.
|
void |
AnnotatableWrapper.addTag(DataManager dm,
String name,
String description)
Adds a newly created tag to the object in OMERO, if possible.
|
void |
Annotatable.addTag(DataManager dm,
String name,
String description)
Adds a newly created tag to the object in OMERO, if possible.
|
default void |
Annotatable.addTags(DataManager dm,
Long... ids)
Adds multiple tags by ID to the object in OMERO, if possible.
|
default void |
Annotatable.addTags(DataManager dm,
Long... ids)
Adds multiple tags by ID to the object in OMERO, if possible.
|
default void |
Annotatable.copyAnnotationLinks(Client client,
Annotatable object)
Copies annotation links from some other object to this one.
|
default void |
Annotatable.copyAnnotationLinks(Client client,
Annotatable object)
Copies annotation links from some other object to this one.
|
default List<AnnotationData> |
Annotatable.getAnnotationData(Browser browser)
Retrieves annotations linked to the object.
|
default List<AnnotationData> |
Annotatable.getAnnotationData(Browser browser)
Retrieves annotations linked to the object.
|
List<Annotation> |
Annotatable.getAnnotations(Browser browser)
Retrieves annotations linked to the object (of known types).
|
List<Annotation> |
AnnotatableWrapper.getAnnotations(Browser browser)
Retrieves annotations linked to the object (of known types).
|
List<Annotation> |
AnnotatableWrapper.getAnnotations(Browser browser)
Retrieves annotations linked to the object (of known types).
|
List<Annotation> |
Annotatable.getAnnotations(Browser browser)
Retrieves annotations linked to the object (of known types).
|
List<RepositoryObject> |
RepositoryObject.getChildren(Browser browser)
Gets the object children.
|
List<RepositoryObject> |
RepositoryObject.getChildren(Browser browser)
Gets the object children.
|
List<FileAnnotation> |
Annotatable.getFileAnnotations(Browser browser)
Returns the file annotations
|
List<FileAnnotation> |
AnnotatableWrapper.getFileAnnotations(Browser browser)
Returns the file annotations
|
List<FileAnnotation> |
AnnotatableWrapper.getFileAnnotations(Browser browser)
Returns the file annotations
|
List<FileAnnotation> |
Annotatable.getFileAnnotations(Browser browser)
Returns the file annotations
|
default List<Map.Entry<String,String>> |
Annotatable.getKeyValuePairs(Browser browser)
Gets the List of Key-Value pairs associated to an object.
|
default List<Map.Entry<String,String>> |
Annotatable.getKeyValuePairs(Browser browser)
Gets the List of Key-Value pairs associated to an object.
|
List<MapAnnotation> |
Annotatable.getMapAnnotations(Browser browser)
Gets all map annotations linked to an object in OMERO, if possible.
|
List<MapAnnotation> |
AnnotatableWrapper.getMapAnnotations(Browser browser)
Gets all map annotations linked to an object in OMERO, if possible.
|
List<MapAnnotation> |
AnnotatableWrapper.getMapAnnotations(Browser browser)
Gets all map annotations linked to an object in OMERO, if possible.
|
List<MapAnnotation> |
Annotatable.getMapAnnotations(Browser browser)
Gets all map annotations linked to an object in OMERO, if possible.
|
int |
Annotatable.getMyRating(Browser browser)
Returns the user rating for this object (averaged if multiple ratings are linked).
|
int |
AnnotatableWrapper.getMyRating(Browser browser)
Returns the user rating for this object (averaged if multiple ratings are linked).
|
int |
AnnotatableWrapper.getMyRating(Browser browser)
Returns the user rating for this object (averaged if multiple ratings are linked).
|
int |
Annotatable.getMyRating(Browser browser)
Returns the user rating for this object (averaged if multiple ratings are linked).
|
List<RepositoryObject> |
RepositoryObject.getParents(Browser browser)
Gets the object parents.
|
List<RepositoryObject> |
RepositoryObject.getParents(Browser browser)
Gets the object parents.
|
Table |
Annotatable.getTable(DataManager dm,
Long fileId)
Gets a certain table linked to the object in OMERO.
|
Table |
AnnotatableWrapper.getTable(DataManager dm,
Long fileId)
Gets a certain table linked to the object in OMERO.
|
Table |
AnnotatableWrapper.getTable(DataManager dm,
Long fileId)
Gets a certain table linked to the object in OMERO.
|
Table |
Annotatable.getTable(DataManager dm,
Long fileId)
Gets a certain table linked to the object in OMERO.
|
default List<Table> |
Annotatable.getTables(DataManager dm)
Gets all tables linked to the object in OMERO.
|
default List<Table> |
Annotatable.getTables(DataManager dm)
Gets all tables linked to the object in OMERO.
|
List<TagAnnotation> |
Annotatable.getTags(Browser browser)
Gets all tags linked to an object in OMERO, if possible.
|
List<TagAnnotation> |
AnnotatableWrapper.getTags(Browser browser)
Gets all tags linked to an object in OMERO, if possible.
|
List<TagAnnotation> |
AnnotatableWrapper.getTags(Browser browser)
Gets all tags linked to an object in OMERO, if possible.
|
List<TagAnnotation> |
Annotatable.getTags(Browser browser)
Gets all tags linked to an object in OMERO, if possible.
|
default List<String> |
Annotatable.getValues(Browser browser,
String key)
Gets the value from a Key-Value pair associated to the object.
|
default List<String> |
Annotatable.getValues(Browser browser,
String key)
Gets the value from a Key-Value pair associated to the object.
|
protected List<Long> |
ImportWrapper.importImage(ConnectionHandler client,
String path)
Imports one image file to the target in OMERO.
|
protected List<Long> |
ImportWrapper.importImage(ConnectionHandler client,
String path)
Imports one image file to the target in OMERO.
|
protected boolean |
ImportWrapper.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the target in OMERO.
|
protected boolean |
ImportWrapper.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the target in OMERO.
|
default <A extends Annotation> |
Annotatable.isLinked(Browser browser,
A annotation)
Checks if a specific annotation is linked to the object.
|
default <A extends Annotation> |
Annotatable.isLinked(Browser browser,
A annotation)
Checks if a specific annotation is linked to the object.
|
default <A extends Annotation> |
Annotatable.link(DataManager dm,
A annotation)
Adds an annotation to the object in OMERO, if possible.
|
default <A extends Annotation> |
Annotatable.link(DataManager dm,
A annotation)
Adds an annotation to the object in OMERO, if possible.
|
default <A extends AnnotationData> |
Annotatable.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
default <A extends AnnotationData> |
Annotatable.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
default void |
Annotatable.link(DataManager dm,
Annotation... annotations)
Adds multiple annotations to the object in OMERO, if possible.
|
default void |
Annotatable.link(DataManager dm,
Annotation... annotations)
Adds multiple annotations to the object in OMERO, if possible.
|
default void |
Annotatable.linkIfNotLinked(Client client,
Annotation... annotations)
Adds multiple annotations to the object in OMERO if they are not already linked.
|
default void |
Annotatable.linkIfNotLinked(Client client,
Annotation... annotations)
Adds multiple annotations to the object in OMERO if they are not already linked.
|
void |
Annotatable.rate(Client client,
int rating)
Rates the object (using a rating annotation).
|
void |
AnnotatableWrapper.rate(Client client,
int rating)
Rates the object (using a rating annotation).
|
void |
AnnotatableWrapper.rate(Client client,
int rating)
Rates the object (using a rating annotation).
|
void |
Annotatable.rate(Client client,
int rating)
Rates the object (using a rating annotation).
|
void |
RepositoryObject.reload(Browser browser)
Reloads the object from OMERO.
|
void |
RepositoryObject.reload(Browser browser)
Reloads the object from OMERO.
|
protected void |
AnnotatableWrapper.removeLink(Client client,
String linkType,
long childId)
Removes the link of the given type with the given child ID.
|
protected void |
AnnotatableWrapper.removeLink(Client client,
String linkType,
long childId)
Removes the link of the given type with the given child ID.
|
void |
ObjectWrapper.saveAndUpdate(DataManager dm)
Saves and updates object.
|
void |
RemoteObject.saveAndUpdate(DataManager dm)
Saves and updates object.
|
void |
RemoteObject.saveAndUpdate(DataManager dm)
Saves and updates object.
|
void |
ObjectWrapper.saveAndUpdate(DataManager dm)
Saves and updates object.
|
<A extends Annotation> |
Annotatable.unlink(Client client,
A annotation)
Unlinks the given annotation from the current object.
|
<A extends Annotation> |
AnnotatableWrapper.unlink(Client client,
A annotation)
Unlinks the given annotation from the current object.
|
<A extends Annotation> |
AnnotatableWrapper.unlink(Client client,
A annotation)
Unlinks the given annotation from the current object.
|
<A extends Annotation> |
Annotatable.unlink(Client client,
A annotation)
Unlinks the given annotation from the current object.
|
| Modifier and Type | Method and Description |
|---|---|
default void |
Table.addRows(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois)
Adds rows from an ImageJ
ResultsTable. |
default void |
Table.addRows(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois)
Adds rows from an ImageJ
ResultsTable. |
void |
Table.addRows(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois,
String roiProperty)
Adds rows from an ImageJ
ResultsTable. |
void |
TableWrapper.addRows(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois,
String roiProperty)
Adds rows from an ImageJ
ResultsTable. |
void |
TableWrapper.addRows(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois,
String roiProperty)
Adds rows from an ImageJ
ResultsTable. |
void |
Table.addRows(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois,
String roiProperty)
Adds rows from an ImageJ
ResultsTable. |
default int |
Annotation.countAnnotationLinks(Browser browser)
Returns the number of annotations links for this object.
|
default int |
Annotation.countAnnotationLinks(Browser browser)
Returns the number of annotations links for this object.
|
List<Dataset> |
Annotation.getDatasets(Browser browser)
Gets all datasets with this annotation from OMERO.
|
List<Dataset> |
AnnotationWrapper.getDatasets(Browser browser)
Gets all datasets with this annotation from OMERO.
|
List<Dataset> |
AnnotationWrapper.getDatasets(Browser browser)
Gets all datasets with this annotation from OMERO.
|
List<Dataset> |
Annotation.getDatasets(Browser browser)
Gets all datasets with this annotation from OMERO.
|
File |
FileAnnotation.getFile(ConnectionHandler client,
String path)
Returns the original file.
|
File |
FileAnnotationWrapper.getFile(ConnectionHandler client,
String path)
Returns the original file.
|
File |
FileAnnotationWrapper.getFile(ConnectionHandler client,
String path)
Returns the original file.
|
File |
FileAnnotation.getFile(ConnectionHandler client,
String path)
Returns the original file.
|
List<Folder> |
Annotation.getFolders(Browser browser)
Gets all folders with this annotation from OMERO.
|
List<Folder> |
AnnotationWrapper.getFolders(Browser browser)
Gets all folders with this annotation from OMERO.
|
List<Folder> |
AnnotationWrapper.getFolders(Browser browser)
Gets all folders with this annotation from OMERO.
|
List<Folder> |
Annotation.getFolders(Browser browser)
Gets all folders with this annotation from OMERO.
|
List<Image> |
Annotation.getImages(Browser browser)
Gets all images with this annotation from OMERO.
|
List<Image> |
AnnotationWrapper.getImages(Browser browser)
Gets all images with this annotation from OMERO.
|
List<Image> |
AnnotationWrapper.getImages(Browser browser)
Gets all images with this annotation from OMERO.
|
List<Image> |
Annotation.getImages(Browser browser)
Gets all images with this annotation from OMERO.
|
List<PlateAcquisition> |
Annotation.getPlateAcquisitions(Browser browser)
Gets all plate acquisitions with this annotation from OMERO.
|
List<PlateAcquisition> |
AnnotationWrapper.getPlateAcquisitions(Browser browser)
Gets all plate acquisitions with this annotation from OMERO.
|
List<PlateAcquisition> |
AnnotationWrapper.getPlateAcquisitions(Browser browser)
Gets all plate acquisitions with this annotation from OMERO.
|
List<PlateAcquisition> |
Annotation.getPlateAcquisitions(Browser browser)
Gets all plate acquisitions with this annotation from OMERO.
|
List<Plate> |
Annotation.getPlates(Browser browser)
Gets all plates with this annotation from OMERO.
|
List<Plate> |
AnnotationWrapper.getPlates(Browser browser)
Gets all plates with this annotation from OMERO.
|
List<Plate> |
AnnotationWrapper.getPlates(Browser browser)
Gets all plates with this annotation from OMERO.
|
List<Plate> |
Annotation.getPlates(Browser browser)
Gets all plates with this annotation from OMERO.
|
List<Project> |
Annotation.getProjects(Browser browser)
Gets all projects with this annotation from OMERO.
|
List<Project> |
AnnotationWrapper.getProjects(Browser browser)
Gets all projects with this annotation from OMERO.
|
List<Project> |
AnnotationWrapper.getProjects(Browser browser)
Gets all projects with this annotation from OMERO.
|
List<Project> |
Annotation.getProjects(Browser browser)
Gets all projects with this annotation from OMERO.
|
List<Screen> |
Annotation.getScreens(Browser browser)
Gets all screens with this annotation from OMERO.
|
List<Screen> |
AnnotationWrapper.getScreens(Browser browser)
Gets all screens with this annotation from OMERO.
|
List<Screen> |
AnnotationWrapper.getScreens(Browser browser)
Gets all screens with this annotation from OMERO.
|
List<Screen> |
Annotation.getScreens(Browser browser)
Gets all screens with this annotation from OMERO.
|
List<Well> |
Annotation.getWells(Browser browser)
Gets all wells with this annotation from OMERO.
|
List<Well> |
AnnotationWrapper.getWells(Browser browser)
Gets all wells with this annotation from OMERO.
|
List<Well> |
AnnotationWrapper.getWells(Browser browser)
Gets all wells with this annotation from OMERO.
|
List<Well> |
Annotation.getWells(Browser browser)
Gets all wells with this annotation from OMERO.
|
| Constructor and Description |
|---|
TableWrapper(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois)
Constructor of the class TableWrapper.
|
TableWrapper(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois)
Constructor of the class TableWrapper.
|
TableWrapper(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois,
String roiProperty)
Constructor of the class TableWrapper.
|
TableWrapper(Client client,
ij.measure.ResultsTable results,
Long imageId,
Collection<? extends Roi> ijRois,
String roiProperty)
Constructor of the class TableWrapper.
|
TagAnnotationWrapper(DataManager dm,
String name,
String description)
Constructor of the TagAnnotationWrapper class.
|
TagAnnotationWrapper(DataManager dm,
String name,
String description)
Constructor of the TagAnnotationWrapper class.
|
| Modifier and Type | Method and Description |
|---|---|
default void |
DataManager.delete(Collection<? extends RemoteObject> objects)
Deletes multiple objects from OMERO.
|
default void |
DataManager.delete(Collection<? extends RemoteObject> objects)
Deletes multiple objects from OMERO.
|
default void |
DataManager.delete(IObject object)
Deletes an object from OMERO.
|
default void |
DataManager.delete(IObject object)
Deletes an object from OMERO.
|
default void |
DataManager.delete(List<IObject> objects)
Deletes multiple objects from OMERO.
|
default void |
DataManager.delete(List<IObject> objects)
Deletes multiple objects from OMERO.
|
default void |
DataManager.delete(RemoteObject object)
Deletes an object from OMERO.
|
default void |
DataManager.delete(RemoteObject object)
Deletes an object from OMERO.
|
default void |
DataManager.delete(Table table)
Deletes a table from OMERO.
|
default void |
DataManager.delete(Table table)
Deletes a table from OMERO.
|
default void |
DataManager.deleteFile(Long id)
Deletes a file from OMERO
|
default void |
DataManager.deleteFile(Long id)
Deletes a file from OMERO
|
default List<IObject> |
Browser.findByQuery(String query)
Finds objects on OMERO through a database query.
|
default List<IObject> |
Browser.findByQuery(String query)
Finds objects on OMERO through a database query.
|
default Dataset |
Browser.getDataset(Long id)
Gets the dataset with the specified id from OMERO.
|
default Dataset |
Browser.getDataset(Long id)
Gets the dataset with the specified id from OMERO.
|
default List<Dataset> |
Browser.getDatasets()
Gets all datasets available from OMERO.
|
default List<Dataset> |
Browser.getDatasets()
Gets all datasets available from OMERO.
|
default List<Dataset> |
Browser.getDatasets(Experimenter experimenter)
Gets all datasets available from OMERO owned by a given user.
|
default List<Dataset> |
Browser.getDatasets(Experimenter experimenter)
Gets all datasets available from OMERO owned by a given user.
|
default List<Dataset> |
Browser.getDatasets(Long... ids)
Gets the datasets with the specified ids from OMERO.
|
default List<Dataset> |
Browser.getDatasets(Long... ids)
Gets the datasets with the specified ids from OMERO.
|
default List<Dataset> |
Browser.getDatasets(String name)
Gets all datasets with a certain name from OMERO.
|
default List<Dataset> |
Browser.getDatasets(String name)
Gets all datasets with a certain name from OMERO.
|
default Folder |
Browser.getFolder(long id)
Gets the folder with the specified ID from OMERO, fully loaded.
|
default Folder |
Browser.getFolder(long id)
Gets the folder with the specified ID from OMERO, fully loaded.
|
default List<Folder> |
Browser.getFolders()
Gets all folders available from OMERO.
|
default List<Folder> |
Browser.getFolders()
Gets all folders available from OMERO.
|
default List<Folder> |
Browser.getFolders(Experimenter experimenter)
Gets all the folders owned by a given user from OMERO.
|
default List<Folder> |
Browser.getFolders(Experimenter experimenter)
Gets all the folders owned by a given user from OMERO.
|
default Group |
AdminManager.getGroup(String groupName)
Returns the group which matches the name.
|
default Group |
AdminManager.getGroup(String groupName)
Returns the group which matches the name.
|
default Image |
Browser.getImage(Long id)
Returns the image with the specified ID from OMERO.
|
default Image |
Browser.getImage(Long id)
Returns the image with the specified ID from OMERO.
|
default List<Image> |
Browser.getImages()
Gets all images owned by the current user.
|
default List<Image> |
Browser.getImages()
Gets all images owned by the current user.
|
default List<Image> |
Browser.getImages(Annotation annotation)
Gets all images with the specified annotation from OMERO.
|
default List<Image> |
Browser.getImages(Annotation annotation)
Gets all images with the specified annotation from OMERO.
|
default List<Image> |
Browser.getImages(Long... ids)
Gets the images with the specified ids from OMERO
|
default List<Image> |
Browser.getImages(Long... ids)
Gets the images with the specified ids from OMERO
|
default List<Image> |
Browser.getImages(String name)
Gets all images with a certain name from OMERO.
|
default List<Image> |
Browser.getImages(String name)
Gets all images with a certain name from OMERO.
|
default List<Image> |
Browser.getImages(String projectName,
String datasetName,
String imageName)
Gets all images with the name specified inside projects and datasets with the given names.
|
default List<Image> |
Browser.getImages(String projectName,
String datasetName,
String imageName)
Gets all images with the name specified inside projects and datasets with the given names.
|
default List<Image> |
Browser.getImagesLike(String motif)
Gets all images with a certain motif in their name from OMERO.
|
default List<Image> |
Browser.getImagesLike(String motif)
Gets all images with a certain motif in their name from OMERO.
|
default List<Image> |
Browser.getImagesWithKey(String key)
Gets all images with a certain key.
|
default List<Image> |
Browser.getImagesWithKey(String key)
Gets all images with a certain key.
|
default List<Image> |
Browser.getImagesWithKeyValuePair(String key,
String value)
Gets all images with a certain key value pair from OMERO
|
default List<Image> |
Browser.getImagesWithKeyValuePair(String key,
String value)
Gets all images with a certain key value pair from OMERO
|
default OMEROMetadataStoreClient |
ConnectionHandler.getImportStore()
Creates or recycles the import store.
|
default OMEROMetadataStoreClient |
ConnectionHandler.getImportStore()
Creates or recycles the import store.
|
default MapAnnotation |
Browser.getMapAnnotation(Long id)
Gets a specific map annotation (key/value pairs) from the OMERO database.
|
default MapAnnotation |
Browser.getMapAnnotation(Long id)
Gets a specific map annotation (key/value pairs) from the OMERO database.
|
default List<MapAnnotation> |
Browser.getMapAnnotations()
Gets the list of map annotations available to the user.
|
default List<MapAnnotation> |
Browser.getMapAnnotations()
Gets the list of map annotations available to the user.
|
default List<MapAnnotation> |
Browser.getMapAnnotations(String key)
Gets the list of map annotations with the specified key available to the user.
|
default List<MapAnnotation> |
Browser.getMapAnnotations(String key)
Gets the list of map annotations with the specified key available to the user.
|
default List<MapAnnotation> |
Browser.getMapAnnotations(String key,
String value)
Gets the list of map annotations with the specified key and value available to the user.
|
default List<MapAnnotation> |
Browser.getMapAnnotations(String key,
String value)
Gets the list of map annotations with the specified key and value available to the user.
|
default Plate |
Browser.getPlate(Long id)
Gets the plate with the specified id from OMERO.
|
default Plate |
Browser.getPlate(Long id)
Gets the plate with the specified id from OMERO.
|
default List<Plate> |
Browser.getPlates()
Gets all plates available from OMERO.
|
default List<Plate> |
Browser.getPlates()
Gets all plates available from OMERO.
|
default List<Plate> |
Browser.getPlates(Experimenter experimenter)
Gets all plates available from OMERO owned by a given user.
|
default List<Plate> |
Browser.getPlates(Experimenter experimenter)
Gets all plates available from OMERO owned by a given user.
|
default List<Plate> |
Browser.getPlates(Long... ids)
Gets the plates with the specified ids from OMERO.
|
default List<Plate> |
Browser.getPlates(Long... ids)
Gets the plates with the specified ids from OMERO.
|
default Project |
Browser.getProject(Long id)
Gets the project with the specified id from OMERO.
|
default Project |
Browser.getProject(Long id)
Gets the project with the specified id from OMERO.
|
default List<Project> |
Browser.getProjects()
Gets all projects available from OMERO.
|
default List<Project> |
Browser.getProjects()
Gets all projects available from OMERO.
|
default List<Project> |
Browser.getProjects(Experimenter experimenter)
Gets all projects available from OMERO owned by a given user.
|
default List<Project> |
Browser.getProjects(Experimenter experimenter)
Gets all projects available from OMERO owned by a given user.
|
default List<Project> |
Browser.getProjects(Long... ids)
Gets the projects with the specified ids from OMERO.
|
default List<Project> |
Browser.getProjects(Long... ids)
Gets the projects with the specified ids from OMERO.
|
default List<Project> |
Browser.getProjects(String name)
Gets all projects with a certain name from OMERO.
|
default List<Project> |
Browser.getProjects(String name)
Gets all projects with a certain name from OMERO.
|
omero.api.IQueryPrx |
Browser.getQueryService()
Returns the
IQueryPrx used to find objects on OMERO. |
default omero.api.IQueryPrx |
Client.getQueryService()
Returns the
IQueryPrx used to find objects on OMERO. |
default omero.api.IQueryPrx |
Client.getQueryService()
Returns the
IQueryPrx used to find objects on OMERO. |
omero.api.IQueryPrx |
Browser.getQueryService()
Returns the
IQueryPrx used to find objects on OMERO. |
default Screen |
Browser.getScreen(Long id)
Gets the screen with the specified id from OMERO.
|
default Screen |
Browser.getScreen(Long id)
Gets the screen with the specified id from OMERO.
|
default List<Screen> |
Browser.getScreens()
Gets all screens available from OMERO.
|
default List<Screen> |
Browser.getScreens()
Gets all screens available from OMERO.
|
default List<Screen> |
Browser.getScreens(Experimenter experimenter)
Gets all screens available from OMERO owned by a given user.
|
default List<Screen> |
Browser.getScreens(Experimenter experimenter)
Gets all screens available from OMERO owned by a given user.
|
default List<Screen> |
Browser.getScreens(Long... ids)
Gets the screens with the specified ids from OMERO.
|
default List<Screen> |
Browser.getScreens(Long... ids)
Gets the screens with the specified ids from OMERO.
|
default TagAnnotation |
Browser.getTag(Long id)
Gets a specific tag from the OMERO database.
|
default TagAnnotation |
Browser.getTag(Long id)
Gets a specific tag from the OMERO database.
|
default List<TagAnnotation> |
Browser.getTags()
Gets the list of tag annotations available to the user.
|
default List<TagAnnotation> |
Browser.getTags()
Gets the list of tag annotations available to the user.
|
default List<TagAnnotation> |
Browser.getTags(String name)
Gets the list of tag annotations with the specified name available to the user.
|
default List<TagAnnotation> |
Browser.getTags(String name)
Gets the list of tag annotations with the specified name available to the user.
|
default Experimenter |
AdminManager.getUser(String username)
Returns the user which matches the username.
|
default Experimenter |
AdminManager.getUser(String username)
Returns the user which matches the username.
|
default Well |
Browser.getWell(Long id)
Gets the well with the specified id from OMERO.
|
default Well |
Browser.getWell(Long id)
Gets the well with the specified id from OMERO.
|
default List<Well> |
Browser.getWells()
Gets all wells available from OMERO.
|
default List<Well> |
Browser.getWells()
Gets all wells available from OMERO.
|
default List<Well> |
Browser.getWells(Experimenter experimenter)
Gets all wells available from OMERO owned by a given user.
|
default List<Well> |
Browser.getWells(Experimenter experimenter)
Gets all wells available from OMERO owned by a given user.
|
default List<Well> |
Browser.getWells(Long... ids)
Gets the wells with the specified ids from OMERO.
|
default List<Well> |
Browser.getWells(Long... ids)
Gets the wells with the specified ids from OMERO.
|
default List<Folder> |
Browser.loadFolders(Long... ids)
Gets the folders with the specified IDs from OMERO (fully loaded).
|
default List<Folder> |
Browser.loadFolders(Long... ids)
Gets the folders with the specified IDs from OMERO (fully loaded).
|
default IObject |
DataManager.save(IObject object)
Saves an object on OMERO.
|
default IObject |
DataManager.save(IObject object)
Saves an object on OMERO.
|
Client |
Client.sudo(String username)
Gets the client associated with the username in the parameters.
|
ConnectionHandler |
ConnectionHandler.sudo(String username)
Returns a ConnectionHandler associated with the given username.
|
Client |
GatewayWrapper.sudo(String username)
Returns a Client associated with the given username.
|
Client |
GatewayWrapper.sudo(String username)
Returns a Client associated with the given username.
|
ConnectionHandler |
ConnectionHandler.sudo(String username)
Returns a ConnectionHandler associated with the given username.
|
Client |
Client.sudo(String username)
Gets the client associated with the username in the parameters.
|
| Modifier and Type | Method and Description |
|---|---|
default Dataset |
Project.addDataset(DataManager dm,
Dataset dataset)
Adds a dataset to the project in OMERO.
|
default Dataset |
Project.addDataset(DataManager dm,
Dataset dataset)
Adds a dataset to the project in OMERO.
|
Dataset |
Project.addDataset(DataManager dm,
String name,
String description)
Creates a dataset and adds it to the project in OMERO. .
|
Dataset |
ProjectWrapper.addDataset(DataManager dm,
String name,
String description)
Creates a dataset and adds it to the project in OMERO. .
|
Dataset |
ProjectWrapper.addDataset(DataManager dm,
String name,
String description)
Creates a dataset and adds it to the project in OMERO. .
|
Dataset |
Project.addDataset(DataManager dm,
String name,
String description)
Creates a dataset and adds it to the project in OMERO. .
|
default void |
Dataset.addImage(DataManager dm,
Image image)
Adds a single image to the dataset in OMERO
|
default void |
Dataset.addImage(DataManager dm,
Image image)
Adds a single image to the dataset in OMERO
|
default void |
Folder.addImages(DataManager dm,
Image... images)
Links images to the folder in OMERO.
|
default void |
Folder.addImages(DataManager dm,
Image... images)
Links images to the folder in OMERO.
|
default void |
Dataset.addImages(DataManager dm,
Iterable<? extends Image> images)
Adds multiple images to the dataset in OMERO.
|
default void |
Dataset.addImages(DataManager dm,
Iterable<? extends Image> images)
Adds multiple images to the dataset in OMERO.
|
default void |
Folder.addROIs(DataManager dm,
Image image,
ROI... rois)
Adds ROIs to the folder and associate them to the provided image.
|
default void |
Folder.addROIs(DataManager dm,
Image image,
ROI... rois)
Adds ROIs to the folder and associate them to the provided image.
|
default void |
Folder.addROIs(DataManager dm,
long imageId,
ROI... rois)
Adds ROIs to the folder and associate them to the provided image ID.
|
default void |
Folder.addROIs(DataManager dm,
long imageId,
ROI... rois)
Adds ROIs to the folder and associate them to the provided image ID.
|
default List<RepositoryObject> |
Dataset.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
Folder.getChildren(Browser browser)
Reloads the folder and gets its children (images and folders).
|
default List<RepositoryObject> |
Project.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
Project.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
Folder.getChildren(Browser browser)
Reloads the folder and gets its children (images and folders).
|
default List<RepositoryObject> |
Dataset.getChildren(Browser browser)
Gets the object children.
|
default List<Dataset> |
Project.getDatasets(Browser browser)
Reloads this project and retrieves the updated list of datasets contained in this project.
|
default List<Dataset> |
Project.getDatasets(Browser browser)
Reloads this project and retrieves the updated list of datasets contained in this project.
|
List<Image> |
Dataset.getImages(Browser browser)
Gets all images in the dataset available from OMERO.
|
List<Image> |
DatasetWrapper.getImages(Browser browser)
Gets all images in the dataset available from OMERO.
|
default List<Image> |
Folder.getImages(Browser browser)
Retrieves the images contained in this folder.
|
List<Image> |
Project.getImages(Browser browser)
Gets all images in the project available from OMERO.
|
List<Image> |
ProjectWrapper.getImages(Browser browser)
Gets all images in the project available from OMERO.
|
List<Image> |
ProjectWrapper.getImages(Browser browser)
Gets all images in the project available from OMERO.
|
List<Image> |
Project.getImages(Browser browser)
Gets all images in the project available from OMERO.
|
default List<Image> |
Folder.getImages(Browser browser)
Retrieves the images contained in this folder.
|
List<Image> |
DatasetWrapper.getImages(Browser browser)
Gets all images in the dataset available from OMERO.
|
List<Image> |
Dataset.getImages(Browser browser)
Gets all images in the dataset available from OMERO.
|
default List<Image> |
Dataset.getImages(Browser browser,
String name)
Gets all images in the dataset with a certain name from OMERO.
|
default List<Image> |
Project.getImages(Browser browser,
String name)
Gets all images in the project with a certain name from OMERO.
|
default List<Image> |
Project.getImages(Browser browser,
String name)
Gets all images in the project with a certain name from OMERO.
|
default List<Image> |
Dataset.getImages(Browser browser,
String name)
Gets all images in the dataset with a certain name from OMERO.
|
default List<Image> |
Project.getImages(Browser browser,
String datasetName,
String imageName)
Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
|
default List<Image> |
Project.getImages(Browser browser,
String datasetName,
String imageName)
Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
|
default List<Image> |
Dataset.getImagesLike(Browser browser,
String motif)
Gets all images in the dataset with a certain motif in their name from OMERO.
|
default List<Image> |
Project.getImagesLike(Browser browser,
String motif)
Gets all images in the project with a certain motif in their name from OMERO.
|
default List<Image> |
Project.getImagesLike(Browser browser,
String motif)
Gets all images in the project with a certain motif in their name from OMERO.
|
default List<Image> |
Dataset.getImagesLike(Browser browser,
String motif)
Gets all images in the dataset with a certain motif in their name from OMERO.
|
default List<Image> |
Dataset.getImagesTagged(Browser browser,
Long tagId)
Gets all images in the dataset tagged with a specified tag from OMERO.
|
default List<Image> |
Project.getImagesTagged(Browser browser,
Long tagId)
Gets all images in the project tagged with a specified tag from OMERO.
|
default List<Image> |
Project.getImagesTagged(Browser browser,
Long tagId)
Gets all images in the project tagged with a specified tag from OMERO.
|
default List<Image> |
Dataset.getImagesTagged(Browser browser,
Long tagId)
Gets all images in the dataset tagged with a specified tag from OMERO.
|
default List<Image> |
Dataset.getImagesTagged(Browser browser,
TagAnnotation tag)
Gets all images in the dataset tagged with a specified tag from OMERO.
|
default List<Image> |
Project.getImagesTagged(Browser browser,
TagAnnotation tag)
Gets all images in the project tagged with a specified tag from OMERO.
|
default List<Image> |
Project.getImagesTagged(Browser browser,
TagAnnotation tag)
Gets all images in the project tagged with a specified tag from OMERO.
|
default List<Image> |
Dataset.getImagesTagged(Browser browser,
TagAnnotation tag)
Gets all images in the dataset tagged with a specified tag from OMERO.
|
default List<Image> |
Dataset.getImagesWithKey(Browser browser,
String key)
Gets all images in the dataset with a certain key
|
default List<Image> |
Project.getImagesWithKey(Browser browser,
String key)
Gets all images in the project with a certain key
|
default List<Image> |
Project.getImagesWithKey(Browser browser,
String key)
Gets all images in the project with a certain key
|
default List<Image> |
Dataset.getImagesWithKey(Browser browser,
String key)
Gets all images in the dataset with a certain key
|
default List<Image> |
Dataset.getImagesWithKeyValuePair(Browser browser,
String key,
String value)
Gets all images in the dataset with a certain key value pair from OMERO
|
default List<Image> |
Project.getImagesWithKeyValuePair(Browser browser,
String key,
String value)
Gets all images in the project with a certain key value pair from OMERO.
|
default List<Image> |
Project.getImagesWithKeyValuePair(Browser browser,
String key,
String value)
Gets all images in the project with a certain key value pair from OMERO.
|
default List<Image> |
Dataset.getImagesWithKeyValuePair(Browser browser,
String key,
String value)
Gets all images in the dataset with a certain key value pair from OMERO
|
default List<RepositoryObject> |
Dataset.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
Folder.getParents(Browser browser)
Reloads the folder and returns its parent as a singleton list.
|
default List<RepositoryObject> |
Folder.getParents(Browser browser)
Reloads the folder and returns its parent as a singleton list.
|
default List<RepositoryObject> |
Dataset.getParents(Browser browser)
Gets the object parents.
|
default List<Project> |
Dataset.getProjects(Browser browser)
Retrieves the projects containing this dataset.
|
default List<Project> |
Dataset.getProjects(Browser browser)
Retrieves the projects containing this dataset.
|
default List<ROI> |
Folder.getROIs(DataManager dm,
Image image)
Gets the ROIs contained in the folder associated with the provided image.
|
default List<ROI> |
Folder.getROIs(DataManager dm,
Image image)
Gets the ROIs contained in the folder associated with the provided image.
|
List<ROI> |
Folder.getROIs(DataManager dm,
long imageId)
Gets the ROIs contained in the folder associated with the provided image ID.
|
List<ROI> |
FolderWrapper.getROIs(DataManager dm,
long imageId)
Gets the ROIs contained in the folder associated with the provided image ID.
|
List<ROI> |
FolderWrapper.getROIs(DataManager dm,
long imageId)
Gets the ROIs contained in the folder associated with the provided image ID.
|
List<ROI> |
Folder.getROIs(DataManager dm,
long imageId)
Gets the ROIs contained in the folder associated with the provided image ID.
|
default List<Long> |
Dataset.importAndReplaceImages(Client client,
String path)
Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their
annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking them.
|
default List<Long> |
Dataset.importAndReplaceImages(Client client,
String path)
Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their
annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking them.
|
default List<Long> |
Dataset.importAndReplaceImages(Client client,
String path,
ReplacePolicy policy)
Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their
annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking or even deleting them.
|
default List<Long> |
Dataset.importAndReplaceImages(Client client,
String path,
ReplacePolicy policy)
Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their
annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking or even deleting them.
|
List<Long> |
Dataset.importImage(ConnectionHandler client,
String path)
Imports one image file to the dataset in OMERO.
|
List<Long> |
DatasetWrapper.importImage(ConnectionHandler client,
String path)
Imports one image file to the dataset in OMERO.
|
List<Long> |
DatasetWrapper.importImage(ConnectionHandler client,
String path)
Imports one image file to the dataset in OMERO.
|
List<Long> |
Dataset.importImage(ConnectionHandler client,
String path)
Imports one image file to the dataset in OMERO.
|
boolean |
Dataset.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the dataset in OMERO.
|
boolean |
DatasetWrapper.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the dataset in OMERO.
|
boolean |
DatasetWrapper.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the dataset in OMERO.
|
boolean |
Dataset.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the dataset in OMERO.
|
default <A extends AnnotationData> |
Folder.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
default <A extends AnnotationData> |
Folder.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
void |
Dataset.reload(Browser browser)
Reloads the dataset from OMERO.
|
void |
DatasetWrapper.reload(Browser browser)
Reloads the dataset from OMERO.
|
void |
Folder.reload(Browser browser)
Reloads the folder from OMERO, to update all links.
|
void |
FolderWrapper.reload(Browser browser)
Reloads the folder from OMERO, to update all links.
|
void |
Project.reload(Browser browser)
Reloads the project from OMERO.
|
void |
ProjectWrapper.reload(Browser browser)
Reloads the project from OMERO.
|
void |
ProjectWrapper.reload(Browser browser)
Reloads the project from OMERO.
|
void |
Project.reload(Browser browser)
Reloads the project from OMERO.
|
void |
FolderWrapper.reload(Browser browser)
Reloads the folder from OMERO, to update all links.
|
void |
Folder.reload(Browser browser)
Reloads the folder from OMERO, to update all links.
|
void |
DatasetWrapper.reload(Browser browser)
Reloads the dataset from OMERO.
|
void |
Dataset.reload(Browser browser)
Reloads the dataset from OMERO.
|
void |
Project.removeDataset(Client client,
Dataset dataset)
Removes a dataset from the project in OMERO.
|
void |
ProjectWrapper.removeDataset(Client client,
Dataset dataset)
Removes a dataset from the project in OMERO.
|
void |
ProjectWrapper.removeDataset(Client client,
Dataset dataset)
Removes a dataset from the project in OMERO.
|
void |
Project.removeDataset(Client client,
Dataset dataset)
Removes a dataset from the project in OMERO.
|
void |
Dataset.removeImage(Client client,
Image image)
Removes an image from the dataset in OMERO.
|
void |
DatasetWrapper.removeImage(Client client,
Image image)
Removes an image from the dataset in OMERO.
|
void |
DatasetWrapper.removeImage(Client client,
Image image)
Removes an image from the dataset in OMERO.
|
void |
Dataset.removeImage(Client client,
Image image)
Removes an image from the dataset in OMERO.
|
default List<Image> |
Dataset.replaceImages(Client client,
Collection<? extends Image> oldImages,
Image newImage)
Replaces (and unlinks) a collection of images from this dataset by a new image, after copying their annotations
and ROIs, and concatenating the descriptions (on new lines).
|
default List<Image> |
Dataset.replaceImages(Client client,
Collection<? extends Image> oldImages,
Image newImage)
Replaces (and unlinks) a collection of images from this dataset by a new image, after copying their annotations
and ROIs, and concatenating the descriptions (on new lines).
|
void |
Folder.unlinkAllROIs(DataManager dm)
Unlink all ROIs associated to this folder.
|
void |
FolderWrapper.unlinkAllROIs(DataManager dm)
Unlink all ROIs associated to this folder.
|
void |
FolderWrapper.unlinkAllROIs(DataManager dm)
Unlink all ROIs associated to this folder.
|
void |
Folder.unlinkAllROIs(DataManager dm)
Unlink all ROIs associated to this folder.
|
default void |
Folder.unlinkAllROIs(DataManager dm,
Image image)
Unlink all ROIs associated to the provided image from the folder.
|
default void |
Folder.unlinkAllROIs(DataManager dm,
Image image)
Unlink all ROIs associated to the provided image from the folder.
|
default void |
Folder.unlinkAllROIs(DataManager dm,
long imageId)
Unlink all ROIs associated to the provided image ID from the folder.
|
default void |
Folder.unlinkAllROIs(DataManager dm,
long imageId)
Unlink all ROIs associated to the provided image ID from the folder.
|
default void |
Folder.unlinkROIs(DataManager dm,
Collection<? extends ROI> rois)
Unlink ROIs from the folder.
|
default void |
Folder.unlinkROIs(DataManager dm,
Collection<? extends ROI> rois)
Unlink ROIs from the folder.
|
default void |
Folder.unlinkROIs(DataManager dm,
ROI... rois)
Unlink ROIs from the folder.
|
default void |
Folder.unlinkROIs(DataManager dm,
ROI... rois)
Unlink ROIs from the folder.
|
| Constructor and Description |
|---|
FolderWrapper(DataManager dm,
String name)
Constructor of the FolderWrapper class.
|
FolderWrapper(DataManager dm,
String name)
Constructor of the FolderWrapper class.
|
ProjectWrapper(DataManager dm,
String name,
String description)
Constructor of the ProjectWrapper class.
|
ProjectWrapper(DataManager dm,
String name,
String description)
Constructor of the ProjectWrapper class.
|
| Modifier and Type | Method and Description |
|---|---|
List<File> |
Image.download(ConnectionHandler client,
String path)
Downloads the original files from the server.
|
List<File> |
ImageWrapper.download(ConnectionHandler client,
String path)
Downloads the original files from the server.
|
List<File> |
ImageWrapper.download(ConnectionHandler client,
String path)
Downloads the original files from the server.
|
List<File> |
Image.download(ConnectionHandler client,
String path)
Downloads the original files from the server.
|
default double[][][][][] |
Pixels.getAllPixels(ConnectionHandler client)
Returns an array containing the value for each voxel
|
default double[][][][][] |
Pixels.getAllPixels(ConnectionHandler client)
Returns an array containing the value for each voxel
|
double[][][][][] |
Pixels.getAllPixels(ConnectionHandler client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds)
Returns an array containing the value for each voxel corresponding to the bounds
|
double[][][][][] |
PixelsWrapper.getAllPixels(ConnectionHandler client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds)
Returns an array containing the value for each voxel corresponding to the bounds
|
double[][][][][] |
PixelsWrapper.getAllPixels(ConnectionHandler client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds)
Returns an array containing the value for each voxel corresponding to the bounds
|
double[][][][][] |
Pixels.getAllPixels(ConnectionHandler client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds)
Returns an array containing the value for each voxel corresponding to the bounds
|
default Color |
Image.getChannelColor(Client client,
int index)
Gets the current color of the channel, or the original if it cannot be retrieved.
|
default Color |
Image.getChannelColor(Client client,
int index)
Gets the current color of the channel, or the original if it cannot be retrieved.
|
default Color |
Image.getChannelImportedColor(Browser browser,
int index)
Gets the original color of the channel.
|
default Color |
Image.getChannelImportedColor(Browser browser,
int index)
Gets the original color of the channel.
|
default String |
Image.getChannelName(Browser browser,
int index)
Gets the name of the channel.
|
default String |
Image.getChannelName(Browser browser,
int index)
Gets the name of the channel.
|
List<Channel> |
Image.getChannels(Browser browser)
Gets the image channels.
|
List<Channel> |
ImageWrapper.getChannels(Browser browser)
Gets the image channels.
|
List<Channel> |
ImageWrapper.getChannels(Browser browser)
Gets the image channels.
|
List<Channel> |
Image.getChannels(Browser browser)
Gets the image channels.
|
default List<Dataset> |
Image.getDatasets(Browser browser)
Retrieves the datasets containing this image from OMERO.
|
default List<Dataset> |
Image.getDatasets(Browser browser)
Retrieves the datasets containing this image from OMERO.
|
default List<Image> |
Image.getFilesetImages(Browser browser)
Returns the list of images sharing the same fileset as the current image.
|
default List<Image> |
Image.getFilesetImages(Browser browser)
Returns the list of images sharing the same fileset as the current image.
|
default List<Folder> |
Image.getFolders(Browser browser)
Gets the list of folders linked to this image.
|
default List<Folder> |
Image.getFolders(Browser browser)
Gets the list of folders linked to this image.
|
default List<RepositoryObject> |
Image.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
Image.getParents(Browser browser)
Gets the object parents.
|
default List<PlateAcquisition> |
Image.getPlateAcquisitions(Browser browser)
Returns the plate acquisitions linked to this image.
|
default List<PlateAcquisition> |
Image.getPlateAcquisitions(Browser browser)
Returns the plate acquisitions linked to this image.
|
default List<Plate> |
Image.getPlates(Browser browser)
Retrieves the plates containing this image.
|
default List<Plate> |
Image.getPlates(Browser browser)
Retrieves the plates containing this image.
|
default List<Project> |
Image.getProjects(Browser browser)
Retrieves the projects containing this image
|
default List<Project> |
Image.getProjects(Browser browser)
Retrieves the projects containing this image
|
default byte[][][][] |
Pixels.getRawPixels(ConnectionHandler client,
int bpp)
Returns an array containing the raw values for each voxel of each plane.
|
default byte[][][][] |
Pixels.getRawPixels(ConnectionHandler client,
int bpp)
Returns an array containing the raw values for each voxel of each plane.
|
byte[][][][] |
Pixels.getRawPixels(ConnectionHandler client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds,
int bpp)
Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
|
byte[][][][] |
PixelsWrapper.getRawPixels(ConnectionHandler client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds,
int bpp)
Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
|
byte[][][][] |
PixelsWrapper.getRawPixels(ConnectionHandler client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds,
int bpp)
Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
|
byte[][][][] |
Pixels.getRawPixels(ConnectionHandler client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds,
int bpp)
Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
|
List<Folder> |
Image.getROIFolders(DataManager dm)
Gets the list of folders linked to the ROIs in this image.
|
List<Folder> |
ImageWrapper.getROIFolders(DataManager dm)
Gets the list of folders linked to the ROIs in this image.
|
List<Folder> |
ImageWrapper.getROIFolders(DataManager dm)
Gets the list of folders linked to the ROIs in this image.
|
List<Folder> |
Image.getROIFolders(DataManager dm)
Gets the list of folders linked to the ROIs in this image.
|
List<ROI> |
Image.getROIs(DataManager dm)
Gets all ROIs linked to the image in OMERO
|
List<ROI> |
ImageWrapper.getROIs(DataManager dm)
Gets all ROIs linked to the image in OMERO
|
List<ROI> |
ImageWrapper.getROIs(DataManager dm)
Gets all ROIs linked to the image in OMERO
|
List<ROI> |
Image.getROIs(DataManager dm)
Gets all ROIs linked to the image in OMERO
|
default List<Screen> |
Image.getScreens(Browser browser)
Retrieves the screens containing this image
|
default List<Screen> |
Image.getScreens(Browser browser)
Retrieves the screens containing this image
|
BufferedImage |
Image.getThumbnail(ConnectionHandler client,
int size)
Retrieves the image thumbnail of the specified size.
|
BufferedImage |
ImageWrapper.getThumbnail(ConnectionHandler client,
int size)
Retrieves the image thumbnail of the specified size.
|
BufferedImage |
ImageWrapper.getThumbnail(ConnectionHandler client,
int size)
Retrieves the image thumbnail of the specified size.
|
BufferedImage |
Image.getThumbnail(ConnectionHandler client,
int size)
Retrieves the image thumbnail of the specified size.
|
default List<Well> |
Image.getWells(Browser browser)
Retrieves the wells containing this image.
|
default List<Well> |
Image.getWells(Browser browser)
Retrieves the wells containing this image.
|
default List<WellSample> |
Image.getWellSamples(Browser browser)
Retrieves the well samples containing this image and updates them from OMERO.
|
default List<WellSample> |
Image.getWellSamples(Browser browser)
Retrieves the well samples containing this image and updates them from OMERO.
|
default boolean |
Image.isOrphaned(Browser browser)
Checks if image is orphaned (not in a WellSample nor linked to a dataset).
|
default boolean |
Image.isOrphaned(Browser browser)
Checks if image is orphaned (not in a WellSample nor linked to a dataset).
|
void |
Pixels.loadPlanesInfo(Browser browser)
Loads the planes information.
|
void |
PixelsWrapper.loadPlanesInfo(Browser browser)
Loads the planes information.
|
void |
PixelsWrapper.loadPlanesInfo(Browser browser)
Loads the planes information.
|
void |
Pixels.loadPlanesInfo(Browser browser)
Loads the planes information.
|
void |
Image.reload(Browser browser)
Reloads the image from OMERO.
|
void |
ImageWrapper.reload(Browser browser)
Reloads the image from OMERO.
|
void |
ImageWrapper.reload(Browser browser)
Reloads the image from OMERO.
|
void |
Image.reload(Browser browser)
Reloads the image from OMERO.
|
List<ROI> |
Image.saveROIs(DataManager dm,
Collection<? extends ROI> rois)
Links ROIs to the image in OMERO.
|
List<ROI> |
ImageWrapper.saveROIs(DataManager dm,
Collection<? extends ROI> rois)
Links ROIs to the image in OMERO.
|
List<ROI> |
ImageWrapper.saveROIs(DataManager dm,
Collection<? extends ROI> rois)
Links ROIs to the image in OMERO.
|
List<ROI> |
Image.saveROIs(DataManager dm,
Collection<? extends ROI> rois)
Links ROIs to the image in OMERO.
|
default List<ROI> |
Image.saveROIs(DataManager dm,
ROI... rois)
Links ROIs to the image in OMERO.
|
default List<ROI> |
Image.saveROIs(DataManager dm,
ROI... rois)
Links ROIs to the image in OMERO.
|
default ij.ImagePlus |
Image.toImagePlus(Client client)
Generates the ImagePlus from the ij library corresponding to the image from OMERO WARNING : you need to include
the ij library to use this function
|
default ij.ImagePlus |
Image.toImagePlus(Client client)
Generates the ImagePlus from the ij library corresponding to the image from OMERO WARNING : you need to include
the ij library to use this function
|
ij.ImagePlus |
Image.toImagePlus(Client client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds)
Gets the imagePlus generated from the image from OMERO corresponding to the bound.
|
ij.ImagePlus |
ImageWrapper.toImagePlus(Client client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds)
Gets the imagePlus generated from the image from OMERO corresponding to the bound.
|
ij.ImagePlus |
ImageWrapper.toImagePlus(Client client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds)
Gets the imagePlus generated from the image from OMERO corresponding to the bound.
|
ij.ImagePlus |
Image.toImagePlus(Client client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds)
Gets the imagePlus generated from the image from OMERO corresponding to the bound.
|
default ij.ImagePlus |
Image.toImagePlus(Client client,
ROI roi)
Gets the imagePlus from the image generated from the ROI.
|
default ij.ImagePlus |
Image.toImagePlus(Client client,
ROI roi)
Gets the imagePlus from the image generated from the ROI.
|
| Modifier and Type | Method and Description |
|---|---|
default <A extends AnnotationData> |
ROI.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
default <A extends AnnotationData> |
Shape.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
default <A extends AnnotationData> |
Shape.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
default <A extends AnnotationData> |
ROI.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
void |
ROI.saveROI(DataManager dm)
Saves the ROI.
|
void |
ROIWrapper.saveROI(DataManager dm)
Saves the ROI.
|
void |
ROIWrapper.saveROI(DataManager dm)
Saves the ROI.
|
void |
ROI.saveROI(DataManager dm)
Saves the ROI.
|
| Modifier and Type | Method and Description |
|---|---|
default List<RepositoryObject> |
Plate.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
PlateAcquisition.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
Screen.getChildren(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
Well.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
WellSample.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
WellSample.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
Well.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
Screen.getChildren(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
PlateAcquisition.getChildren(Browser browser)
Gets the object children.
|
default List<RepositoryObject> |
Plate.getChildren(Browser browser)
Gets the object children.
|
default List<Image> |
Plate.getImages(Browser browser)
Returns the images contained in the wells of this plate.
|
default List<Image> |
PlateAcquisition.getImages(Browser browser)
Retrieves the images contained in the well samples from OMERO.
|
default List<Image> |
Screen.getImages(Browser browser)
Retrieves the images contained in this screen.
|
default List<Image> |
Screen.getImages(Browser browser)
Retrieves the images contained in this screen.
|
default List<Image> |
PlateAcquisition.getImages(Browser browser)
Retrieves the images contained in the well samples from OMERO.
|
default List<Image> |
Plate.getImages(Browser browser)
Returns the images contained in the wells of this plate.
|
default List<RepositoryObject> |
Plate.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
PlateAcquisition.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
Well.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
WellSample.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
WellSample.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
Well.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
PlateAcquisition.getParents(Browser browser)
Gets the object parents.
|
default List<RepositoryObject> |
Plate.getParents(Browser browser)
Gets the object parents.
|
default List<PlateAcquisition> |
Plate.getPlateAcquisitions(Browser browser)
Reloads the plate and returns the plate acquisitions related to it.
|
default List<PlateAcquisition> |
Screen.getPlateAcquisitions(Browser browser)
Returns the plate acquisitions linked to this object, either directly, or through parents/children.
|
default List<PlateAcquisition> |
Well.getPlateAcquisitions(Browser browser)
Refreshes this well and returns the plate acquisitions linked to it.
|
default List<PlateAcquisition> |
Well.getPlateAcquisitions(Browser browser)
Refreshes this well and returns the plate acquisitions linked to it.
|
default List<PlateAcquisition> |
Screen.getPlateAcquisitions(Browser browser)
Returns the plate acquisitions linked to this object, either directly, or through parents/children.
|
default List<PlateAcquisition> |
Plate.getPlateAcquisitions(Browser browser)
Reloads the plate and returns the plate acquisitions related to it.
|
default List<Plate> |
PlateAcquisition.getPlates(Browser browser)
Returns the (updated) parent plate as a singleton list.
|
default List<Plate> |
Screen.getPlates(Browser browser)
Reloads this screen and returns the updated list of plates within.
|
default List<Plate> |
Well.getPlates(Browser browser)
Reloads this well and returns the plate containing it.
|
default List<Plate> |
WellSample.getPlates(Browser browser)
Returns the plates containing the parent Well.
|
default List<Plate> |
WellSample.getPlates(Browser browser)
Returns the plates containing the parent Well.
|
default List<Plate> |
Well.getPlates(Browser browser)
Reloads this well and returns the plate containing it.
|
default List<Plate> |
Screen.getPlates(Browser browser)
Reloads this screen and returns the updated list of plates within.
|
default List<Plate> |
PlateAcquisition.getPlates(Browser browser)
Returns the (updated) parent plate as a singleton list.
|
default List<Screen> |
Plate.getScreens(Browser browser)
Retrieves the screens containing this plate.
|
default List<Screen> |
PlateAcquisition.getScreens(Browser browser)
Retrieves the screens containing the parent plates.
|
default List<Screen> |
Well.getScreens(Browser browser)
Refreshes this well and retrieves the screens containing it.
|
default List<Screen> |
WellSample.getScreens(Browser browser)
Returns the screens containing the parent Well.
|
default List<Screen> |
WellSample.getScreens(Browser browser)
Returns the screens containing the parent Well.
|
default List<Screen> |
Well.getScreens(Browser browser)
Refreshes this well and retrieves the screens containing it.
|
default List<Screen> |
PlateAcquisition.getScreens(Browser browser)
Retrieves the screens containing the parent plates.
|
default List<Screen> |
Plate.getScreens(Browser browser)
Retrieves the screens containing this plate.
|
default Well |
WellSample.getWell(Browser browser)
Retrieves the well containing this well sample.
|
default Well |
WellSample.getWell(Browser browser)
Retrieves the well containing this well sample.
|
List<Well> |
Plate.getWells(Browser browser)
Gets all wells in the plate available from OMERO.
|
default List<Well> |
PlateAcquisition.getWells(Browser browser)
Retrieves the wells containing the well samples for this plate acquisition.
|
List<Well> |
PlateWrapper.getWells(Browser browser)
Gets all wells in the plate available from OMERO.
|
default List<Well> |
Screen.getWells(Browser browser)
Retrieves the wells linked to this object, either directly, or through parents/children.
|
default List<Well> |
Screen.getWells(Browser browser)
Retrieves the wells linked to this object, either directly, or through parents/children.
|
List<Well> |
PlateWrapper.getWells(Browser browser)
Gets all wells in the plate available from OMERO.
|
default List<Well> |
PlateAcquisition.getWells(Browser browser)
Retrieves the wells containing the well samples for this plate acquisition.
|
List<Well> |
Plate.getWells(Browser browser)
Gets all wells in the plate available from OMERO.
|
List<WellSample> |
PlateAcquisition.getWellSamples(Browser browser)
Retrieves the well samples for this plate acquisition and reloads them from OMERO.
|
List<WellSample> |
PlateAcquisitionWrapper.getWellSamples(Browser browser)
Retrieves the well samples for this plate acquisition from OMERO and updates the object.
|
default List<WellSample> |
Well.getWellSamples(Browser browser)
Reloads this well and returns the well samples contained within.
|
default List<WellSample> |
Well.getWellSamples(Browser browser)
Reloads this well and returns the well samples contained within.
|
List<WellSample> |
PlateAcquisitionWrapper.getWellSamples(Browser browser)
Retrieves the well samples for this plate acquisition from OMERO and updates the object.
|
List<WellSample> |
PlateAcquisition.getWellSamples(Browser browser)
Retrieves the well samples for this plate acquisition and reloads them from OMERO.
|
List<Long> |
Screen.importImage(ConnectionHandler client,
String path)
Imports one image file to the screen in OMERO.
|
List<Long> |
ScreenWrapper.importImage(ConnectionHandler client,
String path)
Imports one image file to the screen in OMERO.
|
List<Long> |
ScreenWrapper.importImage(ConnectionHandler client,
String path)
Imports one image file to the screen in OMERO.
|
List<Long> |
Screen.importImage(ConnectionHandler client,
String path)
Imports one image file to the screen in OMERO.
|
boolean |
Screen.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the screen in OMERO.
|
boolean |
ScreenWrapper.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the screen in OMERO.
|
boolean |
ScreenWrapper.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the screen in OMERO.
|
boolean |
Screen.importImages(ConnectionHandler client,
String... paths)
Imports all images candidates in the paths to the screen in OMERO.
|
default <A extends AnnotationData> |
PlateAcquisition.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
default <A extends AnnotationData> |
PlateAcquisition.link(DataManager dm,
A annotation)
Attach an
AnnotationData to this object. |
void |
Plate.reload(Browser browser)
Reloads the plate from OMERO.
|
void |
PlateAcquisition.reload(Browser browser)
Reloads the plate acquisition from OMERO.
|
void |
PlateAcquisitionWrapper.reload(Browser browser)
Reloads the plate acquisition from OMERO.
|
void |
PlateWrapper.reload(Browser browser)
Reloads the plate from OMERO.
|
void |
Screen.reload(Browser browser)
Reloads the screen from OMERO.
|
void |
ScreenWrapper.reload(Browser browser)
Reloads the screen from OMERO.
|
void |
Well.reload(Browser browser)
Reloads the well from OMERO.
|
void |
WellSample.reload(Browser browser)
Reloads the well sample from OMERO.
|
void |
WellSampleWrapper.reload(Browser browser)
Reloads the well sample from OMERO.
|
void |
WellWrapper.reload(Browser browser)
Reloads the well from OMERO.
|
void |
WellWrapper.reload(Browser browser)
Reloads the well from OMERO.
|
void |
WellSampleWrapper.reload(Browser browser)
Reloads the well sample from OMERO.
|
void |
WellSample.reload(Browser browser)
Reloads the well sample from OMERO.
|
void |
Well.reload(Browser browser)
Reloads the well from OMERO.
|
void |
ScreenWrapper.reload(Browser browser)
Reloads the screen from OMERO.
|
void |
Screen.reload(Browser browser)
Reloads the screen from OMERO.
|
void |
PlateWrapper.reload(Browser browser)
Reloads the plate from OMERO.
|
void |
PlateAcquisitionWrapper.reload(Browser browser)
Reloads the plate acquisition from OMERO.
|
void |
PlateAcquisition.reload(Browser browser)
Reloads the plate acquisition from OMERO.
|
void |
Plate.reload(Browser browser)
Reloads the plate from OMERO.
|
| Constructor and Description |
|---|
ScreenWrapper(DataManager dm,
String name,
String description)
Constructor of the ProjectWrapper class.
|
ScreenWrapper(DataManager dm,
String name,
String description)
Constructor of the ProjectWrapper class.
|
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