long |
GenericRepositoryObjectWrapper.addAndReplaceFile(Client client,
java.io.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 |
GenericRepositoryObjectWrapper.addAndReplaceFile(Client client,
java.io.File file,
GenericRepositoryObjectWrapper.ReplacePolicy policy) |
Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
|
void |
GenericRepositoryObjectWrapper.addAndReplaceTable(Client client,
TableWrapper 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 |
GenericRepositoryObjectWrapper.addAndReplaceTable(Client client,
TableWrapper table,
GenericRepositoryObjectWrapper.ReplacePolicy policy) |
Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
|
DatasetWrapper |
ProjectWrapper.addDataset(Client client,
DatasetWrapper dataset) |
Adds a dataset to the project in OMERO.
|
DatasetWrapper |
ProjectWrapper.addDataset(Client client,
java.lang.String name,
java.lang.String description) |
Adds a dataset to the project in OMERO.
|
long |
GenericRepositoryObjectWrapper.addFile(Client client,
java.io.File file) |
Uploads a file and links it to the object
|
void |
GenericRepositoryObjectWrapper.addFileAnnotation(Client client,
FileAnnotationWrapper annotation) |
Links a file annotation to the object
|
void |
DatasetWrapper.addImage(Client client,
ImageWrapper image) |
Adds a single image to the dataset in OMERO
|
void |
DatasetWrapper.addImages(Client client,
java.util.List<? extends ImageWrapper> images) |
Adds a list of image to the dataset in OMERO.
|
void |
GenericRepositoryObjectWrapper.addMapAnnotation(Client client,
MapAnnotationWrapper mapAnnotation) |
Adds a List of Key-Value pair to the object.
|
void |
GenericRepositoryObjectWrapper.addPairKeyValue(Client client,
java.lang.String key,
java.lang.String value) |
Adds a single Key-Value pair to the object.
|
void |
FolderWrapper.addROI(Client client,
ROIWrapper roi) |
Add an ROI to the folder and associate it to the image id set(an image need to be associated)
|
void |
GenericRepositoryObjectWrapper.addTable(Client client,
TableWrapper table) |
Adds a table to the object in OMERO.
|
protected void |
FolderWrapper.addTag(Client client,
TagAnnotationData tagData) |
Private function.
|
void |
GenericRepositoryObjectWrapper.addTag(Client client,
TagAnnotationWrapper tag) |
Adds a tag to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.addTag(Client client,
java.lang.Long id) |
Adds multiple tags to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.addTag(Client client,
java.lang.String name,
java.lang.String description) |
Adds a newly created tag to the object in OMERO, if possible.
|
protected void |
GenericRepositoryObjectWrapper.addTag(Client client,
TagAnnotationData tagData) |
Protected function.
|
protected void |
PlateAcquisitionWrapper.addTag(Client client,
TagAnnotationData tagData) |
Protected function.
|
void |
GenericRepositoryObjectWrapper.addTags(Client client,
TagAnnotationWrapper... tags) |
Adds multiple tag to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.addTags(Client client,
java.lang.Long... ids) |
Adds multiple tags by ID to the object in OMERO, if possible.
|
void |
GenericRepositoryObjectWrapper.copyAnnotationLinks(Client client,
GenericRepositoryObjectWrapper<?> object) |
Copies annotation links from some other object to this one
|
java.util.List<java.io.File> |
ImageWrapper.download(Client client,
java.lang.String path) |
Downloads the original files from the server.
|
double[][][][][] |
PixelsWrapper.getAllPixels(Client client) |
Returns an array containing the value for each voxel
|
double[][][][][] |
PixelsWrapper.getAllPixels(Client client,
int[] xBounds,
int[] yBounds,
int[] cBounds,
int[] zBounds,
int[] tBounds) |
Returns an array containing the value for each voxel corresponding to the bounds
|
java.awt.Color |
ImageWrapper.getChannelColor(Client client,
int index) |
Gets the current color of the channel
|
java.awt.Color |
ImageWrapper.getChannelImportedColor(Client client,
int index) |
Gets the original color of the channel
|
java.lang.String |
ImageWrapper.getChannelName(Client client,
int index) |
Gets the name of the channel
|
java.util.List<ChannelWrapper> |
ImageWrapper.getChannels(Client client) |
Gets the image channels
|
java.util.List<DatasetWrapper> |
ImageWrapper.getDatasets(Client client) |
Retrieves the datasets containing this image
|
java.util.List<FileAnnotationWrapper> |
GenericRepositoryObjectWrapper.getFileAnnotations(Client client) |
Returns the file annotations
|
java.util.List<ImageWrapper> |
ImageWrapper.getFilesetImages(Client client) |
Returns the list of images sharing the same fileset as the current image.
|
FolderWrapper |
ImageWrapper.getFolder(Client client,
java.lang.Long folderId) |
Gets the folder with the specified id on OMERO.
|
java.util.List<FolderWrapper> |
ImageWrapper.getFolders(Client client) |
Gets the list of Folder linked to the image Associate the folder to the image
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImages(Client client) |
Gets all images in the dataset available from OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImages(Client client,
java.lang.String name) |
Gets all images in the dataset with a certain name from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImages(Client client) |
Gets all images in the project available from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImages(Client client,
java.lang.String name) |
Gets all images in the project with a certain name from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImages(Client client,
java.lang.String datasetName,
java.lang.String imageName) |
Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesKey(Client client,
java.lang.String key) |
Gets all images in the dataset with a certain key
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesKey(Client client,
java.lang.String key) |
Gets all images in the project with a certain key
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesLike(Client client,
java.lang.String motif) |
Gets all images in the dataset with a certain motif in their name from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesLike(Client client,
java.lang.String motif) |
Gets all images in the project with a certain motif in their name from OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesPairKeyValue(Client client,
java.lang.String key,
java.lang.String value) |
Gets all images in the dataset with a certain key value pair from OMERO
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesPairKeyValue(Client client,
java.lang.String key,
java.lang.String value) |
Gets all images in the project with a certain key value pair from OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesTagged(Client client,
TagAnnotationWrapper tag) |
Gets all images in the dataset tagged with a specified tag from OMERO.
|
java.util.List<ImageWrapper> |
DatasetWrapper.getImagesTagged(Client client,
java.lang.Long tagId) |
Gets all images in the dataset tagged with a specified tag from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesTagged(Client client,
TagAnnotationWrapper tag) |
Gets all images in the project tagged with a specified tag from OMERO.
|
java.util.List<ImageWrapper> |
ProjectWrapper.getImagesTagged(Client client,
java.lang.Long tagId) |
Gets all images in the project tagged with a specified tag from OMERO.
|
java.util.Map<java.lang.String,java.lang.String> |
GenericRepositoryObjectWrapper.getKeyValuePairs(Client client) |
Gets the List of NamedValue (Key-Value pair) associated to an object.
|
java.util.List<MapAnnotationWrapper> |
GenericRepositoryObjectWrapper.getMapAnnotations(Client client) |
Gets all map annotations linked to an object in OMERO, if possible.
|
java.util.List<PlateWrapper> |
ImageWrapper.getPlates(Client client) |
Retrieves the plates containing this image
|
java.util.List<ProjectWrapper> |
DatasetWrapper.getProjects(Client client) |
Retrieves the projects containing this dataset.
|
java.util.List<ProjectWrapper> |
ImageWrapper.getProjects(Client client) |
Retrieves the projects containing this image
|
byte[][][][] |
PixelsWrapper.getRawPixels(Client client,
int bpp) |
Returns an array containing the raw values for each voxel for each planes
|
byte[][][][] |
PixelsWrapper.getRawPixels(Client 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
|
java.util.List<ROIWrapper> |
FolderWrapper.getROIs(Client client) |
Gets the ROI contained in the folder associated with the image id set (an image need to be associated)
|
java.util.List<ROIWrapper> |
ImageWrapper.getROIs(Client client) |
Gets all ROIs linked to the image in OMERO
|
java.util.List<ScreenWrapper> |
ImageWrapper.getScreens(Client client) |
Retrieves the screens containing this image
|
java.util.List<ScreenWrapper> |
PlateWrapper.getScreens(Client client) |
Retrieves the screens containing this dataset.
|
TableWrapper |
GenericRepositoryObjectWrapper.getTable(Client client,
java.lang.Long fileId) |
Gets a certain table linked to the object in OMERO.
|
java.util.List<TableWrapper> |
GenericRepositoryObjectWrapper.getTables(Client client) |
Gets all tables linked to the object in OMERO.
|
java.util.List<TagAnnotationWrapper> |
GenericRepositoryObjectWrapper.getTags(Client client) |
Gets all tags linked to an object in OMERO, if possible.
|
java.awt.image.BufferedImage |
ImageWrapper.getThumbnail(Client client,
int size) |
Retrieves the image thumbnail of the specified size.
|
java.lang.String |
GenericRepositoryObjectWrapper.getValue(Client client,
java.lang.String key) |
Gets the value from a Key-Value pair associated to the object.
|
WellWrapper |
WellSampleWrapper.getWell(Client client) |
Retrieves the well containing this well sample
|
java.util.List<WellWrapper> |
ImageWrapper.getWells(Client client) |
Retrieves the wells containing this image
|
java.util.List<WellWrapper> |
PlateWrapper.getWells(Client client) |
Gets all wells in the plate available from OMERO.
|
java.util.List<java.lang.Long> |
DatasetWrapper.importAndReplaceImages(Client client,
java.lang.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.
|
java.util.List<java.lang.Long> |
DatasetWrapper.importAndReplaceImages(Client client,
java.lang.String path,
GenericRepositoryObjectWrapper.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.
|
java.util.List<java.lang.Long> |
DatasetWrapper.importImage(Client client,
java.lang.String path) |
Imports one image file to the dataset in OMERO.
|
boolean |
DatasetWrapper.importImages(Client client,
java.lang.String... paths) |
Imports all images candidates in the paths to the dataset in OMERO.
|
boolean |
ImageWrapper.isOrphaned(Client client) |
Checks if image is orphaned (not in a WellSample nor linked to a dataset).
|
void |
PixelsWrapper.loadPlanesInfo(Client client) |
Loads the planes information.
|
void |
DatasetWrapper.refresh(Client client) |
Refreshes the wrapped dataset.
|
void |
ProjectWrapper.refresh(Client client) |
Refreshes the wrapped project.
|
void |
ProjectWrapper.removeDataset(Client client,
DatasetWrapper dataset) |
Removes a dataset from the project in OMERO.
|
void |
DatasetWrapper.removeImage(Client client,
ImageWrapper image) |
Removes an image from the dataset in OMERO.
|
protected void |
GenericRepositoryObjectWrapper.removeLink(Client client,
java.lang.String linkType,
long childId) |
Removes the link of the given type with the given child ID.
|
java.util.List<ImageWrapper> |
DatasetWrapper.replaceImages(Client client,
java.util.Collection<? extends ImageWrapper> oldImages,
ImageWrapper 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 |
ImageWrapper.saveROI(Client client,
ROIWrapper roi) |
Links a ROI to the image in OMERO
|
ImagePlus |
ImageWrapper.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
|
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.
|
ImagePlus |
ImageWrapper.toImagePlus(Client client,
ROIWrapper roi) |
Gets the imagePlus from the image generated from the ROI.
|
<A extends GenericAnnotationWrapper<?>>
void |
GenericRepositoryObjectWrapper.unlink(Client client,
A annotation) |
Unlinks the given annotation from the current object.
|
void |
FolderWrapper.unlinkAllROI(Client client) |
Unlink all ROI, associated to the image set, in the folder.
|
void |
FolderWrapper.unlinkROI(Client client,
ROIWrapper roi) |
Unlink an ROI, associated to the image set, in the folder.
|