DatasetWrapper |
ProjectWrapper.addDataset(Client client,
DatasetWrapper dataset) |
Add a dataset to the project in OMERO.
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DatasetWrapper |
ProjectWrapper.addDataset(Client client,
String name,
String description) |
Add a dataset to the project in OMERO.
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long |
GenericRepositoryObjectWrapper.addFile(Client client,
File file) |
Links a file to the object
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void |
DatasetWrapper.addImage(Client client,
ImageWrapper image) |
Adds a single image to the dataset in OMERO
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void |
DatasetWrapper.addImages(Client client,
List<ImageWrapper> images) |
Adds a list of image to the dataset in OMERO.
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void |
GenericRepositoryObjectWrapper.addMapAnnotation(Client client,
MapAnnotationWrapper mapAnnotation) |
Adds a List of Key-Value pair to the object
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void |
GenericRepositoryObjectWrapper.addPairKeyValue(Client client,
String key,
String value) |
Adds a single Key-Value pair to the object.
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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)
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void |
GenericRepositoryObjectWrapper.addTable(Client client,
TableWrapper table) |
Adds a table to the object in OMERO
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void |
GenericRepositoryObjectWrapper.addTag(Client client,
TagAnnotationWrapper tag) |
Adds a tag to the object in OMERO, if possible.
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void |
GenericRepositoryObjectWrapper.addTag(Client client,
Long id) |
Adds multiple tags to the object in OMERO, if possible.
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void |
GenericRepositoryObjectWrapper.addTag(Client client,
String name,
String description) |
Adds a newly created tag to the object in OMERO, if possible.
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protected void |
GenericRepositoryObjectWrapper.addTag(Client client,
TagAnnotationData tagData) |
Private function.
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void |
GenericRepositoryObjectWrapper.addTags(Client client,
TagAnnotationWrapper... tags) |
Adds multiple tag to the object in OMERO, if possible.
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void |
GenericRepositoryObjectWrapper.addTags(Client client,
Long... ids) |
Adds multiple tags by ID to the object in OMERO, if possible.
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List<File> |
ImageWrapper.download(Client client,
String path) |
Downloads the original files from the server.
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double[][][][][] |
PixelsWrapper.getAllPixels(Client client) |
Returns an array containing the value for each voxels
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double[][][][][] |
PixelsWrapper.getAllPixels(Client client,
int[] xBound,
int[] yBound,
int[] cBound,
int[] zBound,
int[] tBound) |
Returns an array containing the value for each voxels corresponding to the bounds
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Color |
ImageWrapper.getChannelColor(Client client,
int index) |
Gets the current color of the channel
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Color |
ImageWrapper.getChannelImportedColor(Client client,
int index) |
Gets the original color of the channel
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String |
ImageWrapper.getChannelName(Client client,
int index) |
Gets the name of the channel
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List<ChannelWrapper> |
ImageWrapper.getChannels(Client client) |
Gets the image channels
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FolderWrapper |
ImageWrapper.getFolder(Client client,
Long folderId) |
Gets the folder with the specified id on OMERO.
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List<FolderWrapper> |
ImageWrapper.getFolders(Client client) |
Gets the list of Folder linked to the image Associate the folder to the image
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List<ImageWrapper> |
DatasetWrapper.getImages(Client client) |
Gets all images in the dataset available from OMERO.
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List<ImageWrapper> |
DatasetWrapper.getImages(Client client,
String name) |
Gets all images in the dataset with a certain from OMERO.
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List<ImageWrapper> |
ProjectWrapper.getImages(Client client) |
Gets all images in the project available from OMERO.
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List<ImageWrapper> |
ProjectWrapper.getImages(Client client,
String name) |
Gets all images in the project with a certain from OMERO.
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List<ImageWrapper> |
DatasetWrapper.getImagesKey(Client client,
String key) |
Gets all images in the dataset with a certain key
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List<ImageWrapper> |
ProjectWrapper.getImagesKey(Client client,
String key) |
Gets all images in the project with a certain key
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List<ImageWrapper> |
DatasetWrapper.getImagesLike(Client client,
String motif) |
Gets all images in the dataset with a certain motif in their name from OMERO.
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List<ImageWrapper> |
ProjectWrapper.getImagesLike(Client client,
String motif) |
Gets all images in the project with a certain motif in their name from OMERO.
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List<ImageWrapper> |
DatasetWrapper.getImagesPairKeyValue(Client client,
String key,
String value) |
Gets all images in the dataset with a certain key value pair from OMERO
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List<ImageWrapper> |
ProjectWrapper.getImagesPairKeyValue(Client client,
String key,
String value) |
Gets all images in the project with a certain key value pair from OMERO.
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List<ImageWrapper> |
DatasetWrapper.getImagesTagged(Client client,
TagAnnotationWrapper tag) |
Gets all images in the dataset tagged with a specified tag from OMERO.
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List<ImageWrapper> |
DatasetWrapper.getImagesTagged(Client client,
Long tagId) |
Gets all images in the dataset tagged with a specified tag from OMERO.
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List<ImageWrapper> |
ProjectWrapper.getImagesTagged(Client client,
TagAnnotationWrapper tag) |
Gets all images in the project tagged with a specified tag from OMERO.
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List<ImageWrapper> |
ProjectWrapper.getImagesTagged(Client client,
Long tagId) |
Gets all images in the project tagged with a specified tag from OMERO.
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Map<String,String> |
GenericRepositoryObjectWrapper.getKeyValuePairs(Client client) |
Gets the List of NamedValue (Key-Value pair) associated to an object.
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byte[][][][] |
PixelsWrapper.getRawPixels(Client client,
int bpp) |
Returns an array containing the raw values for each voxels for each planes
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byte[][][][] |
PixelsWrapper.getRawPixels(Client client,
int[] xBound,
int[] yBound,
int[] cBound,
int[] zBound,
int[] tBound,
int bpp) |
Returns an array containing the raw values for each voxels for each planes corresponding to the bounds
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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)
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List<ROIWrapper> |
ImageWrapper.getROIs(Client client) |
Gets all ROIs linked to the image in OMERO
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TableWrapper |
GenericRepositoryObjectWrapper.getTable(Client client,
Long fileId) |
Gets a certain table linked to the object in OMERO
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List<TableWrapper> |
GenericRepositoryObjectWrapper.getTables(Client client) |
Gets all table linked to the object in OMERO.
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List<TagAnnotationWrapper> |
GenericRepositoryObjectWrapper.getTags(Client client) |
Gets all tag linked to an object in OMERO, if possible.
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BufferedImage |
ImageWrapper.getThumbnail(Client client,
int size) |
Retrieves the image thumbnail of the specified size.
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String |
GenericRepositoryObjectWrapper.getValue(Client client,
String key) |
Gets the value from a Key-Value pair associated to the object
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List<Long> |
DatasetWrapper.importImage(Client client,
String path) |
Imports one image candidate in the paths to the dataset in OMERO.
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boolean |
DatasetWrapper.importImages(Client client,
String... paths) |
Imports all images candidates in the paths to the dataset in OMERO.
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void |
DatasetWrapper.refresh(Client client) |
Refreshes the wrapped project.
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void |
ProjectWrapper.refresh(Client client) |
Refreshes the wrapped project.
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void |
ImageWrapper.saveROI(Client client,
ROIWrapper roi) |
Links a ROI to the image in OMERO
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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
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ImagePlus |
ImageWrapper.toImagePlus(Client client,
int[] xBound,
int[] yBound,
int[] cBound,
int[] zBound,
int[] tBound) |
Gets the imagePlus generated from the image from OMERO corresponding to the bound
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ImagePlus |
ImageWrapper.toImagePlus(Client client,
ROIWrapper roi) |
Gets the imagePlus from the image generated from the ROI.
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void |
FolderWrapper.unlinkAllROI(Client client) |
Unlink all ROI, associated to the image set, in the folder.
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void |
FolderWrapper.unlinkROI(Client client,
ROIWrapper roi) |
Unlink an ROI, associated to the image set, in the folder.
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