aliby.io.omero.UnsafeImage¶

class UnsafeImage(image_id, **server_info)[source]¶

Bases: Image

Loads images from OMERO and gives access to the data and metadata. This class is a temporary solution while we find a way to use context managers inside napari. It risks resulting in zombie connections and producing freezes in an OMERO server.

Attributes

data
file_annotations
metadata: Store metadata saved in OMERO: image size, number of time points, labels of channels, and image name.
name
ome_class

Methods

`add_file_as_annotation`(file_to_upload, **kwargs)	Upload annotation to object on OMERO server.
`from_h5`(filepath)	Instatiate Image from a hdf5 file.
`server_info_from_h5`(filepath)	Return server info from hdf5 file.

create_gate
set_id

Establishes the connection to the OMERO server via the Argo base class.

Parameters

image_id: integer
server_info: dictionary: Specifies the host, username, and password as strings

Attributes

data
file_annotations
metadata: Store metadata saved in OMERO: image size, number of time points, labels of channels, and image name.
name
ome_class

Methods

`add_file_as_annotation`(file_to_upload, **kwargs)	Upload annotation to object on OMERO server.
`from_h5`(filepath)	Instatiate Image from a hdf5 file.
`server_info_from_h5`(filepath)	Return server info from hdf5 file.

create_gate
set_id

__init__(image_id, **server_info)[source]¶

Establishes the connection to the OMERO server via the Argo base class.

Parameters

image_id: integer
server_info: dictionary: Specifies the host, username, and password as strings

Methods

`__init__`(image_id, **server_info)	Establishes the connection to the OMERO server via the Argo base class.
`add_file_as_annotation`(file_to_upload, **kwargs)	Upload annotation to object on OMERO server.
`create_gate`()	rtype `bool`
`from_h5`(filepath)	Instatiate Image from a hdf5 file.
`server_info_from_h5`(filepath)	Return server info from hdf5 file.
`set_id`(ome_id)

Attributes

`data`
`file_annotations`
`metadata`	Store metadata saved in OMERO: image size, number of time points, labels of channels, and image name.
`name`
`ome_class`

add_file_as_annotation(file_to_upload, **kwargs)¶

Upload annotation to object on OMERO server. Only valid in subclasses.

Parameters

file_to_upload: File to upload
**kwargs: Additional keyword arguments passed on: to BlitzGateway.createFileAnnfromLocalFile

classmethod from_h5(filepath)¶

Instatiate Image from a hdf5 file.

Parameters

clsImage: Image class
filepatht.Union[str, PosixPath]: Location of hdf5 file.

Examples

FIXME: Add docs.

property metadata¶: Store metadata saved in OMERO: image size, number of time points, labels of channels, and image name.

classmethod server_info_from_h5(filepath)¶

Return server info from hdf5 file.

Parameters

clsBridgeOmero: BridgeOmero class
filepatht.Union[str, PosixPath]: Location of hdf5 file.

Examples

FIXME: Add docs.