aliby.io.omero.Dataset¶
- class Dataset(expt_id, **server_info)[source]¶
Bases:
BridgeOmero- Parameters
- hoststring
web address of OMERO host
- username: string
- passwordstring
- ome_id: Optional int
Unique identifier on Omero database. Used to fetch specific objects.
- Attributes
- date
- file_annotations
- files
- name
- ome_class
- tags
- unique_name
Methods
add_file_as_annotation(file_to_upload, **kwargs)Upload annotation to object on OMERO server.
from_h5(filepath)Instatiate Dataset from a hdf5 file.
server_info_from_h5(filepath)Return server info from hdf5 file.
cache_logs
create_gate
get_images
set_id
- __init__(expt_id, **server_info)[source]¶
- Parameters
- hoststring
web address of OMERO host
- username: string
- passwordstring
- ome_id: Optional int
Unique identifier on Omero database. Used to fetch specific objects.
Methods
__init__(expt_id, **server_info)- Parameters
add_file_as_annotation(file_to_upload, **kwargs)Upload annotation to object on OMERO server.
cache_logs(root_dir)create_gate()- rtype
bool
from_h5(filepath)Instatiate Dataset from a hdf5 file.
get_images()server_info_from_h5(filepath)Return server info from hdf5 file.
set_id(ome_id)Attributes
datefile_annotationsfilesnameome_classtagsunique_name- 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)[source]¶
Instatiate Dataset from a hdf5 file.
- Parameters
- clsImage
Image class
- filepatht.Union[str, PosixPath]
Location of hdf5 file.
Examples
FIXME: Add docs.
- 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.