ezomero 0.0.5

A suite of convenience functions for working with OMERO. Written and maintained by the Research IT team at The Jackson Laboratory.

ezomero

A module with convenience functions for writing Python code that interacts with OMERO.

Installation

Just pip install ezomero and you should be good to go! The repo contains a requirements.txt file with the specific package versions we test ezomero with, but any Python>=3.6 and latest omero-py and numpy should work - note that this package is in active development!

Usage

In general, you will need to create a BlitzGateway object using omero-py, successfully do something like conn.connect() and then pass the conn object to most of these helper functions along with function-specific parameters.

Functions

post functions

post_dataset(conn, dataset_name, project_id, description)

Creates a new dataset. Returns a (new) dataset ID.

post_image(conn, image, image_name, description=None, dataset_id=None, source_image_id=None, channel_list=None)

Creates a new OMERO image from a numpy array. Returns a (new) image ID.

post_map_annotation(conn, object_type, object_ids, kv_dict, ns)

Creates a new MapAnnotation and links to images. Returns a (new) MapAnnotation ID.

post_project(conn, project_name, description=None)

Creates a new project. Returns a (new) project ID.

get functions

get_image(conn, image_id, no_pixels=False, start_coords=None, axis_lengths=None, xyzct=False, pad=False)

Gets omero image object along with pixels as a numpy array. Returns an omero.gateway.ImageWrapper object along with an ndarray containing the image pixels.

get_image_ids(conn, dataset=None, well=None)

Returns a list of image ids based on project and dataset. Returns a list of ints with the desired IDs.

get_map_annotation_ids(conn, object_type, object_id, ns=None)

Get IDs of map annotations associated with an object. Returns a list of ints with the desired IDs.

get_map_annotation(conn, map_ann_id)

Get the value of a map annotation object. Returns a dict with the contents of the desired MapAnnotation.

get_group_id(conn, group_name)

Get ID of a group based on group name. Must be an exact match. Case sensitive. Returns a single int.

get_user_id(conn, user_name)

Get ID of a user based on username. Must be an exact match. Case sensitive. Returns a single int.

get_original_filepaths(conn, image_id, fpath='repo')

Get paths to original files for specified image. Returns a list of str.

put functions

put_map_annotation(conn, map_ann_id, kv_dict, ns=None)

Update an existing map annotation with new values (kv pairs).

Filter functions

filter_by_filename(conn, im_ids, imported_filename)

Filter list of image ids by originalFile name. Returns a list of int image IDs that match.

Linking functions

link_images_to_dataset(conn, image_ids, dataset_id)

Adds the images with given IDs to the dataset with given ID.

link_datasets_to_project(conn, dataset_ids, project_id)

Adds the datasets with given IDs to the project with given ID.

print functions

print_map_annotation(conn, map_ann_id)

Print some information and value of a map annotation.

print_groups(conn)

Print all Groups with IDs and membership info.

print_projects(conn)

Print all available Projects.

print_datasets(conn, project=None)

Print all available Datasets for a given Project.

Other functions

set_group(conn, group_id)

Safely switch OMERO group. This function will change the user's current group to that specified by group_id, but only if the user is a member of that group. Returns a boolean with success status.