acia.segm.omero.utils

Utils for OMERO segmenation data

acia.segm.omero.utils.getImage(conn, imageId)

Get omero image by id

Note: only images in your current group are accessible

Parameters:

• conn (BlitzGateway) – current omero connection

• imageId (int) – image id

Returns:

ImageWrapper – image object

Return type:

omero.gateway.ImageWrapper

acia.segm.omero.utils.getDataset(conn, datasetId)

Get omero dataset by id

Note: only datasets in your current group are accessible

Parameters:

• conn (BlitzGateway) – active omero connection

• datasetId (int) – dataset id

Returns:

DatasetWrapper – dataset object

Return type:

omero.gateway.DatasetWrapper

acia.segm.omero.utils.getProject(conn, projectId)

Get omero project by id

Note: only projects in your current group are accessible

Parameters:

• conn (BlitzGateway) – active omero connection

• projectId (int) – project id

Returns:

ProjectWrapper – project object

Return type:

omero.gateway.ProjectWrapper

acia.segm.omero.utils.list_projects(conn)

List projects in the current user group

Note: only projects in your current group are accessible

Parameters:

conn (BlitzGateway) – Current omero BlitzGateway connection

Returns:

List[ProjectWrapper] – List of project wrappers

Return type:

list[omero.gateway.ProjectWrapper]

acia.segm.omero.utils.list_image_ids_in_dataset(conn, datasetId)

[summary]

Parameters:

• conn (BlitzGateway) – active omero connection

• datasetId (int) – dataset id

Returns:

List[int] – array of all image ids of the dataset

Return type:

list[int]

acia.segm.omero.utils.list_images_in_dataset(conn, datasetId)

List all images in the omero dataset

Parameters:

• conn (BlitzGateway) – active omero connection

• datasetId (int) – dataset id

Returns:

List[ImageWrapper] – List of omero images

Return type:

list[omero.gateway.ImageWrapper]

acia.segm.omero.utils.list_datasets_in_project(conn, projectId)

Parameters:

• conn (omero.gateway.BlitzGateway)

• projectId (int)

Return type:

list[omero.gateway.DatasetWrapper]

acia.segm.omero.utils.list_images_in_project(conn, projectId)

Parameters:

• conn (omero.gateway.BlitzGateway)

• projectId (int)

Return type:

list[omero.gateway.ImageWrapper]

acia.segm.omero.utils.list_image_ids_in(omero_id, omero_type, conn)

List all image sequences in an omero source (dataset, project or image)

Parameters:

• omero_id (int) – the omero id specifying the resource on the omero server

• omero_type (str) – the type of the omero source. Can be ‘project’, ‘dataset’ or ‘image’.

• conn (BlitzGateway) – the connection to omero

Raises:

Exception – when wrong omero_type is specified

Returns:

List[int] – list of image ids contained in the OMERO resource

Return type:

list[int]

acia.segm.omero.utils.get_image_name(conn, imageId)

Parameters:

• conn (omero.gateway.BlitzGateway)

• imageId (int)

Return type:

str

acia.segm.omero.utils.get_project_name(conn, projectId)

Parameters:

• conn (omero.gateway.BlitzGateway)

• projectId (int)

Return type:

str

acia.segm.omero.utils.image_iterator(conn, object)

Parameters:

conn (omero.gateway.BlitzGateway)

Return type:

omero.gateway.ImageWrapper

acia.segm.omero.utils.create_project(conn, project_name)

Parameters:

• conn (omero.gateway.BlitzGateway)

• project_name (str)

Return type:

omero.gateway.ProjectWrapper

acia.segm.omero.utils.create_dataset(conn, projectId, dataset_name)

Parameters:

• conn (omero.gateway.BlitzGateway)

• projectId (int)

• dataset_name (str)

Return type:

omero.gateway.DatasetWrapper

class acia.segm.omero.utils.OmeroScaleBar

Bases: ScaleBar

Renderer for scale bar to show metric size of pixels on image

__init__(oss, width, unit='MICROMETER', short_title='μm', color=(255, 255, 255), font_size=25)

Parameters:

oss (OmeroSequenceSource)

draw(image, xstart, ystart)

acia.segm.omero.utils.has_all_tags(object, tag_list=None)

Parameters:

tag_list (list[str] | None)