locan.rois.roi.Roi#

class locan.rois.roi.Roi(region, reference=None, loc_properties=None)[source]#

Bases: object

Class for defining a region of interest for a referenced LocData object.

Parameters:

  • region (Region) – Geometrical region of interest.

  • reference (LocData | dict | locan.data.metadata_pb2.Metadata | locan.data.metadata_pb2.File | None) – Reference to localization data for which the region of interest is defined. It can be a LocData object, a reference to a saved SMLM file, or None for indicating no specific reference. When dict it must have keys file_path`and `file_type. When Metadata message it must have keys file.path and file.type for a path pointing to a localization file and an integer or string indicating the file type. Integer or string should be according to locan.constants.FileType.

  • loc_properties (Sequence[str] | None) – Localization properties in LocData object on which the region selection will be applied (for instance the coordinate_keys).

Variables:

  • region (Region) – Geometrical region of interest.

  • reference (LocData | locan.data.metadata_pb2.Metadata | None) – Reference to localization data for which the region of interest is defined. It can be a LocData object, a reference to a saved SMLM file, or None for indicating no specific reference. When referencing a saved SMLM file, reference has attributes file.path and file.type for a path pointing to a localization file and an integer indicating the file type.

  • loc_properties (tuple[str, ...] | None) – Localization properties in LocData object on which the region selection will be applied (for instance the coordinate_keys).

Methods

__init__(region[, reference, loc_properties])

from_yaml(path)

Read Roi object from yaml format.

locdata([reduce])

Localization data according to roi specifications.

to_yaml([path])

Save Roi object in yaml format.

Attributes

region

classmethod from_yaml(path)[source]#

Read Roi object from yaml format.

Parameters:

path (str | PathLike[Any]) – Path for yaml file.

Return type:

TypeVar(T_Roi, bound= Roi)

locdata(reduce=True)[source]#

Localization data according to roi specifications.

The ROI is applied on locdata properties as specified in self.loc_properties or by taking the first applicable locdata.coordinate_keys.

Parameters:

reduce (bool) – Return the reduced LocData object or keep references alive.

Returns:

A new instance of LocData with all localizations within region of interest.

Return type:

LocData

property region: Region#
to_yaml(path=None)[source]#

Save Roi object in yaml format.

Parameters:

path (UnionType[str, PathLike[str], None]) – Path for yaml file. If None a roi file path is generated from the metadata.

Return type:

None