Orientations#

class Orientations(translations, rotations, scores, details)[source]#

Bases: object

Handle template matching orientations and conversion between formats.

Parameters:

translations: np.ndarray: Array with translations of each orientations (n, d).
rotations: np.ndarray: Array with euler angles of each orientation in zxy convention (n, d).
scores: np.ndarray: Array with the score of each orientation (n, ).
details: np.ndarray: Array with additional orientation details (n, ).

Examples

The following achieves the minimal definition of an Orientations instance

>>> import numpy as np
>>> from tme import Orientations
>>> translations = np.random.randint(low = 0, high = 100, size = (100,3))
>>> rotations = np.random.rand(100, 3)
>>> scores = np.random.rand(100)
>>> details = np.full((100,), fill_value = -1)
>>> orientations = Orientations(
>>>     translations = translations,
>>>     rotations = rotations,
>>>     scores = scores,
>>>     details = details,
>>> )

The created orientations object can be written to disk in a range of formats. See Orientations.to_file() for available formats. The following creates a STAR file

>>> orientations.to_file("test.star")

Orientations.from_file() can create Orientations instances from a range of formats, to enable conversion between formats

>>> orientations_star = Orientations.from_file("test.star")
>>> np.all(orientations.translations == orientations_star.translations)
True

Attributes

`Orientations.translations`	Array with translations of each orientation (n, d).
`Orientations.rotations`	Array with zyx euler angles of each orientation (n, d).
`Orientations.scores`	Array with scores of each orientation (n, ).
`Orientations.details`	Array with additional details of each orientation(n, ).

Methods

`Orientations.copy`()	Create a copy of the current class instance.
`Orientations.from_file`(filename[, file_format])	Create an instance of `Orientations` from a file.
`Orientations.get_extraction_slices`(...[, ...])	Calculate slices for extracting regions of interest within a larger array.
`Orientations.to_file`(filename[, file_format])	Save the current class instance to a file in the specified format.