Chamfer#
- class Chamfer(target_coordinates, template_coordinates, target_weights, template_weights, template_mask_coordinates=None, target_mask_coordinates=None, negate_score=True, **kwargs)[source]#
Bases:
_MatchCoordinatesToCoordinates
The Chamfer distance between the target \(f\) and the template \(g\) is calculated as:
\[\text{d(f,g)} = \frac{1}{|X|} \sum_{\mathbf{f}_i \in X} \inf_{\mathbf{g} \in Y} ||\mathbf{f}_i - \mathbf{g}||_2\]- Parameters:
- targetNDArray
A d-dimensional target to match the template coordinate set to.
- template_coordinatesNDArray
Template coordinate array with shape (d,n).
- template_weightsNDArray
Template weight array with shape (n,).
- template_mask_coordinatesNDArray, optional
Template mask coordinates with shape (d,n).
- target_maskNDArray, optional
A d-dimensional mask to be applied to the target.
- negate_scorebool, optional
Whether the final score should be multiplied by negative one. Default is True.
- return_gradientbool, optional
Invoking __call_ returns a tuple of score and parameter gradient. Default is False.
- **kwargsDict, optional
Keyword arguments propagated to downstream functions.
References
[1]Daven Vasishtan and Maya Topf, “Scoring functions for cryoEM density fitting”, Journal of Structural Biology, vol. 174, no. 2, pp. 333–343, 2011. DOI: https://doi.org/10.1016/j.jsb.2011.01.012
Methods
Chamfer.rotate_array
(arr, rotation_matrix, ...)Compute the matching score for the given transformation parameters.
Computes the score after a given rotation.
Computes the score after a given translation.