Correlation-based peak finding and strain mapping reference
Blobfinder
Deprecated since version 0.4.0: Blobfinder has moved to its own package LiberTEM-blobfinder with a new
structure. Please see
https://libertem.github.io/LiberTEM-blobfinder/index.html for installation
instructions and documentation of the new structure. Imports from
libertem.udf.blobfinder
trigger a FutureWarning
starting from
0.4.0 and are supported until LiberTEM release 0.6.0.
Matching
These modules contain classes and helper functions that extract and manipulate lattices from correlation results.
- class libertem.analysis.gridmatching.CorrelationResult(centers, refineds=None, peak_values=None, peak_elevations=None)[source]
Bases:
object
Container class for the result of correlation-based refinement of peak positions within a frame.
- class libertem.analysis.gridmatching.Match(correlation_result: libertem.analysis.gridmatching.CorrelationResult, selector, zero, a, b, indices)[source]
Bases:
libertem.analysis.gridmatching.PointSelection
Class that represents a lattice match to a subset of a correlation result
The attributes are not guaranteed to be correct or sensible for the given lattice. The methods
weighted_optimize()
andoptimize()
calculate a derivedMatch
with a best fit ofzero
,a
andb
based on the points and the indices.- zero
Declared zero point (y, x) of the lattice
- Type
- a
Declared “a” vector (y, x) of the lattice
- Type
- b
Declared “b” vector (y, x) of the lattice
- Type
- indices
List of indices (i, j) that are declared to express the matched points as linear combination of vectors
a
andb
with reference tozero
. The indices can be integers or floats, and they can be precise or approximate, depending on the matching method.- Type
- calc_coords(indices=None, drop_zero=False, frame_shape=None, r=0)[source]
Shorthand to calculate peak coordinates.
- Parameters
indices (numpy.ndarray) – Indices to calculate coordinates for. Both an array of (y, x) pairs and the output of np.mgrid are supported.
drop_zero (bool) – Drop the zero order peak. This is important for virtual darkfield imaging.
frame_shape (Tuple[int, int]) – If set, the peaks are filtered with
within_frame()
r (float) – Radius for
within_frame()
- Returns
A list of (y, x) coordinate pairs for peaks
- Return type
- Raises
ValueError – If the shape of
indices
is not as expected.
- property calculated_refineds
Calculated peak positions based on lattice parameters and indices.
- Type
- property error
Weighted average distance between calculated and given peak position. numpy.float(‘inf’) if match of length zero.
- Type
- classmethod invalid(correlation_result)[source]
- Match
A
Match
instance with empty selector and all-‘nan’ attributes
- optimize()[source]
Least square optimization of
zero
,a
andb
Optimization to match the given points and indices.
- class libertem.analysis.gridmatching.Matcher(tolerance=3, min_weight=0.1, min_match=3)[source]
Bases:
object
The main job of the Matcher object is managing the matching parameters and making them available for the various matching routines.
- Parameters
- affinematch(centers, indices, refineds=None, peak_values=None, peak_elevations=None)[source]
This function creates a Match object from correlation_result and indices for all points. The indices can be non-integer and relative to any base vectors zero, a, b, including virtual ones like zero=(0, 0), a=(1, 0), b=(0, 1).
Refined values for zero, a and b that match the correlated peaks are then derived.
This match method is very fast, can be robust against a distorted field of view and works without determining a lattice. It matches the full CorrelationResult and does not reject random points or other outliers.
It is mathematically equivalent to calculating an affine transformation, as inspired by Giulio Guzzinati https://arxiv.org/abs/1902.06979
- Parameters
centers (numpy.ndarray) – numpy.ndarray of shape (n, 2) with integer centers (y, x) of peaks
refineds (numpy.ndarray) – numpy.ndarray of shape (n, 2) with float centers (y, x) of peaks (subpixel refinement)
peak_values (numpy.ndarray) – numpy.ndarray of shape (n,) with float maxima of correlation map of peaks
peak_values – numpy.ndarray of shape (n,) with float elevation of correlation map of peaks. See
libertem_blobfinder.base.correlation.peak_elevation()
for details.indices (numpy.ndarray) – The indices assigned to each point of the CorrelationResult.
- Returns
- Return type
- fastmatch(centers, zero, a, b, refineds=None, peak_values=None, peak_elevations=None)[source]
This function creates a Match object from correlation_result and approximates for zero point and lattice vectors a and b. This function is much, much faster than the full match. It works well to match a large number of point sets that share the same lattice vectors, for example from a larger grain or monocrystalline material. It rejects random points or other lattices in the CorrelationResult, provided they are not on near-integer positions of zero, a, b.
- Parameters
centers (numpy.ndarray) – numpy.ndarray of shape (n, 2) with integer centers (y, x) of peaks
refineds (numpy.ndarray) – numpy.ndarray of shape (n, 2) with float centers (y, x) of peaks (subpixel refinement)
peak_values (numpy.ndarray) – numpy.ndarray of shape (n,) with float maxima of correlation map of peaks
peak_elevations (numpy.ndarray) – numpy.ndarray of shape (n,) with float elevation of correlation map of peaks. See
libertem_blobfinder.base.correlation.peak_elevation()
for details.zero (numpy.ndarray) – The near approximate zero point as numpy array (y, x).
a (numpy.ndarray) – The near approximate vectors a, b to match the grid as numpy arrays (y, x).
b (numpy.ndarray) – The near approximate vectors a, b to match the grid as numpy arrays (y, x).
- Returns
Match
object with the optimized matching result.- Return type
- class libertem.analysis.gridmatching.PointSelection(correlation_result: libertem.analysis.gridmatching.CorrelationResult, selector=None)[source]
Bases:
object
Class that represents a subset of a correlation result.
- selector
Boolean mask for all points in the correlation result,
True
indicating selected points.- Type
- libertem.analysis.gridmatching.get_indices(points, zero, a, b)[source]
Find indices to express each point as sum of lattice vectors from zero point
This could solve for arbitrarily many points, i.e. frame stacks instead of frame by frame With that the algorithm could actually match entire frame collections at once.
- libertem.analysis.gridmatching.get_transformation(ref, peaks, center=None, weighs=None)[source]
Inspired by Giulio Guzzinati https://arxiv.org/abs/1902.06979
- class libertem.analysis.fullmatch.FullMatcher(tolerance=3, min_weight=0.1, min_match=3, min_angle=0.3141592653589793, min_points=10, min_delta=0, max_delta=inf, min_candidates=3, max_candidates=7, clusterer=None, min_cluster_size_fraction=4, min_samples_fraction=20)[source]
Bases:
libertem.analysis.gridmatching.Matcher
Extension of
Matcher
will full matchingInclude the ability to guess grid parameters from a point cloud. This is separated from the other code since it currently only works with
HDBSCAN
, which can be problematic to install on some platforms. For that reason it is an optional dependency.- Parameters
tolerance (float) – Position tolerance in px for peaks to be considered matches
min_weight (float) – Minimum peak elevation of a peak to be considered for matching
min_match (int) – Minimum number of matching peaks to be considered a match.
min_angle (float) – Minimum angle in radians between two vectors to be considered candidates
min_points (int) – Minimum points to try clustering matching. Otherwise match directly
min_delta (float) – Minimum length of a potential grid vector
max_delta (float) – Maximum length of a potential grid vector
min_candidates (int) – Minimum number of candidates to consider clustering matching successful. If not enough are found, the algorithm uses a brute-force search with all pairwise vectors between points
max_candidates (int) – Maximum number of candidates to return from clustering matching
clusterer – Instance of sklearn.cluster compatible clusterer. Default is
HDBSCAN
.min_cluster_size_fraction (float) – Tuning parameter for clustering matching with
HDBSCAN
. Larger values allow smaller or fuzzier clusters. This is used to adapt themin_cluster_size
parameter ofHDBSCAN
dynamically to the number of points to be matched. Set this toNone
to disable dynamic adjustment ofmin_cluster_size
. If you like to setmin_cluster_size
to a constant value, you can set this toNone
and additionally set theclusterer
parameter with your own clusterer object to have direct control over all parameters.min_samples_fraction (float) – Tuning parameter for clustering matching with
HDBSCAN
. Larger values allow smaller or fuzzier clusters. This is used to adapt themin_samples
parameter ofHDBSCAN
dynamically to the number of points to be matched. Set this toNone
to disable dynamic adjustment ofmin_samples
. If you like to setmin_samples
to a constant value, you can set this toNone
and additionally set theclusterer
parameter with your own clusterer object to have direct control over all parameters.
- full_match(centers, zero=None, cand=None, refineds=None, peak_values=None, peak_elevations=None)[source]
This function extracts a list of Match objects as well two PointSelection objects for unmatched and weak points from correlation_result and zero point. The zero point is included in each of the matches because it is shared between all grids.
- Parameters
centers (numpy.ndarray) – numpy.ndarray of shape (n, 2) with integer centers (y, x) of peaks. This would typically be extracted with
libertem_blobfinder.common.correlation.get_peaks()
zero (numpy.ndarray) – Zero point as numpy array (y, x).
cand (list or numpy.ndarray) – Optional list of candidate vectors (y, x) to use in a first matching round before guessing.
refineds (numpy.ndarray) – numpy.ndarray of shape (n, 2) with float centers (y, x) of peaks (subpixel refinement)
peak_values (numpy.ndarray) – numpy.ndarray of shape (n,) with float maxima of correlation map of peaks
peak_elevations (numpy.ndarray) – numpy.ndarray of shape (n,) with float elevation of correlation map of peaks. See
libertem_blobfinder.base.correlation.peak_elevation()
for details.
- Returns
matches: list of
Match
instances,unmatched: instance of
PointSelection
,weak: instance of
PointSelection
- Return type
Tuple[List[libertem.analysis.gridmatching.Match, …], libertem.analysis.gridmatching.PointSelection, libertem.analysis.gridmatching.PointSelection]
Example
>>> peaks = np.array([ ... # First peak is zero if not specified otherwise ... # Base lattice vectors (32, 0) and (0, 32) ... (64, 64), ... (32, 32), (32, 64), (32, 96), ... (64, 32), (64, 96), ... (96, 32), (96, 64), (96, 96), ... ]) >>> matcher = FullMatcher() >>> (matches, unmatched, weak) = matcher.full_match(peaks) >>> m = matches[0] >>> assert np.allclose(m.zero, (64, 64)) >>> assert np.allclose(m.a, (32, 0)) >>> assert np.allclose(m.b, (0, 32))
- make_polar_vectors(coords)[source]
Calculate all unique pairwise connecting polar vectors between points in coords.
The pairwise connecting vectors are converted to polar coordinates and filtered with parameters
min_delta
andmax_delta
to avoid calculating for unwanted higher order or random smaller vectors.All calculated vectors have a positive or zero x direction.