amd.reconstruct.reconstruct() - Code Metrics - Inspection of "-" - dwiddo/average-minimum-distance - Measure and Improve Code Quality continuously with Scrutinizer

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by Daniel

created 2023-05-01 20:39 UTC

amd.reconstruct.reconstruct() C

↳ Parent: amd.reconstruct

Complexity

Conditions

Size

Total Lines	96
Code Lines	51

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	51
dl	0
loc	96
rs	5.8036
c	0
b	0
f	0
cc	10
nop	2

How to fix Long Method Complexity

"""Functions for resconstructing a periodic set up to isometry from its
PDD. This is possible 'in a general position', see our papers for more.
"""

from itertools import combinations, permutations, product

import numpy as np
import numba
from scipy.spatial.distance import cdist
from scipy.spatial import KDTree

from ._nearest_neighbours import generate_concentric_cloud
from .utils import diameter

__all__ = ['reconstruct']


def reconstruct(pdd: np.ndarray, cell: np.ndarray) -> np.ndarray:
    """Reconstruct a motif from a PDD and unit cell. This function will
    only work if ``pdd`` has enough columns, such that the last column
    has all values larger than 2 times the diameter of the unit cell. It
    also expects an uncollapsed PDD with no weights column. Do not use
    ``amd.PDD`` to compute the PDD for this function, instead use
    ``amd.PDD_reconstructable`` which returns a version of the PDD which
    is passable to this function. This function is quite slow and run
    time may vary a lot arbitrarily depending on input.

    Parameters
    ----------
    pdd : :class:`numpy.ndarray`
        The PDD of the periodic set to reconstruct. Needs `k` at least
        large enough so all values in the last column of pdd are greater
        than :code:`2 * diameter(cell)`, and needs to be uncollapsed
        without weights. Use amd.PDD_reconstructable to get a PDD which
        is acceptable for this argument.
    cell : :class:`numpy.ndarray`
        Unit cell of the periodic set to reconstruct.

    Returns
    -------
    :class:`numpy.ndarray`
        The reconstructed motif of the periodic set.
    """

    # TODO: get a more reduced neighbour set
    # TODO: find all shared distances in a big operation at the start
    # TODO: move PREC variable to its proper place
    PREC = 1e-10

    dims = cell.shape[0]
    if dims not in (2, 3):
        raise ValueError(
            'Reconstructing from PDD only implemented for 2 and 3 dimensions'
        )
    diam = diameter(cell)
    motif = [np.zeros((dims, ))]
    if pdd.shape[0] == 1:
        return np.array(motif)

    # finding lattice distances so we can ignore them
    cloud_generator = generate_concentric_cloud(np.array(motif), cell)
    next(cloud_generator)  # is just the origin
    cloud = []
    layer = next(cloud_generator)
    while np.any(np.linalg.norm(layer, axis=-1) <= diam):
        cloud.append(layer)
        layer = next(cloud_generator)
    cloud = np.concatenate(cloud)

    # is (a superset of) lattice points close enough to Voronoi domain
    nn_set = _neighbour_set(cell, PREC)
    lattice_dists = np.linalg.norm(cloud, axis=-1)
    lattice_dists = lattice_dists[lattice_dists <= diam]
    lattice_dists = _unique_within_tol(lattice_dists, PREC)

    # remove lattice distances from first and second rows
    row1_reduced = _remove_vals(pdd[0], lattice_dists, PREC)
    row2_reduced = _remove_vals(pdd[1], lattice_dists, PREC)
    # get shared dists between first and second rows
    shared_dists = _shared_vals(row1_reduced, row2_reduced, PREC)
    shared_dists = _unique_within_tol(shared_dists, PREC)

    # all combinations of vecs in neighbour set forming a basis
    bases = []
    for vecs in combinations(nn_set, dims):
        vecs = np.asarray(vecs)
        if np.abs(np.linalg.det(vecs)) > PREC:
            bases.extend(basis for basis in permutations(vecs, dims))

    q = _find_second_point(shared_dists, bases, cloud, PREC)
    if q is None:
        raise RuntimeError('Second point of motif could not be found.')
    motif.append(q)

    if pdd.shape[0] == 2:
        return np.array(motif)

    for row in pdd[2:, :]:
        row_reduced = _remove_vals(row, lattice_dists, PREC)
        shared_dists1 = _shared_vals(row1_reduced, row_reduced, PREC)
        shared_dists2 = _shared_vals(row2_reduced, row_reduced, PREC)
        shared_dists1 = _unique_within_tol(shared_dists1, PREC)
        shared_dists2 = _unique_within_tol(shared_dists2, PREC)
        q_ = _find_further_point(
            shared_dists1, shared_dists2, bases, cloud, q, PREC
        )
        if q_ is None:
            raise RuntimeError('Further point of motif could not be found.')
        motif.append(q_)

    motif = np.array(motif)
    motif = np.mod(motif @ np.linalg.inv(cell), 1) @ cell
    return motif


def _find_second_point(shared_dists, bases, cloud, prec):
    dims = cloud.shape[-1]
    abs_q = shared_dists[0]
    sphere_intersect_func = _trilaterate if dims == 3 else _bilaterate

    for distance_tup in combinations(shared_dists[1:], dims):
        for basis in bases:
            res = sphere_intersect_func(*basis, *distance_tup, abs_q, prec)
            if res is None:
                continue
            cloud_res_dists = np.linalg.norm(cloud - res, axis=-1)
            if np.all(cloud_res_dists - abs_q + prec > 0):
                return res


def _find_further_point(shared_dists1, shared_dists2, bases, cloud, q, prec):
    # distance from origin (first motif point) to further point
    dims = cloud.shape[-1]
    abs_q_ = shared_dists1[0]

    # try all ordered subsequences of distances shared between first and
    # further row, with all combinations of the vectors in the neighbour set
    # forming a basis, see if spheres centered at the vectors with the shared
    # distances as radii intersect at 4 (3 dims) points.
    sphere_intersect_func = _trilaterate if dims == 3 else _bilaterate
    for distance_tup in combinations(shared_dists1[1:], dims):
        for basis in bases:
            res = sphere_intersect_func(*basis, *distance_tup, abs_q_, prec)
            if res is None:
                continue
            # check point is in the voronoi domain
            cloud_res_dists = np.linalg.norm(cloud - res, axis=-1)
            if not np.all(cloud_res_dists - abs_q_ + prec > 0):
                continue
            # check |p - point| is among the row's shared distances
            dist_diff = np.abs(shared_dists2 - np.linalg.norm(q - res))
            if np.any(dist_diff < prec):
                return res


def _neighbour_set(cell, prec):
    """(A superset of) the neighbour set of origin for a lattice."""

    k_ = 5
    coeffs = np.array(list(product((-1, 0, 1), repeat=cell.shape[0])))
    coeffs = coeffs[coeffs.any(axis=-1)]    # remove (0,0,0)

    # half of all combinations of basis vectors
    vecs = []
    for c in coeffs:
        vecs.append(np.sum(cell * c[None, :].T, axis=0) / 2)
    vecs = np.array(vecs)

    origin = np.zeros((1, cell.shape[0]))
    cloud_generator = generate_concentric_cloud(origin, cell)
    cloud = np.concatenate((next(cloud_generator), next(cloud_generator)))
    tree = KDTree(cloud, compact_nodes=False, balanced_tree=False)
    dists, inds = tree.query(vecs, k=k_)
    dists_ = np.empty_like(dists)

    while not np.allclose(dists, dists_, atol=0, rtol=1e-12):
        dists = dists_
        cloud = np.vstack(
            (cloud, next(cloud_generator), next(cloud_generator))
        )
        tree = KDTree(cloud, compact_nodes=False, balanced_tree=False)
        dists_, inds = tree.query(vecs, k=k_)

    tmp_inds = np.unique(inds[:, 1:].flatten())
    tmp_inds = tmp_inds[tmp_inds != 0]
    neighbour_set = cloud[tmp_inds]

    # reduce neighbour set
    # half the lattice points and find their nearest neighbours in the lattice
    neighbour_set_half = neighbour_set / 2
    # for each of these vectors, check if 0 is a nearest neighbour.
    # so, check if the dist to 0 is leq (within tol) than dist to all other
    # lattice points.
    nn_norms = np.linalg.norm(neighbour_set, axis=-1)
    halves_norms = nn_norms / 2
    halves_to_lattice_dists = cdist(neighbour_set_half, neighbour_set)

    # Do I need to + PREC?
    # inds of voronoi neighbours in cloud
    voronoi_neighbours = np.all(
        halves_to_lattice_dists - halves_norms + prec >= 0, axis=-1
    )
    neighbour_set = neighbour_set[voronoi_neighbours]
    return neighbour_set


@numba.njit(cache=True)
def _bilaterate(p1, p2, r1, r2, abs_val, prec):
    """Return the intersection of three circles."""

    d = np.sqrt((p2[0] - p1[0]) ** 2 + (p2[1] - p1[1]) ** 2)
    v = (p2 - p1) / d

    if d > r1 + r2:
        return None
    if d < abs(r1 - r2):
        return None
    if d == 0 and r1 == r2:
        return None

    a = (r1 ** 2 - r2 ** 2 + d ** 2) / (2 * d)
    h = np.sqrt(r1 ** 2 - a ** 2)
    x2 = p1[0] + a * v[0]
    y2 = p1[1] + a * v[1]
    x3 = x2 + h * v[1]
    y3 = y2 - h * v[0]
    x4 = x2 - h * v[1]
    y4 = y2 + h * v[0]
    q1 = np.array((x3, y3))
    q2 = np.array((x4, y4))

    if np.abs(np.sqrt(x3 ** 2 + y3 ** 2) - abs_val) < prec:
        return q1
    if np.abs(np.sqrt(x4 ** 2 + y4 ** 2) - abs_val) < prec:
        return q2
    return None


@numba.njit(cache=True)
def _trilaterate(p1, p2, p3, r1, r2, r3, abs_val, prec):
    """Return the intersection of four spheres."""

    if np.linalg.norm(p1) > abs_val + r1 - prec:
        return None
    if np.linalg.norm(p2) > abs_val + r2 - prec:
        return None
    if np.linalg.norm(p3) > abs_val + r3 - prec:
        return None
    if np.linalg.norm(p1 - p2) > r1 + r2 - prec:
        return None
    if np.linalg.norm(p1 - p3) > r1 + r3 - prec:
        return None
    if np.linalg.norm(p2 - p3) > r2 + r3 - prec:
        return None

    temp1 = p2 - p1
    d = np.linalg.norm(temp1)
    e_x = temp1 / d
    temp2 = p3 - p1
    i = np.dot(e_x, temp2)
    temp3 = temp2 - i * e_x
    e_y = temp3 / np.linalg.norm(temp3)

    j = np.dot(e_y, temp2)
    x = (r1 * r1 - r2 * r2 + d * d) / (2 * d)
    y = (r1 * r1 - r3 * r3 - 2 * i * x + i * i + j * j) / (2 * j)
    temp4 = r1 * r1 - x * x - y * y

    if temp4 < 0:
        return None

    e_z = np.cross(e_x, e_y)
    z = np.sqrt(temp4)
    p_12_a = p1 + x * e_x + y * e_y + z * e_z
    p_12_b = p1 + x * e_x + y * e_y - z * e_z

    if np.abs(np.linalg.norm(p_12_a) - abs_val) < prec:
        return p_12_a
    if np.abs(np.linalg.norm(p_12_b) - abs_val) < prec:
        return p_12_b
    return None


def _unique_within_tol(arr, prec):
    """Return only unique values in a vector within ``prec``."""
    return arr[~np.any(np.triu(np.abs(arr[:, None] - arr) < prec, 1), axis=0)]


def _remove_vals(vec, vals_to_remove, prec):
    """Remove specified values in vec, within ``prec``."""
    return vec[~np.any(np.abs(vec[:, None] - vals_to_remove) < prec, axis=-1)]


def _shared_vals(v1, v2, prec):
    """Return values shared between v1, v2 within ``prec``."""
    return v1[np.argwhere(np.abs(v1[:, None] - v2) < prec)[:, 0]]


1			"""Functions for resconstructing a periodic set up to isometry from its
2			PDD. This is possible 'in a general position', see our papers for more.
3			"""
4
5			from itertools import combinations, permutations, product
6
7			import numpy as np
8			import numba
9			from scipy.spatial.distance import cdist
10			from scipy.spatial import KDTree
11
12			from ._nearest_neighbours import generate_concentric_cloud
13			from .utils import diameter
14
15			__all__ = ['reconstruct']
16
17
18			def reconstruct(pdd: np.ndarray, cell: np.ndarray) -> np.ndarray:
19			"""Reconstruct a motif from a PDD and unit cell. This function will
20			only work if ``pdd`` has enough columns, such that the last column
21			has all values larger than 2 times the diameter of the unit cell. It
22			also expects an uncollapsed PDD with no weights column. Do not use
23			``amd.PDD`` to compute the PDD for this function, instead use
24			``amd.PDD_reconstructable`` which returns a version of the PDD which
25			is passable to this function. This function is quite slow and run
26			time may vary a lot arbitrarily depending on input.
27
28			Parameters
29			----------
30			pdd : :class:`numpy.ndarray`
31			The PDD of the periodic set to reconstruct. Needs `k` at least
32			large enough so all values in the last column of pdd are greater
33			than :code:`2 * diameter(cell)`, and needs to be uncollapsed
34			without weights. Use amd.PDD_reconstructable to get a PDD which
35			is acceptable for this argument.
36			cell : :class:`numpy.ndarray`
37			Unit cell of the periodic set to reconstruct.
38
39			Returns
40			-------
41			:class:`numpy.ndarray`
42			The reconstructed motif of the periodic set.
43			"""
44
45			# TODO: get a more reduced neighbour set
46			# TODO: find all shared distances in a big operation at the start
47			# TODO: move PREC variable to its proper place
48			PREC = 1e-10
49
50			dims = cell.shape[0]
51			if dims not in (2, 3):
52			raise ValueError(
53			'Reconstructing from PDD only implemented for 2 and 3 dimensions'
54			)
55			diam = diameter(cell)
56			motif = [np.zeros((dims, ))]
57			if pdd.shape[0] == 1:
58			return np.array(motif)
59
60			# finding lattice distances so we can ignore them
61			cloud_generator = generate_concentric_cloud(np.array(motif), cell)
62			next(cloud_generator) # is just the origin
63			cloud = []
64			layer = next(cloud_generator)
65			while np.any(np.linalg.norm(layer, axis=-1) <= diam):
66			cloud.append(layer)
67			layer = next(cloud_generator)
68			cloud = np.concatenate(cloud)
69
70			# is (a superset of) lattice points close enough to Voronoi domain
71			nn_set = _neighbour_set(cell, PREC)
72			lattice_dists = np.linalg.norm(cloud, axis=-1)
73			lattice_dists = lattice_dists[lattice_dists <= diam]
74			lattice_dists = _unique_within_tol(lattice_dists, PREC)
75
76			# remove lattice distances from first and second rows
77			row1_reduced = _remove_vals(pdd[0], lattice_dists, PREC)
78			row2_reduced = _remove_vals(pdd[1], lattice_dists, PREC)
79			# get shared dists between first and second rows
80			shared_dists = _shared_vals(row1_reduced, row2_reduced, PREC)
81			shared_dists = _unique_within_tol(shared_dists, PREC)
82
83			# all combinations of vecs in neighbour set forming a basis
84			bases = []
85			for vecs in combinations(nn_set, dims):
86			vecs = np.asarray(vecs)
87			if np.abs(np.linalg.det(vecs)) > PREC:
88			bases.extend(basis for basis in permutations(vecs, dims))
89
90			q = _find_second_point(shared_dists, bases, cloud, PREC)
91			if q is None:
92			raise RuntimeError('Second point of motif could not be found.')
93			motif.append(q)
94
95			if pdd.shape[0] == 2:
96			return np.array(motif)
97
98			for row in pdd[2:, :]:
99			row_reduced = _remove_vals(row, lattice_dists, PREC)
100			shared_dists1 = _shared_vals(row1_reduced, row_reduced, PREC)
101			shared_dists2 = _shared_vals(row2_reduced, row_reduced, PREC)
102			shared_dists1 = _unique_within_tol(shared_dists1, PREC)
103			shared_dists2 = _unique_within_tol(shared_dists2, PREC)
104			q_ = _find_further_point(
105			shared_dists1, shared_dists2, bases, cloud, q, PREC
106			)
107			if q_ is None:
108			raise RuntimeError('Further point of motif could not be found.')
109			motif.append(q_)
110
111			motif = np.array(motif)
112			motif = np.mod(motif @ np.linalg.inv(cell), 1) @ cell
113			return motif
114
115
116			def _find_second_point(shared_dists, bases, cloud, prec):
117			dims = cloud.shape[-1]
118			abs_q = shared_dists[0]
119			sphere_intersect_func = _trilaterate if dims == 3 else _bilaterate
120
121			for distance_tup in combinations(shared_dists[1:], dims):
122			for basis in bases:
123			res = sphere_intersect_func(basis, distance_tup, abs_q, prec)
124			if res is None:
125			continue
126			cloud_res_dists = np.linalg.norm(cloud - res, axis=-1)
127			if np.all(cloud_res_dists - abs_q + prec > 0):
128			return res
129
130
131			def _find_further_point(shared_dists1, shared_dists2, bases, cloud, q, prec):
132			# distance from origin (first motif point) to further point
133			dims = cloud.shape[-1]
134			abs_q_ = shared_dists1[0]
135
136			# try all ordered subsequences of distances shared between first and
137			# further row, with all combinations of the vectors in the neighbour set
138			# forming a basis, see if spheres centered at the vectors with the shared
139			# distances as radii intersect at 4 (3 dims) points.
140			sphere_intersect_func = _trilaterate if dims == 3 else _bilaterate
141			for distance_tup in combinations(shared_dists1[1:], dims):
142			for basis in bases:
143			res = sphere_intersect_func(basis, distance_tup, abs_q_, prec)
144			if res is None:
145			continue
146			# check point is in the voronoi domain
147			cloud_res_dists = np.linalg.norm(cloud - res, axis=-1)
148			if not np.all(cloud_res_dists - abs_q_ + prec > 0):
149			continue
150			# check \|p - point\| is among the row's shared distances
151			dist_diff = np.abs(shared_dists2 - np.linalg.norm(q - res))
152			if np.any(dist_diff < prec):
153			return res
154
155
156			def _neighbour_set(cell, prec):
157			"""(A superset of) the neighbour set of origin for a lattice."""
158
159			k_ = 5
160			coeffs = np.array(list(product((-1, 0, 1), repeat=cell.shape[0])))
161			coeffs = coeffs[coeffs.any(axis=-1)] # remove (0,0,0)
162
163			# half of all combinations of basis vectors
164			vecs = []
165			for c in coeffs:
166			vecs.append(np.sum(cell * c[None, :].T, axis=0) / 2)
167			vecs = np.array(vecs)
168
169			origin = np.zeros((1, cell.shape[0]))
170			cloud_generator = generate_concentric_cloud(origin, cell)
171			cloud = np.concatenate((next(cloud_generator), next(cloud_generator)))
172			tree = KDTree(cloud, compact_nodes=False, balanced_tree=False)
173			dists, inds = tree.query(vecs, k=k_)
174			dists_ = np.empty_like(dists)
175
176			while not np.allclose(dists, dists_, atol=0, rtol=1e-12):
177			dists = dists_
178			cloud = np.vstack(
179			(cloud, next(cloud_generator), next(cloud_generator))
180			)
181			tree = KDTree(cloud, compact_nodes=False, balanced_tree=False)
182			dists_, inds = tree.query(vecs, k=k_)
183
184			tmp_inds = np.unique(inds[:, 1:].flatten())
185			tmp_inds = tmp_inds[tmp_inds != 0]
186			neighbour_set = cloud[tmp_inds]
187
188			# reduce neighbour set
189			# half the lattice points and find their nearest neighbours in the lattice
190			neighbour_set_half = neighbour_set / 2
191			# for each of these vectors, check if 0 is a nearest neighbour.
192			# so, check if the dist to 0 is leq (within tol) than dist to all other
193			# lattice points.
194			nn_norms = np.linalg.norm(neighbour_set, axis=-1)
195			halves_norms = nn_norms / 2
196			halves_to_lattice_dists = cdist(neighbour_set_half, neighbour_set)
197
198			# Do I need to + PREC?
199			# inds of voronoi neighbours in cloud
200			voronoi_neighbours = np.all(
201			halves_to_lattice_dists - halves_norms + prec >= 0, axis=-1
202			)
203			neighbour_set = neighbour_set[voronoi_neighbours]
204			return neighbour_set
205
206
207			@numba.njit(cache=True)
208			def _bilaterate(p1, p2, r1, r2, abs_val, prec):
209			"""Return the intersection of three circles."""
210
211			d = np.sqrt((p2[0] - p1[0]) 2 + (p2[1] - p1[1]) 2)
212			v = (p2 - p1) / d
213
214			if d > r1 + r2:
215			return None
216			if d < abs(r1 - r2):
217			return None
218			if d == 0 and r1 == r2:
219			return None
220
221			a = (r1 2 - r2 2 + d ** 2) / (2 * d)
222			h = np.sqrt(r1 2 - a 2)
223			x2 = p1[0] + a * v[0]
224			y2 = p1[1] + a * v[1]
225			x3 = x2 + h * v[1]
226			y3 = y2 - h * v[0]
227			x4 = x2 - h * v[1]
228			y4 = y2 + h * v[0]
229			q1 = np.array((x3, y3))
230			q2 = np.array((x4, y4))
231
232			if np.abs(np.sqrt(x3 2 + y3 2) - abs_val) < prec:
233			return q1
234			if np.abs(np.sqrt(x4 2 + y4 2) - abs_val) < prec:
235			return q2
236			return None
237
238
239			@numba.njit(cache=True)
240			def _trilaterate(p1, p2, p3, r1, r2, r3, abs_val, prec):
241			"""Return the intersection of four spheres."""
242
243			if np.linalg.norm(p1) > abs_val + r1 - prec:
244			return None
245			if np.linalg.norm(p2) > abs_val + r2 - prec:
246			return None
247			if np.linalg.norm(p3) > abs_val + r3 - prec:
248			return None
249			if np.linalg.norm(p1 - p2) > r1 + r2 - prec:
250			return None
251			if np.linalg.norm(p1 - p3) > r1 + r3 - prec:
252			return None
253			if np.linalg.norm(p2 - p3) > r2 + r3 - prec:
254			return None
255
256			temp1 = p2 - p1
257			d = np.linalg.norm(temp1)
258			e_x = temp1 / d
259			temp2 = p3 - p1
260			i = np.dot(e_x, temp2)
261			temp3 = temp2 - i * e_x
262			e_y = temp3 / np.linalg.norm(temp3)
263
264			j = np.dot(e_y, temp2)
265			x = (r1 * r1 - r2 * r2 + d * d) / (2 * d)
266			y = (r1 * r1 - r3 * r3 - 2 * i * x + i * i + j * j) / (2 * j)
267			temp4 = r1 * r1 - x * x - y * y
268
269			if temp4 < 0:
270			return None
271
272			e_z = np.cross(e_x, e_y)
273			z = np.sqrt(temp4)
274			p_12_a = p1 + x * e_x + y * e_y + z * e_z
275			p_12_b = p1 + x * e_x + y * e_y - z * e_z
276
277			if np.abs(np.linalg.norm(p_12_a) - abs_val) < prec:
278			return p_12_a
279			if np.abs(np.linalg.norm(p_12_b) - abs_val) < prec:
280			return p_12_b
281			return None
282
283
284			def _unique_within_tol(arr, prec):
285			"""Return only unique values in a vector within ``prec``."""
286			return arr[~np.any(np.triu(np.abs(arr[:, None] - arr) < prec, 1), axis=0)]
287
288
289			def _remove_vals(vec, vals_to_remove, prec):
290			"""Remove specified values in vec, within ``prec``."""
291			return vec[~np.any(np.abs(vec[:, None] - vals_to_remove) < prec, axis=-1)]
292
293
294			def _shared_vals(v1, v2, prec):
295			"""Return values shared between v1, v2 within ``prec``."""
296			return v1[np.argwhere(np.abs(v1[:, None] - v2) < prec)[:, 0]]
297

dwiddo / average-minimum-distance

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amd.reconstruct.reconstruct() C

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