def convex_hull_inflation(ch: ss.ConvexHull,
inflation_ratio: float = 0.2,
vertices_only: bool = True) -> ss.ConvexHull:
"""
TODO: consider the choice of "center_of_mass"
Parameters
----------
to write
Returns
-------
to write
"""
ch_vertices = ch.points[ch.vertices]
center_of_mass = np.mean(ch.points, axis=0)
ch_vertices = ch_vertices - center_of_mass # relative coord.
ch_vertices = ch_vertices * (1 + inflation_ratio)
ch_vertices = ch_vertices + center_of_mass
if vertices_only:
inflated_ch = ss.ConvexHull(ch_vertices)
else:
inflated_ch = ss.ConvexHull(ch_vertices, incremental=True)
inflated_ch.add_points(ch.points[is_in_hull(ch.points, inflated_ch)])
inflated_ch.close()
return inflated_ch
def plot(self, axis=-1, coords=[], label="", **kwargs):
"""
Plots the polytope on the given axis.
"""
if self.isLowerDimensional() or self.isEmpty():
# Will not plot empty or lower-dimensional polytopes
return
num_coords = len(coords)
if num_coords > 1 and num_coords <= 3:
vertices = self.project(coords)
if num_coords == 1 or num_coords > 3:
raise AssertionError("Cannot plot projection onto more than 3 "
"dimensions or onto 1 dimension")
if self.n > 3 and num_coords == 0:
raise AssertionError("Cannot plot higher dimensional polytope than"
"3D")
no_axis = axis == -1
if no_axis:
# Axis not passed in, create a new figure
fig = plt.figure()
if self.n == 2 or num_coords == 2:
axis = fig.add_subplot(111)
if self.n == 3 or num_coords == 3:
axis = fig.add_subplot(111, projection='3d')
# TODO plotting for self.n == 1
if self.n == 2 or num_coords == 2:
# 2D plot
if num_coords == 0:
# The polytope is 2D and we plot it as such
vertices = self.vrep(return_as_matrix=True)
co = ss.ConvexHull(vertices)
# Filled region
axis.fill(vertices[co.vertices, 0],
vertices[co.vertices, 1],
label=label,
**kwargs)
if self.n == 3 or num_coords == 3:
# 3D plot
if num_coords == 0:
# The polytope is 3D and we plot is as such
vertices = self.vrep(return_as_matrix=True)
co = ss.ConvexHull(vertices)
tri = matplotlib.tri.Triangulation(vertices[:, 0],
vertices[:, 1],
triangles=co.simplices)
axis.plot_trisurf(vertices[:, 0],
vertices[:, 1],
vertices[:, 2],
triangles=tri.triangles,
**kwargs)
if no_axis:
plt.show()
def get_orientation_features(mask):
if type(mask) == sitk.SimpleITK.Image:
mask = sitk.GetArrayFromImage(mask)
# Get nonzero point indices if convex hull for memory reduction
data = np.transpose(np.nonzero(mask))
try:
points = sp.ConvexHull(data).points
success = False
while not success:
try:
center, radii, evecs, v = of.ellipsoid_fit(points)
success = True
except np.linalg.linalg.LinAlgError:
print(
"Encountered singular matrix, segmentation too small, dilating."
)
elem = morphology.ball(2)
mask = morphology.binary_dilation(mask, elem)
data = np.transpose(np.nonzero(mask))
points = sp.ConvexHull(data).points
points = of.data_regularize(points, divs=8)
# Convert evecs to angles
X = evecs[:, 0]
Y = evecs[:, 1]
Z = evecs[:, 2]
alpha = np.arctan2(Z[0], Z[1])
beta = np.arccos(Z[2])
gamma = np.arctan2(X[2], Y[2])
except sp.qhull.QhullError:
# TODO: 2D ellipse fit
alpha = 0
beta = 0
gamma = 0
panda_labels = ['of_theta_x', 'of_theta_y', 'of_theta_z']
orientation_features = [alpha, beta, gamma]
panda_dict = dict(zip(panda_labels, orientation_features))
orientation_dict = dict()
orientation_dict['all'] = pd.Series(panda_dict)
orientation_features = pd.Series(orientation_dict)
return orientation_features
def generate_image_and_stats(data, cluster_coords, regions_image,
optional_params, axes):
"""Adds cluster shape to shapes image and also returns regionprops of that shape"""
one_region_image = np.zeros((data["dimensions"][0], data["dimensions"][1]),
np.uint8)
concave_hull = alphashape.alphashape(cluster_coords)
border_points = concave_hull.exterior.coords
list_array = []
for coord in border_points:
list_array.append(coord)
# border_points = cluster_coords[spatial.ConvexHull(cluster_coords).vertices]
hull = spatial.ConvexHull(cluster_coords)
border_points = np.array(list_array, dtype='int32')
regions_image = cv2.fillPoly(regions_image, np.int32([border_points]),
(255, 255, 255))
one_region_image = cv2.fillPoly(one_region_image,
np.int32([border_points]), 255)
labeled_image = label(one_region_image, background=0)
properties = regionprops(labeled_image)
degrees = math.degrees(properties[0].orientation)
parameters = ((properties[0].centroid[1], properties[0].centroid[0]),
(int(properties[0].major_axis_length),
int(properties[0].minor_axis_length)), float(degrees))
regions_image = cv2.ellipse(regions_image, parameters, (0, 0, 255))
add_outline(border_points, axes, optional_params, properties)
ellipticity = compute_ellipticity_area_based(data, border_points)
return regions_image, properties, ellipticity, hull.area, hull.volume
def get_hulls(exp, ts):
hulls = []
for t in ts:
nx_graph = exp.nx_graph[t]
threshold = 0.1
S = [
nx_graph.subgraph(c).copy()
for c in nx.connected_components(nx_graph)
]
selected = [
g for g in S
if g.size(weight="weight") * len(g.nodes) / 10**6 >= threshold
]
polys = Polygon()
if len(selected) >= 0:
area_max = 0
for g in selected:
nodes = np.array([
node.pos(t) for node in exp.nodes if node.is_in(t)
and np.all(is_in_study_zone(node, t, 1000, 150)) and (
node.label in g.nodes)
])
if len(nodes) > 3:
hull = spatial.ConvexHull(nodes)
poly = Polygon(
[nodes[vertice] for vertice in hull.vertices])
area_hull = poly.area * 1.725**2 / (1000**2)
polys = polys.union(poly)
print(t, len(selected), polys.area)
hulls.append(polys)
return hulls
def planar_hull(points, normal, origin=None, input_convex=False):
'''
Find the convex outline of a set of points projected to a plane.
Arguments
-----------
points: (n,3) float, input points
normal: (3) float vector, normal vector of plane
origin: (3) float, location of plane origin
input_convex: bool, if True we assume the input points are already from
a convex hull which provides a speedup.
Returns
-----------
hull_lines: (n,2,2) set of unordered line segments
T: (4,4) float, transformation matrix
'''
from .points import project_to_plane
if origin is None:
origin = np.zeros(3)
if not input_convex:
pass
planar, T = project_to_plane(points,
plane_normal=normal,
plane_origin=origin,
return_planar=False,
return_transform=True)
hull_edges = spatial.ConvexHull(planar[:, 0:2]).simplices
hull_lines = planar[hull_edges]
planar_z = planar[:, 2]
height = np.array([planar_z.min(),
planar_z.max()])
return hull_lines, T, height
def __init__(self,
list_hulls,
name="unnamed",
mask=None,
check_mask_outofbounds=True):
"""
Initializes a bounding convex hull around a list of bounding
convex hulls or series of points.
A unity-weighted mask is computed for the region that
falls within this convex hull
if a mask of (y, x) coordinates is not provided.
Otherwise if a mask is provided and the
check_mask_outofbounds value is set the
masked coordinates are not verified to fall within
the hull. The latter should thus be used with some
caution by the user, but can potentially
significantly speed up the mask creation process for
axis aligned regions.
"""
self._name = name
self._check_mask_outofbounds = check_mask_outofbounds
self._cached_filled_mask = None
self._vertices = points = np.vstack([
b.corners if hasattr(b, "corners") else [b[0], b[1]]
for b in list_hulls
])
self._hull = spat.ConvexHull(points)
if mask is None:
self._mask, self._mask_weights = self.init_mask()
else:
self.sparse_mask = mask
def max_dist(point_list):
"""
Find the maximum distance between two points in a point list using convex hull.
"""
# Find the convex hull of the point set
conv_hull = spatial.ConvexHull(point_list)
# Find the vertices on the convex hull
vertices = np.vstack(point_list[conv_hull.vertices])
# Find the pairwise distances
dists = spatial.distance.pdist(vertices)
dists = spatial.distance.squareform(dists)
# Find the indices of the furthest points
idx = np.unravel_index(np.argmax(dists), dists.shape)
idx = list(idx)
idx1, idx2 = conv_hull.vertices[idx]
p1, p2 = vertices[idx]
print('The furthest points are:')
print('Index: {}, coordinates: {}'.format(idx1, tuple(p1)))
print('Index: {}, coordinates: {}'.format(idx2, tuple(p2)))
return np.max(dists)
def get_pareto_frontier(pts):
"""
Iteratively filter points based on the convex hull heuristic
"""
pareto_groups = []
# loop while there are points remaining
while pts.shape[0]:
# brute force if there are few points:
if pts.shape[0] < 10:
pareto_groups.append(get_pareto_undominated_by(pts))
break
# compute vertices of the convex hull
hull_vertices = spatial.ConvexHull(pts).vertices
# get corresponding points
hull_pts = pts[hull_vertices]
# get points in pts that are not convex hull vertices
nonhull_mask = np.ones(pts.shape[0], dtype=bool)
nonhull_mask[hull_vertices] = False
pts = pts[nonhull_mask]
# get points in the convex hull that are on the Pareto frontier
pareto = get_pareto_undominated_by(hull_pts)
pareto_groups.append(pareto)
# filter remaining points to keep those not dominated by
# Pareto points of the convex hull
pts = get_pareto_undominated_by(pts, pareto)
return np.vstack(pareto_groups)
def find_vectors_in_matrix(data, graph: bool = False, file_name: str = ""):
""" Finds and returns vectors in a 2D matrix """
labeled_array, num_features = label(
data, structure=[[1, 1, 1], [1, 1, 1], [1, 1, 1]]
) # group and label
print(f"Group count: {config.CC_OKCYAN}%d{config.CC_ENDC}" % num_features)
if graph:
np.savetxt(fna(file_name, "matrix_labeled", "txt"), labeled_array, fmt="%d")
vectors = []
for i in range(num_features):
index = i + 1
indices = np.argwhere(labeled_array == index) # find the group
if len(indices) < THRESHOLD: # not an important line if under threshold
continue
candidates = indices[spatial.ConvexHull(indices).vertices] # convex hull
dist_mat = spatial.distance_matrix(candidates, candidates) # distance btw
points = np.unravel_index(dist_mat.argmax(), dist_mat.shape) # furthest cands
vectors.append(
[
candidates[points[0]][1],
candidates[points[0]][0],
candidates[points[1]][1],
candidates[points[1]][0],
]
)
print(f"Vector count: {config.CC_OKCYAN}%d{config.CC_ENDC}" % len(vectors))
return np.array(vectors)
def InROI(file, Coordinates, TMin, TMax):
from matplotlib import path
import numpy as np
from scipy import spatial as sp
K = sp.ConvexHull(Coordinates).vertices
K = np.append(K, K[0])
XVert = Coordinates[K, 0]
YVert = Coordinates[K, 1]
XY = np.stack((XVert, YVert), axis=1)
data_in = [0] * len(file['T'])
data_out = [0] * len(file['T'])
for i in range(len(file['X'])):
# is it in the prescribed interval
if i >= TMin and i <= TMax:
p = path.Path(XY)
if p.contains_points([(file['X'][i], file['Y'][i])]):
data_in[i] = 1
else:
data_out[i] = 1
for i, number in enumerate(data_in):
data_in[i] = number > 0
for i, number in enumerate(data_out):
data_out[i] = number > 0
return data_in, data_out
def plot(self, dim_proj=[0,1], largest_ball=False, **kwargs):
"""
Plots a 2d projection of the polytope.
INPUTS:
dim_proj: dimensions in which to project the polytope
"""
if self.empty:
print('Cannot plot empty polytope')
return
if len(dim_proj) != 2:
raise ValueError('Only 2d polytopes!')
# extract vertices components
vertices_proj = np.hstack(self.vertices).T[:,dim_proj]
hull = spatial.ConvexHull(vertices_proj)
verts = [hull.points[i].tolist() for i in hull.vertices]
verts += [verts[0]]
codes = [Path.MOVETO] + [Path.LINETO]*(len(verts)-2) + [Path.CLOSEPOLY]
path = Path(verts, codes)
ax = plt.gca()
patch = patches.PathPatch(path, **kwargs)
ax.add_patch(patch)
plt.xlabel(r'$x_' + str(dim_proj[0]+1) + '$')
plt.ylabel(r'$x_' + str(dim_proj[1]+1) + '$')
ax.autoscale_view()
if largest_ball:
circle = plt.Circle((self.center[0], self.center[1]), self.radius, facecolor='white', edgecolor='black')
ax.add_artist(circle)
return
def orthogonal_projection(self, residual_variables, method='convex_hull'):
if method == 'convex_hull':
A_proj, b_proj, v_proj = orthogonal_projection_CHM(self.lhs_min, self.rhs_min, residual_variables)
p_proj = Polytope(A_proj, b_proj)
p_proj.assemble(redundant=False, vertices=v_proj)
# elif method == 'block_elimination':
# drop_variables = [i+1 for i in range(self.n_variables) if i not in residual_variables]
# M = np.hstack((self.rhs_min, -self.lhs_min))
# M = cdd.Matrix([list(m) for m in M])
# M.rep_type = cdd.RepType.INEQUALITY
# M_proj = M.block_elimination(drop_variables)
# M_proj.canonicalize()
# A_proj = - np.array([list(M_proj[i])[1:] for i in range(M_proj.row_size)])
# b_proj = np.array([list(M_proj[i])[:1] for i in range(M_proj.row_size)])
# p_proj = Polytope(A_proj, b_proj)
# p_proj.assemble()
elif method == 'vertex_enumeration':
v_proj = np.hstack(self.vertices).T[:,residual_variables]
if len(residual_variables) > 1:
hull = spatial.ConvexHull(v_proj)
A_proj = np.array(hull.equations)[:, :-1]
b_proj = - np.array(hull.equations)[:, -1:]
else:
A_proj = np.array([[1.],[-1.]])
b_proj = np.array([[max(v_proj)[0]],[-min(v_proj)[0]]])
p_proj = Polytope(A_proj, b_proj)
p_proj.assemble()
return p_proj
def compute_empirical_nodal_width(self, mode='mean') -> float:
r"""
Compute the set's nodal width.
"""
cvx_hull = sp.ConvexHull(self.vec.transpose())
cols = np.roll(cvx_hull.simplices, shift=1, axis=-1).reshape(-1)
rows = cvx_hull.simplices.reshape(-1)
# Form sparse coo_matrix from extracted pairs
affinity_matrix = sparse.coo_matrix((cols * 0 + 1, (rows, cols)), shape=(cvx_hull.points.shape[0],
cvx_hull.points.shape[0]))
# Symmetrize the matrix to obtain an undirected graph.
extended_row = np.concatenate([affinity_matrix.row, affinity_matrix.col])
extended_col = np.concatenate([affinity_matrix.col, affinity_matrix.row])
affinity_matrix.row = extended_row
affinity_matrix.col = extended_col
affinity_matrix.data = np.concatenate([affinity_matrix.data, affinity_matrix.data])
affinity_matrix = affinity_matrix.tocsr().tocoo() # Delete potential duplicate pairs
distance = np.linalg.norm(cvx_hull.points[affinity_matrix.row, :] - cvx_hull.points[affinity_matrix.col, :],
axis=-1)
if mode is 'mean':
nodal_distance = np.mean(distance) # average distance to neighbors
elif mode is 'max':
nodal_distance = np.max(distance)
elif mode is 'median':
nodal_distance = np.median(distance)
else:
raise TypeError("Parameter mode must be one of ['mean', 'max', 'median']")
return nodal_distance
def crown_from_points(pts):
if len(pts) > 3:
hull = spatial.ConvexHull(np.stack(pts))
return hull.simplices, np.array(
[[hull.points[f[0]], hull.points[f[1]], hull.points[f[2]]]
for f in hull.simplices])
def _prepare_hull(coordinates, hull):
"""
Construct a hull from the coordinates given a hull type
Will either return:
- a bounding box array of [xmin, ymin, xmax, ymax]
- a scipy.spatial.ConvexHull object from the Qhull library
- a shapely shape using alpha_shape_auto
"""
if isinstance(hull, numpy.ndarray):
assert len(
hull
) == 4, f"bounding box provided is not shaped correctly! {hull}"
assert hull.ndim == 1, f"bounding box provided is not shaped correctly! {hull}"
return hull
if (hull is None) or (hull == "bbox"):
return _bbox(coordinates)
if HAS_SHAPELY: # protect the isinstance check if import has failed
if isinstance(hull, (_ShapelyPolygon, _ShapelyMultiPolygon)):
return hull
if HAS_PYGEOS:
if isinstance(hull, pygeos.Geometry):
return hull
if isinstance(hull, str):
if hull.startswith("convex"):
return spatial.ConvexHull(coordinates)
elif hull.startswith("alpha") or hull.startswith("α"):
return alpha_shape_auto(coordinates)
elif isinstance(hull, spatial.qhull.ConvexHull):
return hull
raise ValueError(f"Hull type {hull} not in the set of valid options:"
f" (None, 'bbox', 'convex', 'alpha', 'α', "
f" shapely.geometry.Polygon, pygeos.Geometry)")
def make(self, key):
density = 110000 # per cubic mm
xyz = np.stack((design.Geometry.EPixel() & key).fetch('e_loc'))
margin = 75
bounds_min = xyz.min(axis=0) - margin
bounds_max = xyz.max(axis=0) + margin
volume = (bounds_max - bounds_min).prod() * 1e-9
npoints = int(volume * density + 0.5)
# generate random points that aren't too close
min_distance = 10.0 # cells aren't not allowed any closer
points = np.empty((npoints, 3), dtype='float32')
replace = np.r_[:npoints]
while replace.size:
points[replace, :] = np.random.rand(replace.size, 3) * (bounds_max - bounds_min) + bounds_min
replace = spatial.cKDTree(points).query_pairs(min_distance, output_type='ndarray')[:, 0]
# eliminate points that are too distant
inner = (spatial.Delaunay(xyz).find_simplex(points)) != -1
d, _ = spatial.cKDTree(points[inner, :]).query(points[~inner, :], distance_upper_bound=margin)
points = np.vstack((points[inner, :], points[~inner, :][d < margin, :]))
self.insert1(dict(
key, margin=margin,
density=density,
npoints=points.shape[0], min_distance=min_distance,
points=points,
volume=spatial.ConvexHull(points).volume * 1e-9,
inner_count=inner.sum()))
def find_footprint(self, points):
"""This function will take in an numpy.array of points in 2D and create
a convex polygon that encapsilates every point provided.\
Arguments to pass in:
points = 2D array of points numpy.array([:,:])
Returns a Polygon"""
footprint = Polygon()
if self.halo_density:
buffed_points = self.halo_buffer(points, self.halo_radius,
self.halo_density)
else:
buffed_points = points
if not points.size:
pass
else:
hull = spatial.ConvexHull(buffed_points)
for vertex in hull.vertices:
point = Point32()
point.x = buffed_points[vertex, 0]
point.y = buffed_points[vertex, 1]
point.z = 0.0
footprint.points.append(point)
return footprint
def overlap(rec1, rec2):
if not collisionCheck(rec1, rec2): return 0.
x1, y1, theta1, l1, w1 = rec1
x2, y2, theta2, l2, w2 = rec2
cos1 = np.cos(theta1)
sin1 = np.sin(theta1)
diffx = x2 - x1
diffy = y2 - y1
x2 = diffx * cos1 + diffy * sin1
y2 = -diffx * sin1 + diffy * cos1
cos2 = np.cos(theta2 - theta1)
sin2 = np.sin(theta2 - theta1)
A = np.array([[1, 0, 1], [-1, 0, 1], [0, 1, 1], [0, -1, 1],
[cos2, sin2, 1], [-cos2, -sin2, 1], [-sin2, cos2, 1],
[sin2, -cos2, 1]])
b = np.array([
l1, l1, w1, w1, l2 + cos2 * x2 + sin2 * y2, l2 - cos2 * x2 - sin2 * y2,
w2 - sin2 * x2 + cos2 * y2, w2 + sin2 * x2 - cos2 * y2
])
res = linprog(np.array([0, 0, -1]),
A_ub=A,
b_ub=b,
bounds=(-np.inf, np.inf))
assert res.success
interior = res.x[:2]
halfspaces = np.append(A[:, :2], -b[:, None], axis=1)
hs = spspatial.HalfspaceIntersection(halfspaces, interior).intersections
return spspatial.ConvexHull(hs).volume
def plot_points(data, fig=None, ax=None, inp_color=None):
# Takes as input all the points
if fig is None:
fig = plt.figure()
# If no plot is defined
ax = fig.gca(projection='3d')
for i in range(len(data)):
points = np.asarray(data[i])
hull = sp.ConvexHull(points)
# Plotting the points with scatter
if not inp_color:
ax.plot_trisurf(points[:, 0],
points[:, 1],
points[:, 2],
triangles=hull.simplices,
color='b')
else:
ax.plot_trisurf(points[:, 0],
points[:, 1],
points[:, 2],
triangles=hull.simplices,
color=inp_color)
# Checking if there are a prismatic joint that needs to be denoted
# Label the axis
ax.set_xlabel('X'), ax.set_ylabel('Y'), ax.set_zlabel('Z')
ax.set_xlim([-2, 5]), ax.set_ylim([-2.5, 1]), ax.set_zlim([-1, 1])
plt.savefig("test.png")
plt.show()
return (fig, ax)
def hull_points(obj, qhull_options='QbB Pp'):
"""
Try to extract a convex set of points from multiple input formats.
Parameters
---------
obj: Trimesh object
(n,d) points
(m,) Trimesh objects
Returns
--------
points: (o,d) convex set of points
"""
if hasattr(obj, 'convex_hull'):
return obj.convex_hull.vertices
initial = np.asanyarray(obj, dtype=np.float64)
if len(initial.shape) != 2:
raise ValueError('points must be (n, dimension)!')
hull = spatial.ConvexHull(initial, qhull_options=qhull_options)
points = hull.points[hull.vertices]
return points
def get_convex_hull(locations):
array = []
for i in locations:
array.append([i.x, i.y])
hullArray = np.array(array)
hull = sp.ConvexHull(hullArray)
return hull.volume
def RandPolytope(n, m):
import scipy.spatial as sp
import random
# Hyperspheroid coordinates take the form
# x_1 = r*cos(t_1)
# x_2 = r*sin(t_1)*cos(t_2)
# x_3 = r*sin(t_1)*sin(t_2)*cos(t_3)
# ...
# x_n = r*sin(t_1)*...*sin(t_n-1)*cos(t_n)
r = random.uniform(1.0, 10.0)
arr = []
for i in range(m):
angles = [np.deg2rad(random.randint(1, 360)) for a in range(n - 1)]
arr.append(nsphere_to_cartesian(r, angles))
#arr.append([random.uniform(0.0,50.0) for a in range(n)])
# For now we just have the point (0) as our guaranteed point
arr.append(np.array([0 for a in range(n)]))
hull = sp.ConvexHull(arr)
A = hull.equations[:, 0:-1]
b = hull.equations[:, -1]
#return A, b
return hull.points
def _bresenham(self, faces, dx):
r'''
A Bresenham line function to generate points to fill in for the fibers
'''
line_points = []
for face in faces:
# Get in hull order
fx = face[:, 0]
fy = face[:, 1]
fz = face[:, 2]
# Find the axis with the smallest spread and remove it to make 2D
if (np.std(fx) < np.std(fy)) and (np.std(fx) < np.std(fz)):
f2d = np.vstack((fy, fz)).T
elif (np.std(fy) < np.std(fx)) and (np.std(fy) < np.std(fz)):
f2d = np.vstack((fx, fz)).T
else:
f2d = np.vstack((fx, fy)).T
hull = sptl.ConvexHull(f2d, qhull_options='QJ Pp')
face = np.around(face[hull.vertices].astype(float), 6)
for i in range(len(face)):
vec = face[i] - face[i - 1]
vec_length = np.linalg.norm(vec)
increments = np.ceil(vec_length / dx)
check_p_old = np.array([-1, -1, -1])
for x in np.linspace(0, 1, increments):
check_p_new = face[i - 1] + (vec * x)
if np.sum(check_p_new - check_p_old) != 0:
line_points.append(check_p_new)
check_p_old = check_p_new
return np.asarray(line_points)
def planar_hull(points, normal, origin=None):
"""
Find the convex outline of a set of points projected to a plane.
Parameters
-----------
points: (n,3) float, input points
normal: (3) float vector, normal vector of plane
origin: (3) float, location of plane origin
Returns
-----------
hull_lines: (n,2,2) set of unordered line segments
T: (4,4) float, transformation matrix
height: (2,) float, [Z min, Z max]
"""
from .points import project_to_plane
if origin is None:
origin = np.zeros(3)
planar, T = project_to_plane(points,
plane_normal=normal,
plane_origin=origin,
return_planar=False,
return_transform=True)
hull_edges = spatial.ConvexHull(planar[:, 0:2]).simplices
hull_lines = planar[hull_edges]
planar_z = planar[:, 2]
height = np.array([planar_z.min(), planar_z.max()])
return hull_lines, T, height
def compute_cell_diameter(self) -> float:
cell_mask = self.get_cell_mask()
cell_mask_points = np.argwhere(cell_mask == 1)
convex_hull = spatial.ConvexHull(cell_mask_points)
boundary_points = cell_mask_points[convex_hull.vertices]
d = np.max(pairwise_distances(boundary_points))
return d
def hull_points(obj):
'''
Try to extract a convex set of points from multiple input formats.
Arguments
---------
obj: Trimesh object
(n,d) points
(m,) Trimesh objects
Returns
--------
points: (o,d) convex set of points
'''
if hasattr(obj, 'convex_hull'):
points = obj.convex_hull.vertices
elif util.is_sequence(obj):
initial = np.asanyarray(obj)
if len(initial.shape) != 2:
raise ValueError('Points must be (n, dimension)!')
hull = spatial.ConvexHull(initial, qhull_options='QbB Pp')
points = hull.points[hull.vertices]
else:
raise ValueError('Can\'t extract hull points from %s',
obj.__class__.__name__)
return points
def _export_vor_fibres(self):
r"""
Run through the throat vertices, compute the convex hull order and save
the vertices and ordered faces in a pickle dictionary to be used in
blender
"""
import pickle as pickle
Indices = []
for t in self.throats():
indices = list(self["throat.vert_index"][t].keys())
verts = self._vor.vertices[indices]
# Need to order the indices in convex hull order
# Compute the standard deviation in all coordinates and eliminate
# the axis with the smallest to make 2d
stds = [
np.std(verts[:, 0]),
np.std(verts[:, 1]),
np.std(verts[:, 2])
]
if np.argmin(stds) == 0:
verts2d = np.vstack((verts[:, 1], verts[:, 2])).T
elif np.argmin(stds) == 1:
verts2d = np.vstack((verts[:, 0], verts[:, 2])).T
else:
verts2d = np.vstack((verts[:, 0], verts[:, 1])).T
# 2d convexhull returns vertices in hull order
hull2d = sptl.ConvexHull(verts2d, qhull_options='QJ Pp')
# Re-order the vertices and save as list (blender likes them as lists)
Indices.append(np.asarray(indices)[hull2d.vertices].tolist())
# Create dictionary to pickle
data = {}
data["Verts"] = self._vor.vertices
data["Indices"] = Indices
pickle.dump(data, open("fibres.p", "wb"))
def hull(x, T, data):
# getting minimal G for each x - solution phases
Fgy = [fase.G(x, T) for fase in data if fase.kind == 'sol']
Gmin = np.amin(Fgy, axis=0)
Gmin = np.column_stack((x, Gmin))
# adding stoichiometric phases
for fase in data:
if fase.kind == 'stq':
point = [[fase.xB, fase.G(T)]]
Gmin = np.append(Gmin, point, axis=0)
# ordering array by composition
Gmin = Gmin[np.argsort(Gmin[:, 0])]
# getting convex hull for solution phases
hull = spa.ConvexHull(Gmin)
# shifting first position to end
vertices = np.roll(hull.vertices, -1)
# separating points belonging to hull
points = hull.points[vertices, :]
return Gmin, points, vertices
def find_ball(mask):
contours, _ = cv2.findContours(mask, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)
if contours:
contour = max(contours, key=cv2.contourArea)
if cv2.contourArea(contour) > BALL_MIN_AREA:
test = np.array(contour.reshape(-1, 2))
# two points which are fruthest apart will occur as vertices of the convex hull
candidates = test[spatial.ConvexHull(test).vertices]
# get distances between each pair of candidate points
dist_mat = spatial.distance_matrix(candidates, candidates)
# get indices of candidates that are furthest apart
i, j = np.unravel_index(dist_mat.argmax(), dist_mat.shape)
p1, p2 = candidates[i], candidates[j]
delta_x = abs((p1[0] - p2[0]) / 2)
delta_y = abs((p1[1] - p2[1]) / 2)
x = int(min(p1[0], p2[0]) + delta_x)
y = int(min(p1[1], p2[1]) + delta_y)
dist = int(math.sqrt((x - p1[0])**2 + (y - p1[1])**2))
return (x, y), dist
return (0, 0), 0
