def intersection_of_plane_with_slice(slice_index, plane):
"""
ASSUMING AXIAL ORIENTATION, finds the line that repreents the interection
between the two planes IN 2D
Parameters
----------
slice_index : int
the z index of the axial slice.
plane : sympy Plane object
The plane of interest.
Returns
-------
sympy Line2D object.
"""
# set up the plane of the slice
flat_plane = sp.Plane((1, 0, slice_index), (-1, 0, slice_index),
(0, 1, slice_index))
inter = plane.intersection(flat_plane)[0]
intersection_2d = sp.Line((inter.p1[0], inter.p1[1]),
(inter.p2[0], inter.p2[1]))
return intersection_2d
def _check_intersection(self, ray0, ray1, tri0, tri1, tri2):
from pascal3d.utils.geometry import intersect3d_ray_triangle
n_rays = len(ray0)
assert len(ray1) == n_rays
assert len(tri0) == n_rays
assert len(tri1) == n_rays
assert len(tri2) == n_rays
l1 = sympy.Line3D(sympy.Point3D(*ray0.tolist()),
sympy.Point3D(*ray1.tolist()))
p1 = sympy.Plane(sympy.Point3D(*tri0.tolist()),
sympy.Point3D(*tri1.tolist()),
sympy.Point3D(*tri2.tolist()))
t1 = sympy.Triangle(sympy.Point3D(*tri0.tolist()),
sympy.Point3D(*tri1.tolist()),
sympy.Point3D(*tri2.tolist()))
i1 = p1.intersection(l1)
if len(i1) == 0:
ret1 = False
else:
ret1 = t1.encloses(i1[0])
ret2, i2 = intersect3d_ray_triangle(ray0, ray1, tri0, tri1, tri2)
nose.tools.assert_equal(ret2.shape, (1, ))
nose.tools.assert_equal(ret2[0] == 1, ret1)
nose.tools.assert_equal(i2.shape, (1, 3))
if ret1:
np.testing.assert_allclose(i2[0],
map(float, [i1[0].x, i1[0].y, i1[0].z]))
def default_plane(pick: int) -> sy.Plane:
"""
"""
x = sy.Point3D([30, 0, 0])
y = sy.Point3D([0, 30, 0])
z = sy.Point3D([0, 0, 30])
c = sy.Point3D([0, 0, 0])
if pick == 0:
return sy.Plane(y, c, x)
elif pick == 1:
return sy.Plane(x, c, z)
elif pick == 2:
return sy.Plane(z, c, y)
else:
raise ValueError('Selection must be between 0 and 2')
def plane_1(a,b,c):
'''
a,b,c : tuples with three element (x,y,z)
'''
x, y , z = sp.symbols("x y z")
plane_temp = sp.Plane(sp.Point3D(*a),sp.Point3D(*b),sp.Point3D(*c))
vn = plane_temp.normal_vector;
return -(vn[0]*(x-a[0])+vn[1]*(y-a[1]))/vn[2] + a[2]
def make_angles_and_distances(pieces: Dict) -> pd.DataFrame:
"""Calculates the angles and distances from the vectors and planes.
:param pieces: The SSE pieces to calculate the vectors from.
"""
data = {
'sse': [],
'layer': [],
'angles_layer': [],
'angles_floor': [],
'angles_side': [],
'points_layer': [],
'points_floor': [],
'points_side': [],
'tilted_layer': [],
'tilted_floor': [],
'tilted_side': []
}
for layer in sorted(set([x[0] for x in pieces if len(x) == 1])):
for sse in [x for x in pieces if len(x) == 3]:
if abs(ascii_uppercase.find(layer) -
ascii_uppercase.find(sse[0])) <= 1:
data['sse'].append(sse)
data['layer'].append(layer)
for iplane, plane in enumerate(pieces[layer]):
if TBcore.get_option('system', 'debug'):
sys.stdout.write(
'PDB:{} geometry plane {} vs. sse {}\n'.format(
plane, layer, sse))
syPlane = sy.Plane(sy.Point3D(pieces[layer][plane][0]),
sy.Point3D(pieces[layer][plane][1]),
sy.Point3D(pieces[layer][plane][2]))
syLine = sy.Line(pieces[sse]['vector'][0],
pieces[sse]['vector'][-1])
syPoint = sy.Point3D(*pieces[sse]['vector'][1])
data[f'angles_{plane}'].append(
math.degrees(syPlane.angle_between(syLine)))
data[f'points_{plane}'].append(
float(syPlane.distance(syPoint)))
data[f'tilted_{plane}'].append(
float(syPlane.distance(default_plane(iplane))))
return pd.DataFrame(data)
def offset_face(self, fid):
connected_edges = [
self.get_connected_edge(self.faces[fid][i], fid) for i in range(4)
]
plane = self.face2plane(fid)
origin = self.face_centre(fid)
norm = sp.Point3D(plane.normal_vector)
offset_vector = (sp.Point3D(self.center) - origin)
offset_vector /= sp.Segment3D(sp.Point3D(0, 0, 0),
offset_vector).length
origin += offset_vector * random.uniform(-self.max_offset,
self.max_offset)
plane = sp.Plane(origin, normal_vector=norm)
# find new points for face
new_face_points = []
for ce in connected_edges:
line = sp.Line3D(sp.Point3D(self.points[ce[0]]),
sp.Point3D(self.points[ce[1]]))
intersections = plane.intersection(line)
if len(intersections) == 0:
print("skip face offsetting - hex will not be valid")
return
new_point = intersections[0]
new_point = [
new_point.x.evalf(),
new_point.y.evalf(),
new_point.z.evalf()
]
new_face_points.append(new_point)
if not self.is_b_not_far_than_a(self.points[ce[0]],
self.points[ce[1]], new_point):
print("skip face offsetting - hex will not be valid")
return
# replace old points with new
for i in range(4):
pid = self.faces[fid][i]
self.points[pid] = new_face_points[i]
def rotate_face(self, fid):
connected_edges = [
self.get_connected_edge(self.faces[fid][i], fid) for i in range(4)
]
# rotate face plane around random axis with origin at face centre
plane = self.face2plane(fid)
origin = self.face_centre(fid)
axis = plane.random_point() - plane.random_point()
transform_matrix = Quaternion.from_axis_angle((axis[0], axis[1], axis[2]),
random.uniform(-self.max_angle_offset, self.max_angle_offset)
)\
.to_rotation_matrix((origin[0], origin[1], origin[2]))
norm = sp.Point3D(plane.normal_vector)
plane = sp.Plane(origin,
normal_vector=norm.transform(transform_matrix))
# find new points for face
new_face_points = []
for ce in connected_edges:
line = sp.Line3D(sp.Point3D(self.points[ce[0]]),
sp.Point3D(self.points[ce[1]]))
new_point = plane.intersection(line)[0]
new_point = [
new_point.x.evalf(),
new_point.y.evalf(),
new_point.z.evalf()
]
new_face_points.append(new_point)
if not self.is_b_not_far_than_a(self.points[ce[0]],
self.points[ce[1]], new_point):
print("skip face rotating - hex will not be valid")
return
# replace old points with new
for i in range(4):
pid = self.faces[fid][i]
self.points[pid] = new_face_points[i]
# -*- coding: utf-8 -*-
"""
Main entry point for neurosegment
"""
import sympy as sp
import matplotlib.pyplot as plt
from preprocessing import read_nifti, skull_strip, sobelize, binary_by_percentile_threshold
from preprocessing import calculate_projected_plane_coords, is_partnered, intersection_of_plane_with_slice
from preprocessing import score_midsagittal
px, py = (238, 242)
arbitrary_plane = sp.Plane((0, 0, 10), (300, 300, 20), (300, 300, 10))
slice_num = 23
img_path = r'/Users/manusdonahue/Documents/Sky/Infarcts/Donahue_114402.XMLPARREC.dcm2niix/NIFTI/Donahue_114402.04.01.14-42-52.WIP_MJD_FLAIR_AX_3MM_SENSE.01.nii'
img = read_nifti(img_path)
stripped_img, mask = skull_strip(img)
sobel_img = sobelize(stripped_img)
edge_img, abs_thresh = binary_by_percentile_threshold(sobel_img,
3,
invert=True)
# note that when plotting with imshow, imaging conventions for coordinates are used
# essentially x and y are swapped and the origin is at the upper left corner
raw_data = img[:, :, slice_num]
fig, ax = plt.subplots(2, 2)
def as_sympy_plane(self) -> S.Plane:
return S.Plane(*self.sympy_vertices, normal_vector=self.normal)
def face2plane(self, fid):
p1 = sp.Point3D(self.points[self.faces[fid][0]])
p2 = sp.Point3D(self.points[self.faces[fid][1]])
p3 = sp.Point3D(self.points[self.faces[fid][2]])
return sp.Plane(p1, p2, p3)
normvec[i] = edgevec[i] / edgelength
wrappedmidpt = geometry.wrap_positions([mid], cell)[0]
print("wrapped midpoint: ", wrappedmidpt)
print("cut: ", cutrad, "midpoint: ", mid[0], mid[1], mid[2], "vec: ",
edgevec[0], edgevec[1], edgevec[2], "normvec: ", normvec[0], normvec[1],
normvec[2])
# declare sympy Point3D from UNWRAPPED midpoint
# FIXME: not sure if this is the best thing to do though? should not matter if it is wrapped
midpoint = sympy.Point3D(mid[0], mid[1], mid[2])
nodepoint1 = sympy.Point3D(node1[0], node1[1], node1[2])
nodepoint2 = sympy.Point3D(node2[0], node2[1], node2[2])
vecline = sympy.geometry.Line(nodepoint1, nodepoint2)
# declare sympy Plane
plane = sympy.Plane(sympy.Point3D(mid[0], mid[1], mid[2]),
normal_vector=normvec)
# declare radii dictionary
radii = dict()
# declare containers to store atoms within cutoff
atomname = [] # atom names
point3D = [] # atom centers
projection3D = [] # projection of atom centers onto 3D plane
projection2D = [] # parameterization of atom centers onto a 2D plane
radius = [] # radius of atoms
indices = []
allatomnames = []
allatompos = []
allatomnames_supercell = []
allatompos_supercell = []
import platform platform.platform() platform.python_version() import numpy as np import numpy.linalg as LA import math import sympy from sympy import var H = sympy.Point3D(-69.2, 89.23, 70.43) tockanax = -(-33.21 / 80.86) ravnina = sympy.Plane(sympy.Point3D(tockanax, 0, 0), (80.86, -66.12, -18.29)) presjeknaravnini = ravnina.projection(H) Hc = presjeknaravnini + H.direction_ratio(presjeknaravnini) E = sympy.Point3D(-32.6, 67.92, -51.91) print(round(Hc.distance(E), 5))
def reconstruct_room(candidate_virtual_sources,
loudspeaker,
dist_thresh,
shoebox=True):
"""
This method uses the first-order virtual-sources to reconstruct the room:
it processes the candidate virtual sources in the order of increasing distance
from the loudspeaker to find the first-order virtual sources and add their planes
to the list of half-spaces whose intersection determines the final room.
:param candidate_virtual_sources: list of the coordinates of all the individuated
virtual sources (it could contain even higher-order virtual sources)
:param loudspeaker: x, y, z coordinates of the speaker location in the room
:param dist_thresh: distance threshold (epsilon)
:param shoebox: boolean to identify if the room is a shoebox
:return: list of planes corresponding to the first-order virtual sources
"""
def combine(s1, s2):
"""
This method combines the virtual sources s1 and s2 to generate a higher-order
virtual source; it is used as a criterion to discard higher-order virtual sources.
:param s1: first virtual source coordinates
:param s2: second virtual source coordinates
:return: the coordinates of the higher order virtual source generated through
the combination of s1 and s2
"""
# p2 is a point on the hypothetical wall defined by s2, that is, a point on
# the median plane between the loudspeaker and s2
p2 = (loudspeaker + s2) / 2
# n2 is the outward pointing unit normal
n2 = (loudspeaker - s2) / np.linalg.norm(loudspeaker - s2)
return s1 + 2 * np.dot((p2 - s1), n2) * n2
def perpendicular(a):
"""
This method computes the perpendicular to a given vector.
:param a: the given vector
:return: the perpendicular vector
"""
b = np.empty_like(a)
b[0] = -a[1]
b[1] = a[0]
return b
# Instantiating the array to contain the distance of each virtual source from the loudspeaker
distances_from_speaker = []
# Computing the distances
for source in candidate_virtual_sources:
distances_from_speaker.append(np.linalg.norm(source - loudspeaker))
# Re-ordering the list of virtual sources according to their distance from the loudspeaker
candidate_virtual_sources = np.array(candidate_virtual_sources)
sorted_virtual_sources = candidate_virtual_sources[np.array(
distances_from_speaker).argsort()][1:]
# Initialize the list of planes that constitutes the room
room = []
vertices = []
# Initialize the boolean mask to identify the first-order virtual sources
deleted = np.array([False] * len(sorted_virtual_sources), dtype=bool)
for i in range(len(sorted_virtual_sources)):
for j in range(i):
for k in range(i):
# The following two conditions verify if the current virtual source is a combination of lower order
# virtual sources: if so, it is deleted from the available candidates
if j != k and k < i:
if np.linalg.norm(
combine(sorted_virtual_sources[j],
sorted_virtual_sources[k]) -
sorted_virtual_sources[i]) < dist_thresh:
deleted[i] = True
# If the room is a "Shoebox" it is possible to exploit geometric properties to filter out
# "ghost" image sources from the first order reflections.
if shoebox:
# Array containing the direction of the axes passing through the source position
directions = []
if len(loudspeaker) == 2:
x = sp.Line(loudspeaker, loudspeaker + [0, 1])
y = sp.Line(loudspeaker, loudspeaker + [1, 0])
directions.append(x)
directions.append(y)
elif len(loudspeaker) == 3:
planes = []
x = sp.Plane(loudspeaker, [1, 0, 0])
y = sp.Plane(loudspeaker, [0, 1, 0])
z = sp.Plane(loudspeaker, [0, 0, 1])
planes.append(x)
planes.append(y)
planes.append(z)
for i in range(3):
for j in range(i):
directions.append(planes[i].intersection(planes[j])[0])
for i in range(len(sorted_virtual_sources)):
if not deleted[i]:
for index, direction in enumerate(directions):
if direction.distance(sp.Point(
sorted_virtual_sources[i])) < dist_thresh:
break
else:
if index == len(directions) - 1:
deleted[i] = True
# If the virtual source is not a combination of lower order virtual sources, the corresponding plane
# is built and it is added to the room's walls list
for i in range(len(sorted_virtual_sources)):
if not deleted[i]:
# pi is a point on the hypothetical wall defined by si, that is, a point on
# the median plane between the loudspeaker and si
pi = (loudspeaker + sorted_virtual_sources[i]) / 2
# ni is the outward pointing unit normal
ni = (loudspeaker - sorted_virtual_sources[i]
) / np.linalg.norm(loudspeaker - sorted_virtual_sources[i])
plane = {}
if len(pi) == 2:
ni_perp = perpendicular(ni)
pi2 = pi + ni_perp
plane = sp.Line(pi, pi2)
elif len(pi) == 3:
plane = sp.Plane(sp.Point3D(pi), normal_vector=ni)
# If the room is empty, we add the first plane to the list of half-spaces whose intersection
# determines the final room
if len(room) == 0:
room.append(plane)
else:
for wall in room:
if len(plane.intersection(wall)) > 0:
room.append(plane)
break
if plane not in room:
deleted[i] = True
if room[0].ambient_dimension == 2:
for wall1 in range(len(room)):
for wall2 in range(wall1):
if wall1 != wall2:
intersections = room[wall2].intersection(room[wall1])
if len(intersections) > 0:
for intersection in intersections:
if abs(float(intersection.x)) < 100 and abs(
float(intersection.y)) < 100:
vertices.append(intersection)
if room[0].ambient_dimension == 3:
planes_intersections = []
for wall1 in range(len(room)):
for wall2 in range(wall1):
if wall1 != wall2:
planes_intersections.append(room[wall2].intersection(
room[wall1]))
for inter1 in range(len(planes_intersections)):
for inter2 in range(inter1):
if inter1 != inter2:
intersections = planes_intersections[inter2][
0].intersection(planes_intersections[inter1][0])
if len(intersections) > 0:
for intersection in intersections:
if abs(float(intersection.x)) < 100 and abs(
float(intersection.y)) < 100 and abs(
float(intersection.z)
) < 100 and intersection not in vertices:
vertices.append(intersection)
return room, vertices
import platform
platform.platform()
platform.python_version()
import numpy as np
import numpy.linalg as LA
import math
import sympy
from sympy import var
#Zadavanje ravnine pomoću tri nekolinearne točke
T1 = sympy.Point3D(35, 33, -46)
T2 = sympy.Point3D(-36, -40, -44)
T3 = sympy.Point3D(0, -11, 48)
rav = sympy.Plane(T1, T2, T3)
print("Zadavanje ravnine pomoću tri nekolinearne točke: ", rav)
#dvije ravnine
pi1 = sympy.Plane(sympy.Point3D(0.92857, 0, 0), (-14, 7, -8))
print(pi1.equation())
pi2 = sympy.Plane(sympy.Point3D(0, 1.869565, 0), (21, -23, 32))
print(pi2.equation())
normala1 = pi1.intersection(pi2)[0]
print(normala1.equation())
kut = rav.angle_between(normala1)
print(kut)
print(kut)
kut2 = (round(kut, 10) * 180 / np.pi)
import sympy from sympy import var H = sympy.Point3D(18, -95, 56) pravac1 = sympy.Line3D(sympy.Point3D(10, -27, 24), sympy.Point3D(-17, -65, 63)) pravac2 = sympy.Line3D(sympy.Point3D(41, 54, 86), sympy.Point3D(43, 129, 32)) s1 = sympy.Matrix(pravac1.direction_ratio) s2 = sympy.Matrix(pravac2.direction_ratio) nor = s1.cross(s2) nor_pi1 = s1.cross(nor) pi1 = sympy.Plane(sympy.Point3D(10, -27, 24), nor_pi1) nor_pi2 = s2.cross(nor) pi2 = sympy.Plane(sympy.Point3D(41, 54, 86), nor_pi2) normala = pi1.intersection(pi2)[0] N1 = normala.intersection(pravac1)[0] N2 = normala.intersection(pravac2)[0] pravaca = sympy.Line3D(H, N1) pravacb = sympy.Line3D(H, N2) vektora = sympy.Matrix(pravaca.direction_ratio) vektorb = sympy.Matrix(pravacb.direction_ratio) cross = vektora.cross(vektorb).norm()
print("tocke A, B i D nisu kolinearne: ", sympy.Point3D.are_collinear(A, B, D),
"\n")
#kosinus smjera radij vektora
A = sympy.Point3D(1, -2, 3)
O = sympy.Point3D(0, 0, 0)
print("kosinus smjera radij vektora: ", O.direction_cosine(A), "\n")
#kosinus smjera vektora odredjenog s dvije tocke
A = sympy.Point3D(1, 4, -2)
B = sympy.Point3D(0, -2, 1)
print("kosinus smjera vektora odredjenog s dvije tocke: ",
A.direction_cosine(B), "\n")
#zadavanje ravnine pomocu tocke i vektora normale
rav = sympy.Plane(sympy.Point3D(1, 2, 1), (-2, 3, -1))
print("Ravnina uz pomoc tocke i vektora normale: ", rav)
#opci oblik jednadzbe ravnine
print("opci oblik jednadzbe ravnine: ", rav.equation())
#slucajana tocka u ravnini
ranT = rav.random_point()
print("Slucajna tocak u ravnini: ", ranT)
from sympy import var
#parametarska jednadzba ravnine
u, v = var('u v')
par = rav.arbitrary_point(u, v)
print("parametarska jednadzba ravnine: ", par)
