/
bezier_cyl_3d_with_detail.py
171 lines (146 loc) · 6.65 KB
/
bezier_cyl_3d_with_detail.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
#!/usr/bin/env python3
# a 3D Bezier branch/trunk
# Inherits from 3D bezier curve
# - The 3D bezier curve
# - Start and end radii
# Adds
# - placing buds/bud geometry
# - profile curve - making the outside "bumpy"
#
# Can:
# - Evaluate points along the curve
# - Make a cylinderical mesh
# - Project self into an image
import numpy as np
from json import load
from bezier_cyl_3d import BezierCyl3D
from scipy.spatial.transform import Rotation as R
class BezierCyl3DWithDetail(BezierCyl3D):
_profiles = None
_type_names = {"trunk", "sidebranch", "branch"}
_bud_shape = None
_data_dir = "./data/"
def __init__(self, bezier_crv=None):
""" Initialize a 3D curve, built from a quadratic Bezier with radii
@param bezier_crv - 3D bezier curve to start with"""
if bezier_crv:
super(BezierCyl3DWithDetail, self).__init__()
bezier_crv.copy(bezier_crv=self, b_compute_mesh=True)
else:
super(BezierCyl3DWithDetail, self).__init__()
self.start_is_junction = False
self.end_is_bud = False
self.start_bud = 0.7
self.bud_angle = 0.8 * np.pi / 2
self.bud_length = 0.1
# Read in global data/profiles
BezierCyl3DWithDetail._read_profiles(self._data_dir)
BezierCyl3DWithDetail._make_bud_shape()
@staticmethod
def _read_profiles(data_dir):
""" Read in all the profile curves for the various branch types"""
if BezierCyl3DWithDetail._profiles is not None:
return
BezierCyl3DWithDetail._profiles = {}
for t in BezierCyl3DWithDetail._type_names:
try:
fname = data_dir + "/" + t + "_profiles.json"
with open(fname, "r") as fp:
BezierCyl3DWithDetail._profiles[t] = load(fp)
except FileNotFoundError:
pass
@staticmethod
def _make_bud_shape():
if BezierCyl3DWithDetail._bud_shape is None:
n_pts = 10
BezierCyl3DWithDetail._bud_shape = np.zeros((2, n_pts))
BezierCyl3DWithDetail._bud_shape[0, :] = np.linspace(0, 1.0, n_pts)
BezierCyl3DWithDetail._bud_shape[0, -2] = 0.5 * BezierCyl3DWithDetail._bud_shape[0, -2] + 0.5 * BezierCyl3DWithDetail._bud_shape[0, -1]
BezierCyl3DWithDetail._bud_shape[1, 0] = 1.0
BezierCyl3DWithDetail._bud_shape[1, 1] = 0.95
BezierCyl3DWithDetail._bud_shape[1, 2] = 1.05
BezierCyl3DWithDetail._bud_shape[1, 3] = 1.1
BezierCyl3DWithDetail._bud_shape[1, 4] = 1.05
BezierCyl3DWithDetail._bud_shape[1, 5] = 0.8
BezierCyl3DWithDetail._bud_shape[1, 6] = 0.7
BezierCyl3DWithDetail._bud_shape[1, 7] = 0.5
BezierCyl3DWithDetail._bud_shape[1, 8] = 0.3
BezierCyl3DWithDetail._bud_shape[1, 9] = 0.0
def _make_cyl(self, profiles):
""" Make a 3D generalized cylinder
@param profiles - variations to the radii """
if profiles:
self._calc_cyl_vertices()
else:
self._calc_cyl_vertices()
def set_radii_and_junction(self, start_radius=1.0, end_radius=1.0, b_start_is_junction=False, b_end_is_bud=False):
""" Set the radius of the branch
@param start_radius - radius at pt1
@param end_radius - radius at pt3
@param b_start_is_junction - is the start of the curve a junction?
@param b_end_is_bud - is the end a bud? """
self.set_radii(start_radius, end_radius)
self.start_is_junction = b_start_is_junction
self.end_is_bud = b_end_is_bud
def make_branch_segment(self, pt1, pt2, pt3, radius_start, radius_end, start_is_junction, end_is_bud):
""" Output a 3D generalized cylinder"""
self.set_pts(pt1, pt2, pt3)
self.set_radii_and_junction(start_radius=radius_start, end_radius=radius_end, b_start_is_junction=start_is_junction, b_end_is_bud=end_is_bud)
try:
self._make_cyl(BezierCyl3DWithDetail._profiles["sidebranches"])
except KeyError:
self._make_cyl(None)
def place_buds(self, locs):
""" Position and orientation of buds,
@param locs - t along, radius loc tuples in a list
@
@return [(pt1, pt2, pt3) """
ts = np.linspace(0, 1, self.n_along)
radii = self._calc_radii()
pt = np.ones((4,))
zero_pt = np.ones((4,))
zero_pt[0:3] = 0.0
vec = np.zeros((4,))
ret_list = []
for loc in locs:
mat = self.frenet_frame(loc[0])
r = np.interp(loc[0], ts, radii)
pt_on_crv = mat @ zero_pt
pt[0] = np.cos(loc[1]) * r
pt[1] = np.sin(loc[1]) * r
pt[2] = 0
pt_on_srf = mat @ pt
vec[0] = np.cos(loc[1])
vec[1] = np.sin(loc[1])
vec[2] = 0
vec_rotate = np.cross(vec[0:3], np.array([0, 0, 1]))
vec_rotate = vec_rotate / np.linalg.norm(vec_rotate)
mat_rotate_bud = R.from_rotvec(self.bud_angle * vec_rotate)
# Note - newer versions use as_matrix
mat_rot = mat_rotate_bud.as_dcm()
vec[0:3] = mat_rot @ vec[0:3]
vec_on_crv = mat @ vec
vec_on_crv = vec_on_crv * (self.bud_length / np.linalg.norm(vec_on_crv))
pt_end_bud = pt_on_srf + vec_on_crv
pt_mid = 0.7 * pt_on_srf + 0.3 * pt_on_crv
ret_list.append((pt_mid[0:3], pt_on_srf[0:3], pt_end_bud[0:3]))
return ret_list
if __name__ == '__main__':
branch = BezierCyl3DWithDetail()
branch.set_pts([506.5, 156.0, 0.0], [457.49999996771703, 478.9999900052037, 0.0], [521.5, 318.0, 0.0])
branch.set_radii_and_junction(start_radius=10.5, end_radius=8.25, b_start_is_junction=True, b_end_is_bud=False)
branch.write_mesh("data/jos.obj")
branch.set_pts([-0.5, 0.0, 0.0], [0.0, 0.1, 0.05], [0.5, 0.0, 0.0])
branch.set_radii_and_junction(start_radius=0.5, end_radius=0.25, b_start_is_junction=True, b_end_is_bud=False)
branch.write_mesh("data/cyl.obj")
branch.set_dims(n_along=30, n_radial=32)
branch.set_pts([-0.5, 0.0, 0.0], [0.0, 0.1, 0.05], [0.5, 0.0, 0.0])
branch.set_radii_and_junction(start_radius=0.1, end_radius=0.075, b_start_is_junction=False, b_end_is_bud=True)
branch.write_mesh("data/cyl_bud.obj")
bud_loc = branch.place_buds(((0.2, 0), (0.3, np.pi/4), (0.4, 3.0 * np.pi/4)))
bud = BezierCyl3DWithDetail()
bud.start_bud = 0.2
for i, b in enumerate(bud_loc):
bud.set_pts(b[0], b[1], b[2])
bud.make_branch_segment(b[0], b[1], b[2], radius_start=0.025, radius_end=0.03, start_is_junction=False, end_is_bud=True)
bud.write_mesh(f"data/bud_{i}.obj")