-
Notifications
You must be signed in to change notification settings - Fork 0
/
utils.py
213 lines (191 loc) · 7.53 KB
/
utils.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
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
import numpy as np
from random import sample, choice
from unionfind import unionfind
import xml.etree.ElementTree as ET
voxel_dict = {
'#': 1,
'_': 0,
'+': 2
}
array_dict = {
1: '#',
0: '_',
2: '+'
}
def string_to_array(input_shape_string, input_shape_sizes):
"""A simple function to convert burr-tools xml voxel shape string to numpy array
Args:
input_shape_string (str): input voxel string in xml
input_shape_sizes (tuple): input voxel sizes in xml, should in z,y,x order
"""
voxel_int = [voxel_dict[x] for x in input_shape_string]
voxel_array = np.array(voxel_int)
voxel_array.shape = input_shape_sizes
return voxel_array
def array_to_string(input_shape_array):
"""the reverse of string to array, use the array to generate xml string
Args:
input_shape_array (numpy array): the input shape array
"""
shape_array = input_shape_array.copy()
shape_array.shape = (-1)
input_shape_list = list(shape_array)
input_shape_list = [array_dict[x] for x in input_shape_list]
return ''.join(input_shape_list)
def validate_shape(input_voxel_array):
"""validate voxel shape, make sure the voxels in the shape is all connected by utilizing union find algorithm
Args:
input_voxel_array (numpy array): the input shape in numpy array
"""
pos = np.argwhere(input_voxel_array == 1)
pos = [tuple(x) for x in pos]
pos_dict = {item:ind for ind, item in enumerate(pos)}
u = unionfind(len(pos))
for t_pos in pos:
z,y,x = t_pos
if (z,y,x+1) in pos_dict:
u.unite(pos_dict[t_pos], pos_dict[(z,y,x+1)])
if (z,y,x-1) in pos_dict:
u.unite(pos_dict[t_pos], pos_dict[(z,y,x-1)])
if (z,y-1,x) in pos_dict:
u.unite(pos_dict[t_pos], pos_dict[(z,y-1,x)])
if (z,y+1,x) in pos_dict:
u.unite(pos_dict[t_pos], pos_dict[(z,y+1,x)])
if (z-1,y,x) in pos_dict:
u.unite(pos_dict[t_pos], pos_dict[(z-1,y,x)])
if (z+1,y,x) in pos_dict:
u.unite(pos_dict[t_pos], pos_dict[(z+1,y,x)])
if len(u.groups()) > 1:
return False
elif len(u.groups()) == 1:
return True
def validate_shape_by_string(input_voxel_string, input_shape_size):
"""validate the shape by input string
Args:
input_voxel_string (str): input voxel string
input_shape_size (tuple): the input shape size
"""
input_voxel_array = string_to_array(input_voxel_string, input_shape_size)
return validate_shape(input_voxel_array)
def find_valid_shape_by_string(input_voxel_string,
input_voxel_shape,
additional_size):
"""find a valid shape by randomly sample the input voxel template
Args:
input_voxel_string (str): the input shape template
input_voxel_shape (tuple): the input shape
additional_size(int): the additional voxel size
"""
voxel_array = string_to_array(input_voxel_string, input_voxel_shape)
while True:
base_shape_candidate = generate_base_shape(voxel_array, additional_size)
validation = validate_shape(base_shape_candidate)
if validation:
break
return base_shape_candidate
def generate_base_shape(template_shape, voxel_num):
"""generate a base shape by random sampling the viable voxels
Args:
template_shape (numpy array): the template shape which have viable voxels
voxel_num (int): the mininum number for the base shape
"""
ori_shape = template_shape.shape
template_shape = template_shape.flatten()
pos = np.argwhere(template_shape == 2)
pos = np.array(pos)
pos.shape = (-1)
sampled_pos = sample(list(pos), k=voxel_num)
template_shape[template_shape==2] = 0
template_shape[sampled_pos] = 1
template_shape.shape = ori_shape
return template_shape
def crossover(xml_a, xml_b, template_xml):
"""make a crossover os parent xmls
Args:
xml_a (xml tree): parent a
xml_b (xml tree): parent b
template_xml (str): template xml file
"""
root_a = xml_a.getroot()
root_b = xml_b.getroot()
template_tree = ET.parse(template_xml)
template_root = template_tree.getroot()
for voxel_a, voxel_b, voxel_template in zip(root_a.iter('voxel'), root_b.iter('voxel'), template_root.iter('voxel')):
voxel_a_dict = voxel_a.attrib
voxel_a_string = list(voxel_a.text)
voxel_b_string = list(voxel_b.text)
z = int(voxel_a_dict['z'])
y = int(voxel_a_dict['y'])
x = int(voxel_a_dict['x'])
name = voxel_a_dict['name']
if name != 'Goal':
while True:
crosspoint = np.random.randint(len(voxel_a_string))
t_string = voxel_a_string
t_string[crosspoint:] = voxel_b_string[crosspoint:]
voxel_template.text = ''.join(t_string)
if validate_shape_by_string(voxel_template.text, (z,y,x)):
break
return template_tree
def mutation(xml, template_xml):
"""make a mutation to the voxel by adding or removing a voxel randomly
Args:
xml (xml tree): the input candidate
"""
root = xml.getroot()
template_tree = ET.parse(template_xml)
template_root = template_tree.getroot()
for voxel, voxel_template in zip(root.iter('voxel'), template_root.iter('voxel')):
voxel_string = voxel.text
voxel_dict = voxel.attrib
oz = int(voxel_dict['z'])
oy = int(voxel_dict['y'])
ox = int(voxel_dict['x'])
name = voxel_dict['name']
if name != 'Goal':
voxel_array = string_to_array(voxel_string, (oz,oy,ox))
while True:
pos = np.argwhere(voxel_array == 1)
t_voxel_array = voxel_array.copy()
pos = [tuple(x) for x in pos]
mutation_times = np.random.randint(1,5)
for _ in range(mutation_times):
t_pos = choice(pos)
z,y,x = t_pos
if np.random.uniform(0,1)<0.5:
t_voxel_array[z,y,x] = 0
else:
mode = np.random.randint(6)
if mode == 0:
t_voxel_array[z,y,x-1] = 1
if mode == 1:
t_voxel_array[z,y,np.minimum(x+1,ox-1)] = 1
if mode == 2:
t_voxel_array[z,y-1,x] = 1
if mode == 3:
t_voxel_array[z,np.minimum(y+1,oy-1),x] = 1
if mode == 4:
t_voxel_array[z-1,y,x] = 1
if mode == 5:
t_voxel_array[np.minimum(z+1,oz-1),y,x] = 1
t_string = array_to_string(t_voxel_array)
if validate_shape_by_string(''.join(t_string), (oz,oy,ox)):
voxel_template.text = ''.join(t_string)
break
return template_tree
def find_size_by_name(xml, shape_name):
"""find the frame size by name
Args:
xml (xml): the input xml tree
"""
root = xml.getroot()
for voxel in root.iter('voxel'):
voxel_dict = voxel.attrib
name = voxel_dict['name']
oz = int(voxel_dict['z'])
oy = int(voxel_dict['y'])
ox = int(voxel_dict['x'])
if name == shape_name:
voxel_string = voxel.text
voxel_array = string_to_array(voxel_string, (oz, oy, ox))
return np.sum(voxel_array)