-
Notifications
You must be signed in to change notification settings - Fork 0
/
parse_arborization.py
executable file
·221 lines (180 loc) · 8.13 KB
/
parse_arborization.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
214
215
216
217
218
219
220
221
#!/usr/bin/env python
"""
Central Complex arborization data parser.
"""
import itertools
from parsimonious import Grammar, NodeVisitor
class NeuronArborizationParser(NodeVisitor):
grammar = Grammar(
"""
label = arborization (hyphen arborization)*
arborization = neuropil slash regions slash neurite
regions = region (bar region)*
neuropil = "BU" / "bu" / "CRE" / "cre" / "EB" / "FB" / "IB" / "ib" / "LAL" / "lal" / "NO" / "no" / "PB" / "PS" / "ps" / "WED" / "wed"
region = tuple2 / tuple3 / name
tuple2 = lparen name comma name rparen
tuple3 = lparen name comma name comma name rparen
name = "LRB" / (side? (integer / range / alpha / list)) / (side !(integer / range / alpha / list))
side = "LR" / "RL" / "L" / "R"
neurite = "sb" / "bs" / "s" / "b"
range = lbracket integer hyphen integer rbracket
list = lbracket alpha (comma alpha)* rbracket
integer = ~"[0-9]+"
alpha = ~"[a-zA-Z0-9]+"
hyphen = "-"
bar = "|"
slash = "/"
comma = ","
lparen = "("
rparen = ")"
lbracket = "["
rbracket = "]"
""")
def visit_label(self, node, vc):
if len(vc) > 1:
return [vc[0]]+[c[1] for c in vc[1]]
else:
return vc
def visit_arborization(self, node, vc):
return {'neuropil': vc[0],
'regions': set(vc[2:-2][0]),
'neurite': vc[-1]}
def visit_regions(self, node, vc):
if len(vc) > 1:
if isinstance(vc[0], list):
tmp = vc[0]
else:
tmp = [vc[0]]
return tmp+[c[1] if not isinstance(c[1], list) else c[1][0] for c in vc[1]]
else:
return vc
def visit_neuropil(self, node, vc):
return node.text
def visit_side(self, node, vc):
return list(node.text)
def visit_region(self, node, vc):
if isinstance(vc[0], list) or isinstance(vc[0], tuple):
return vc[0]
else:
return node.text
def visit_tuple2(self, node, vc):
a = vc[1]
b = vc[3]
return [(x, y) for (x, y) in itertools.product(a, b)]
def visit_tuple3(self, node, vc):
a = vc[1]
b = vc[3]
c = vc[5]
return [(x, y, z) for (x, y, z) in itertools.product(a, b, c)]
def visit_name(self, node, vc):
# Special case to prevent LRB from being interpreted as LB and RB:
if node.text == 'LRB':
return [node.text]
tmp = []
for c in vc[0]:
if not c:
continue
elif isinstance(c[0], list):
tmp.append(c[0])
else:
tmp.append(c)
return [''.join(a) for a in itertools.product(*tmp)]
def visit_neurite(self, node, vc):
return set(list(node.text))
def visit_range(self, node, vc):
return map(str, range(int(vc[1]), int(vc[3])+1))
def visit_list(self, node, vc):
if isinstance(vc[1], list):
tmp = vc[1]
else:
tmp = [vc[1]]
return tmp+[c[1] if not isinstance(c[1], list) else c[1][0] for c in vc[2]]
def visit_integer(self, node, vc):
return node.text
def visit_alpha(self, node, vc):
return node.text
def _visit_nothing(self, node, vc):
pass
visit_hyphen = _visit_nothing
visit_bar = _visit_nothing
visit_slash = _visit_nothing
visit_comma = _visit_nothing
visit_lparen = _visit_nothing
visit_rparen = _visit_nothing
visit_lbracket = _visit_nothing
visit_rbracket = _visit_nothing
def generic_visit(self, node, vc):
return vc
if __name__ == '__main__':
from unittest import main, TestCase
class test_cx_label(TestCase):
def setUp(self):
self.v = NeuronArborizationParser()
def test_single_arb_region_name_1(self):
self.assertEqual(self.v.parse('PB/L1/s'),
[{'neurite': set(['s']), 'neuropil': 'PB', 'regions': set(['L1'])}])
def test_single_arb_region_name_2(self):
self.assertEqual(self.v.parse('LAL/LHB/b'),
[{'neurite': set(['b']), 'neuropil': 'LAL', 'regions': set(['LHB'])}])
def test_single_arb_region_name_3(self):
self.assertEqual(self.v.parse('cre/LRB/b'),
[{'neurite': set(['b']), 'neuropil': 'cre', 'regions': set(['LRB'])}])
def test_single_arb_region_name_sb(self):
self.assertEqual(self.v.parse('PB/L1/sb'),
[{'neurite': set(['s', 'b']), 'neuropil': 'PB', 'regions': set(['L1'])}])
self.assertEqual(self.v.parse('PB/L1/bs'),
[{'neurite': set(['s', 'b']), 'neuropil': 'PB', 'regions': set(['L1'])}])
def test_single_arb_region_name_lr_1(self):
self.assertEqual(self.v.parse('PB/LR1/b'),
[{'neurite': set(['b']), 'neuropil': 'PB', 'regions': set(['L1', 'R1'])}])
self.assertEqual(self.v.parse('PB/RL1/b'),
[{'neurite': set(['b']), 'neuropil': 'PB', 'regions': set(['L1', 'R1'])}])
def test_single_arb_region_name_lr_2(self):
self.assertEqual(self.v.parse('PB/RL[1-2]/b'),
[{'neurite': set(['b']), 'neuropil': 'PB',
'regions': set(['L1', 'L2', 'R1', 'R2'])}])
self.assertEqual(self.v.parse('PB/LR[1-2]/b'),
[{'neurite': set(['b']), 'neuropil': 'PB',
'regions': set(['L1', 'L2', 'R1', 'R2'])}])
def test_single_arb_region_tuple2_1(self):
self.assertEqual(self.v.parse('PB/(1,R1)/s'),
[{'neurite': set(['s']), 'neuropil': 'PB', 'regions': set([('1', 'R1')])}])
def test_single_arb_region_tuple2_2(self):
self.assertEqual(self.v.parse('NO/(1,R)/b'),
[{'neurite': set(['b']), 'neuropil': 'NO', 'regions': set([('1', 'R')])}])
def test_single_arb_region_tuple3_1(self):
self.assertEqual(self.v.parse('EB/(L7,[P,M],1)/b'),
[{'neurite': set(['b']), 'neuropil': 'EB',
'regions': set([('L7', 'P', '1'), ('L7', 'M', '1')])}])
def test_single_arb_region_tuple3_2(self):
self.assertEqual(self.v.parse('EB/([L1,R1],P,1)/b'),
[{'neurite': set(['b']), 'neuropil': 'EB',
'regions': set([('L1', 'P', '1'),
('R1', 'P', '1')])}])
def test_single_arb_multiple_regions_explicit(self):
self.assertEqual(self.v.parse('PB/L1|L2/s'),
[{'neurite': set(['s']), 'neuropil': 'PB', 'regions': set(['L1', 'L2'])}])
def test_single_arb_multiple_regions_range(self):
self.assertEqual(self.v.parse('PB/L[1-2]/s'),
[{'neurite': set(['s']), 'neuropil': 'PB', 'regions': set(['L1', 'L2'])}])
def test_single_arb_multiple_regions_tuple_range_first(self):
self.assertEqual(self.v.parse('FB/([3-4],L4)/s'),
[{'neurite': set(['s']), 'neuropil': 'FB',
'regions': set([('3', 'L4'), ('4', 'L4')])}])
def test_single_arb_multiple_regions_tuple_range_second(self):
self.assertEqual(self.v.parse('PB/(1,L[1-2])/s'),
[{'neurite': set(['s']), 'neuropil': 'PB',
'regions': set([('1', 'L1'), ('1', 'L2')])}])
def test_single_arb_single_region_list(self):
self.assertEqual(self.v.parse('PB/[L1]/s'),
[{'neurite': set(['s']), 'neuropil': 'PB', 'regions': set(['L1'])}])
def test_single_arb_multiple_regions_list(self):
self.assertEqual(self.v.parse('PB/[L1,L2]/s'),
[{'neurite': set(['s']), 'neuropil': 'PB', 'regions': set(['L1', 'L2'])}])
def test_multiple_arbs_region_name(self):
self.assertEqual(self.v.parse('PB/L1/s-EB/1/b'),
[{'neurite': set(['s']), 'neuropil': 'PB',
'regions': set(['L1'])},
{'neurite': set(['b']), 'neuropil': 'EB',
'regions': set(['1'])}])
main()