-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathReferenceAxis.hoc
213 lines (168 loc) · 6.17 KB
/
ReferenceAxis.hoc
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
if (name_declared("pkgversions") != 4 ) { execute("strdef pkgversions") }
sprint(pkgversions,"%sReferenceAxis = $Revision: 1.5 $, ",pkgversions)
load_file("Segment.hoc")
/*
ReferenceAxis
ra = new ReferenceAxis()
ra.setup_with_secrefs(SecRef base, SecRef apex)
Sets up a new ReferenceAxis with base at the location of the 0th line
segment of the section referred to by the SecRef base and the and apex
located at the 0th line segment of the section referred to by the
SecRef apex.
ra.apply_expr_to_segref(SegmentRef seg, String expr)
Returns the value of expr computed for the segment referred to by seg
with respect to the axis defined by ra. This expression is in fact
computed for each geometric line segment and then these values are
summed to give a total for the electrical segment. Quantities that
may appear in expr are:
H - the projection of the centre of the line segment onto the axis
contained in ra (its "height").
l - the length of the line segment
d - the mean diameter of the line segment
If a geometrical line segment overlaps the boundary between electrical
segments, the quantities are appropriately interpolated.
Example:
ra.apply_expr_to_segref(seg, "h*l")
returns the sum of the products of the height and the length for each
line segment.
*/
begintemplate ReferenceAxis
// Public variables
public base, apex // SectionRefs of base and apex
objref base, apex
public axis, normaxis // Vector joining base and apex
objref axis
public verb // Verbose output
public adjustment
// Public functions
public setup_with_segrefs
public apply_expr_to_segref
// Private variables
objref pt3dbase, pt3dapex // Coordinates of base and apex
objref normaxis // Normalised axis
objref r, r0 // Final and initial points of line segments
objref mean_r // Mean position of line segment
objref Delta_r // Direction of line segment
objref this
strdef tmpstr
// Function definitions
proc init() {
rp = 0 // Relative probablity of connection in segment
verb = 0
adjustment = 0
}
// proc setup_with_secrefs () {
// $o1.secref.sec base = new SegmentRef(0)
// $o2.secref.sec apex = new SegmentRef(0)
// }
proc setup_with_segrefs () {
base = $o1
apex = $o2
if (numarg() == 3) {
adjustment = $3
}
pt3dbase = new Vector()
pt3dapex = new Vector()
axis = new Vector()
// Get the location of the base section. We will assume that the
// 0th element of the line segment list is a good enough indicator
// of the location
base.secref.sec {
pt3dbase.append(x3d(base.x))
pt3dbase.append(y3d(base.x))
pt3dbase.append(z3d(base.x))
}
// Get the location of the apex segment
apex.secref.sec {
pt3dapex.append(x3d(apex.x))
pt3dapex.append(y3d(apex.x))
pt3dapex.append(z3d(apex.x))
}
// Find unormalised axis
// axis = apex - base
axis = pt3dapex.c // Copying syntax
axis.sub(pt3dbase)
normaxis = axis.c
normaxis.div(sqrt(axis.sumsq()))
r = new Vector(3)
r0 = new Vector(3)
mean_r = new Vector(3)
Delta_r = new Vector(3)
}
func apply_expr_to_segref() { local s_beg s_end l s0 p i d d0 s d1seg d0seg
// args: SegRef, probexpr
rp = 0 // rp can't be local since it must be accesed by execute
p = 0 // Probability of synapse in segment
// Find out the start and end points along the segment
if ( ( $o1.x != 0 ) && ($o1.x != 1) ) {
$o1.secref.sec s_beg = ($o1.x - 0.5/nseg) * L
$o1.secref.sec s_end = s_beg + L/nseg
if (verb==1) print "s_beg, s_end: ", s_beg, s_end
// Now look through each geometric segment in turn
s = 0
s0 = 0 // Old value of s
$o1.secref.sec for i=1,(n3d()-1) {
if (verb==1) print "coords: ", x3d(i), y3d(i), z3d(i)
r.x(0) = x3d(i)
r.x(1) = y3d(i)
r.x(2) = z3d(i)
r0.x(0) = x3d(i-1)
r0.x(1) = y3d(i-1)
r0.x(2) = z3d(i-1)
d1 = diam3d(i)
d0 = diam3d(i-1)
Delta_r = r.c
Delta_r.sub(r0)
s0 = s
ds = sqrt(Delta_r.sumsq())
s = s + ds
if (verb==1) print "s, area: ", s, s*PI*diam3d(i)
if (s <= s_beg) {
continue
}
if (s0 >= s_end) {
break
}
l = ds // Length of line segment
d0seg = d0
d1seg = d1
// Begining of segment
if ((s>s_beg) && (s0<s_beg)) {
r0.add(Delta_r.mul((s_beg-s0)/ds))
l = l - (s_beg - s0)
d0seg = d0 + (d1-d0)/ds*(s_beg - s0)
}
// End of segment
if ((s>s_end) && (s0<s_end)) {
r.sub(Delta_r.mul((s-s_end)/ds))
l = l - (s - s_end)
d1seg = d1 - (d1-d0)/ds*(s - s_end)
}
mean_r = r0.c
mean_r.add(r)
mean_r.div(2)
mean_r.sub(pt3dbase)
H = mean_r.dot(normaxis) + adjustment
d = (d0seg + d1seg)/2
if (verb==1) print "h, d, l, area: ", H, d, l, PI*d*l
sprint(tmpstr,"rp += %s",$s2)
execute(tmpstr,this)
if (verb==1) print rp
}
} else { // x == 0 or x == 1
l = 0
if ( $o1.x == 0 ) { i = 0 }
if ( $o1.x == 1 ) { i = n3d()-1 }
d = diam3d(i)
r.x(0) = x3d(i)
r.x(1) = y3d(i)
r.x(2) = z3d(i)
r.sub(pt3dbase)
H = mean_r.dot(normaxis) + adjustment
if (verb==1) print "h, d, l, area: ", H, d, l, PI*d*l
sprint(tmpstr,"rp = %s",$s2)
execute(tmpstr,this)
}
return rp
}
endtemplate ReferenceAxis