def get_nseg( mysec ):
"""
return the number of segments necesary to sample the smallest distance
between 2 consequtive 3D coordinates in a segment according to the
Nysquid criterum (in our case 2 times smaller than the smallest
distance).
"""
ncoord = int( h.n3d( sec = mysec) )
# calculate distance between 0 and 1 coordinate
x = h.x3d(0, sec = mysec) - h.x3d(1, sec = mysec)
y = h.y3d(0, sec = mysec) - h.y3d(1, sec = mysec)
z = h.z3d(0, sec = mysec) - h.z3d(1, sec = mysec)
dist = sqrt(x*x + y*y + z*z)
for i in range(1, ncoord-1):
x = h.x3d(i, sec = mysec) - h.x3d(i+1, sec = mysec)
y = h.y3d(i, sec = mysec) - h.y3d(i+1, sec = mysec)
z = h.z3d(i, sec = mysec) - h.z3d(i+1, sec = mysec)
value = sqrt(x*x + y*y + z*z)
dist = value if value < dist else dist
nseg = int((mysec.L/dist)*2.0) + 1 # odd number
return( nseg )
def _indices_from_sec_x(self, sec, position):
# TODO: the assert is here because the diameter is not computed correctly
# unless it coincides with a 3d point, which we only know to exist at the
# endpoints and because the section does not proceed linearly between
# the endpoints (in general)... which affects the computation of the
# normal vector as well
assert(position in (0, 1))
# NOTE: some care is necessary in constructing normal vector... must be
# based on end frusta, not on vector between end points
if position == 0:
x = h.x3d(0, sec=sec)
y = h.y3d(0, sec=sec)
z = h.z3d(0, sec=sec)
nx = h.x3d(1, sec=sec) - x
ny = h.y3d(1, sec=sec) - y
nz = h.z3d(1, sec=sec) - z
elif position == 1:
n = int(h.n3d(sec=sec))
x = h.x3d(n - 1, sec=sec)
y = h.y3d(n - 1, sec=sec)
z = h.z3d(n - 1, sec=sec)
# NOTE: sign of the normal is irrelevant
nx = x - h.x3d(n - 2, sec=sec)
ny = y - h.y3d(n - 2, sec=sec)
nz = z - h.z3d(n - 2, sec=sec)
else:
raise RxDException('should never get here')
# x, y, z = x * x1 + (1 - x) * x0, x * y1 + (1 - x) * y0, x * z1 + (1 - x) * z1
r = sec(position).diam * 0.5
plane_of_disc = geometry3d.graphicsPrimitives.Plane(x, y, z, nx, ny, nz)
potential_coordinates = []
mesh = self._mesh
xs, ys, zs = mesh._xs, mesh._ys, mesh._zs
xlo, ylo, zlo = xs[0], ys[0], zs[0]
# locate the indices of the cube containing the sphere containing the disc
# TODO: write this more efficiently
i_indices = [i for i, a in enumerate(xs) if abs(a - x) < r]
j_indices = [i for i, a in enumerate(ys) if abs(a - y) < r]
k_indices = [i for i, a in enumerate(zs) if abs(a - z) < r]
sphere_indices = [(i, j, k)
for i, j, k in itertools.product(i_indices, j_indices, k_indices)
if (xs[i] - x) ** 2 + (ys[j] - y) ** 2 + (zs[k] - z) ** 2 < r ** 2]
dx2 = self.dx * 0.5
dx = self.dx
disc_indices = []
for i, j, k in sphere_indices:
# a, b, c = xs[i], ys[j], zs[k]
# TODO: no need to compute all; can stop when some True and some False
# on_side1 = [plane_of_disc.distance(x, y, z) >= 0 for x, y, z in itertools.product([a - dx2, a + dx2], [b - dx2, b + dx2], [c - dx2, c + dx2])]
# NOTE: the expression is structured this way to make sure it tests the exact same corner coordinates for corners shared by multiple voxels and that there are no round-off issues (an earlier attempt had round-off issues that resulted in double-thick discs when the frustum ended exactly on a grid plane)
on_side1 = [plane_of_disc.distance(x, y, z) >= 0 for x, y, z in itertools.product([(xlo + (i - 1) * dx) + dx2, (xlo + i * dx) + dx2], [(ylo + (j - 1) * dx) + dx2, (ylo + j * dx) + dx2], [(zlo + (k - 1) * dx) + dx2, (zlo + k * dx) + dx2])]
# need both sides to have at least one corner
if any(on_side1) and not all(on_side1):
# if we're here, then we've found a point on the disc.
disc_indices.append((i, j, k))
return disc_indices
def retrieve_coordinate(sec):
sec.push()
x, y, z, d = [],[],[],[]
area = 0
tot_points = 0
connect_next = False
for i in range(int(h.n3d())):
present = False
x_i = h.x3d(i)
y_i = h.y3d(i)
z_i = h.z3d(i)
d_i = h.diam3d(i)
a_i = h.area(0.5)
if x_i in x:
ind = len(x) - 1 - x[::-1].index(x_i) # Getting the index of last value
if y_i == y[ind]:
if z_i == z[ind]:
present = True
if not present:
k =(x_i, y_i, z_i)
x.append(x_i)
y.append(y_i)
z.append(z_i)
d.append(d_i)
area += np.sum(a_i)
h.pop_section()
#adding num 3d points per section
n3dpoints[sec.name()] = [np.array(x),np.array(y),np.array(z),np.array(d)]
return (np.array(x),np.array(y),np.array(z),np.array(d),area)
def coarse(hoc_filename,cube_length,save_filename): # INPUT: NEURON .hoc filename to import (str), voxel cube side length (fl/str for gcd), name of file to create for mesh output (str) # >> cube_length: 'gcd' (gcd of box dims) OR floating-point (must be common factor of all box dims) # This function reads in NEURON data and passes their info to # coarse_gen(), then associates the tets of the STEPS Tetmesh object returned # to the NEURON sections which exist inside of them. # Returns a tet_hoc dictionary -- tet_hoc[tet_index] = [encapsulated hoc section references] -- as well as the Tetmesh object ## GET HOC SECTION INFO ## h.load_file(hoc_filename) allp = [[],[],[]] for s in h.allsec(): for j in range(int(h.n3d())): allp[0].append(h.x3d(j)) allp[1].append(h.y3d(j)) allp[2].append(h.z3d(j)) maxl = [max(allp[0]),max(allp[1]),max(allp[2])] minl = [min(allp[0]),min(allp[1]),min(allp[2])] bdim = [ maxl[0] - minl[0], maxl[1] - minl[1], maxl[2] - minl[2] ] print "dims: ", bdim print "mins: ", minl ## CREATE COARSE MESH ## if (cube_length == 'gcd'): gcd = fractions.gcd(fractions.gcd(bdim[0],bdim[1]),fractions.gcd(bdim[2],bdim[1])) print "GCD: ", gcd cube_length = gcd sm = coarse_gen(cube_length,bdim,minl,save_filename) ## ASSOCIATE HOC SECTIONS WITH THEIR TETS ## tet_hoc = tet_associate(sm[0]) return tet_hoc, sm[0]
def morphology_to_dict(sections, outfile=None):
section_map = {sec: i for i, sec in enumerate(sections)}
result = []
h.define_shape()
for sec in sections:
my_parent = parent(sec)
my_parent_loc = -1 if my_parent is None else parent_loc(sec, my_parent)
my_parent = -1 if my_parent is None else section_map[my_parent]
n3d = int(h.n3d(sec=sec))
result.append({
'section_orientation': h.section_orientation(sec=sec),
'parent': my_parent,
'parent_loc': my_parent_loc,
'x': [h.x3d(i, sec=sec) for i in xrange(n3d)],
'y': [h.y3d(i, sec=sec) for i in xrange(n3d)],
'z': [h.z3d(i, sec=sec) for i in xrange(n3d)],
'diam': [h.diam3d(i, sec=sec) for i in xrange(n3d)],
'name': sec.hname()
})
if outfile is not None:
with open(outfile, 'w') as f:
json.dump(result, f)
return result
def get_section_path(h,sec):
n3d = int(h.n3d(sec=sec))
xyz = []
for i in range(0,n3d):
xyz.append([h.x3d(i,sec=sec),h.y3d(i,sec=sec),h.z3d(i,sec=sec)])
xyz = np.array(xyz)
return xyz
def rotateZ(self, theta):
"""Rotate the cell about the Z axis."""
rot_m = numpy.array([[sin(theta), cos(theta)], [cos(theta), -sin(theta)]])
for sec in self.all:
for i in range(int(h.n3d())):
xy = numpy.dot([h.x3d(i), h.y3d(i)], rot_m)
h.pt3dchange(i, xy[0], xy[1], h.z3d(i), h.diam3d(i))
def mkmitral(gid):
nrn = getmitral(gid)
m = h.Mitral()
m.createsec(len(nrn.dend), len(nrn.tuft))
m.subsets()
m.topol(0) # need to connect secondary dendrites explicitly
for i, d in enumerate(nrn.dend):
# <<< check my changed if
if(d.parent == nrn.soma): # <<< changed name
m.secden[i].connect(m.soma(.5))
else:
m.secden[i].connect(m.secden[d.parent.index](1)) # <<< changed name
m.geometry()
m.segments() # depends on geometry
m.geometry() # again to get the hillock stylized shape
fillall(nrn, m)
m.segments() # again to get the proper number of segments for tuft and secden
m.soma.push()
m.x = h.x3d(0)
m.y = h.y3d(0)
m.z = h.z3d(0)
h.pop_section()
m.memb()
return m
def get_pos_data_short():
"""
Get positions of all segments currently loaded in Neuron in a simple matrix.
Section position information is not available.
:returns:
Matrix (3 x nSegments) With x,y,z positions.
:rtype: :class:`~numpy.ndarray`
Example:
.. code-block:: python
data = get_pos_data_short()
"""
n = 0
for sec in h.allsec():
n += int(h.n3d())
data = np.zeros([4, n])
cnt = 0
for sec in h.allsec():
for i in xrange(int(h.n3d())):
data[0, cnt] = h.x3d(i)
data[1, cnt] = h.y3d(i)
data[2, cnt] = h.z3d(i)
data[3, cnt] = h.diam3d(i)
cnt += 1
return data
def get_pos_data():
"""
Get positions x, y, z for all segments and their diameter.
:returns:
4 lists: x,y,z,d. One element per section where each element is
a :class:`~numpy.ndarray`.
Example:
.. code-block:: python
x,y,z,d = get_pos_data()
for sec in xrange(len(x)):
for seg in xrange(len(x[sec]):
print x[sec][seg], y[sec][seg], z[sec][seg]
"""
x = []
y = []
z = []
d = []
for sec in h.allsec():
n3d = int(h.n3d())
x_i, y_i, z_i = np.zeros(n3d), np.zeros(n3d), np.zeros(n3d),
d_i = np.zeros(n3d)
for i in xrange(n3d):
x_i[i] = h.x3d(i)
y_i[i] = h.y3d(i)
z_i[i] = h.z3d(i)
d_i[i] = h.diam3d(i)
x.append(x_i)
y.append(y_i)
z.append(z_i)
d.append(d_i)
return x, y, z, d
def retrieve_coordinate(self, sec):
"""Retrieve the coordinates of the section avoiding duplicates"""
sec.push()
x, y, z, d = [],[],[],[]
tot_points = 0
connect_next = False
for i in range(int(h.n3d())):
present = False
x_i = h.x3d(i)
y_i = h.y3d(i)
z_i = h.z3d(i)
d_i = h.diam3d(i)
# Avoiding duplicates in the sec
if x_i in x:
ind = len(x) - 1 - x[::-1].index(x_i) # Getting the index of last value
if y_i == y[ind]:
if z_i == z[ind]:
present = True
if not present:
k =(x_i, y_i, z_i)
x.append(x_i)
y.append(y_i)
z.append(z_i)
d.append(d_i)
h.pop_section()
#adding num 3d points per section
self.n3dpoints_per_sec[sec.name()] = len(d)
return (np.array(x),np.array(y),np.array(z),np.array(d))
def rotateZ(self, theta):
"""Rotate the cell about the Z axis."""
for sec in self.all:
for i in range(2):
x = h.x3d(i) * sin(theta) + h.y3d(i) * cos(theta)
y = h.x3d(i) * cos(theta) + h.y3d(i) * -sin(theta)
h.pt3dchange(i, x, y, h.z3d(i), h.diam3d(i))
def retrieve_coordinates(self, sec):
xyzds = []
sec.push()
for ii in xrange(int(nrn.n3d())):
xyzds.append([nrn.x3d(ii),
nrn.y3d(ii),
nrn.z3d(ii),
nrn.diam3d(ii)])
nrn.pop_section()
return xyzds
def build_tree(self):
print "-"*100
def append_data(sec, xyzdv, parent_id, connections):
""" Append data to xyzdv """
if self.var is 'v':
v = sec.v
else:
raise AttributeError('Variable %s not implemented' % self.var)
sec.push()
for ii in xrange(1, int(nrn.n3d())):
x = nrn.x3d(ii)
y = nrn.y3d(ii)
z = nrn.z3d(ii)
d = nrn.diam3d(ii)
xyzdv.append([x,y,z,d,v])
child_id = len(xyzdv)-1
if len(xyzdv)>1:
connections.append([child_id, parent_id])
parent_id = child_id
nrn.pop_section()
return xyzdv, connections
def append_children_data(parent, parent_id, xyzdv, connections):
parent.push()
sref = nrn.SectionRef()
nrn.pop_section()
if sref.child:
for child in sref.child:
xyzdv, connections = append_data(child, xyzdv, parent_id, connections)
xyzdv, connections = append_children_data(parent = child,
parent_id = len(xyzdv)-1,
xyzdv = xyzdv,
connections = connections)
return xyzdv, connections
# Find data and connections
root_section = self.root_section()
root_section.push()
xyzdv = [[nrn.x3d(0),
nrn.y3d(0),
nrn.z3d(0),
nrn.diam3d(0),
root_section.v]]
nrn.pop_section()
xyzdv, connections = append_data(root_section, xyzdv, 0, [])
xyzdv, connections = append_children_data(root_section,
len(xyzdv)-1,
xyzdv,
connections)
self.xyzdv = array(xyzdv)
self.connections = array(connections)
def set_position(self, x, y, z):
"""
Set the base location in 3D and move all other
parts of the cell relative to that location.
"""
for sec in self.all:
for i in range(int(h.n3d())):
h.pt3dchange(i,
x - self.x + h.x3d(i),
y - self.y + h.y3d(i),
z - self.z + h.z3d(i),
h.diam3d(i))
self.x, self.y, self.z = x, y, z
def computeCenter(seg):
"""Compute the distance from soma
Assuming soma is at (0,0,0)
"""
# n3d returns the number of 3d points in a segment.
xpoints = ypoints = zpoints = np.zeros(h.n3d(seg))
for i in range(len(xpoints)):
xpoints[i] = h.x3d(i, seg)
ypoints[i] = h.y3d(i, seg)
zpoints[i] = h.z3d(i, seg)
center = np.array([xpoints.mean(), ypoints.mean(), zpoints.mean()])
r = np.sqrt(np.mean(center))
return r, center
def make_sec_dict(self, dendTypeList):
d = {}
for dendType in dendTypeList:
d[dendType] = {}
dend = dendTypeList[dendType]
for ii in range(len(dend)):
dend[ii].push()
idx = h.n3d() - 1
dist = np.sum(
(np.array([h.x3d(idx), h.y3d(idx),
h.z3d(idx)]) - self.center)**2)**0.5
d[dendType][dist] = dend[ii]
h.pop_section()
return d
def getMaxExtent(self, dendTypeList):
maxExtent = {}
for dendType in dendTypeList:
dend = dendTypeList[dendType]
values = []
for i in range(len(dend)):
dend[i].push()
for j in range(int(h.n3d())):
swc = np.array([h.x3d(j), h.y3d(j), h.z3d(j)])
distance = abs(np.dot(self.new_axis, swc - self.center))
values.append(distance)
h.pop_section()
maxExtent[dendType] = max(values)
return maxExtent
def get_soma_pos(self):
n3dsoma = 0
r3dsoma = np.zeros(3)
for sec in self.hobj.soma:
n3d = int(h.n3d(sec=sec)) # get number of n3d points in each section
r3d = np.zeros((3, n3d)) # to hold locations of 3D morphology for the current section
n3dsoma += n3d
for i in range(n3d):
r3dsoma[0] += h.x3d(i, sec=sec)
r3dsoma[1] += h.y3d(i, sec=sec)
r3dsoma[2] += h.z3d(i, sec=sec)
r3dsoma /= n3dsoma
return r3dsoma
def find_middle_coordinates(self) :
cell_list = []
self.m_coordinates = []
for n in range(self.num_neurons) :
cell = []
print "Neuron ", n
for i in range(self.NSize[n]):
exec "cell.append(h.neuron"+str(n)+"_tree["+str(i)+"])";
cell[i].push()
middle = int(h.n3d()/2)# It has to be integer!!
self.m_coordinates.append((h.x3d(middle),h.y3d(middle),h.z3d(middle)))
#print "Yo(", i, ") Middle is ", middle, Coordinates[i]
h.pop_section()
cell_list.append(cell)
self.m_coordinates
def set_position(self, x, y, z):
"""
Set the base location in 3D and move all other
parts of the cell relative to that location.
"""
for sec in self.all:
for i in range(int(nrn.n3d())):
nrn.pt3dchange(i, \
x-self.x+nrn.x3d(i), \
y-self.y+nrn.y3d(i), \
z-self.z+nrn.z3d(i), \
nrn.diam3d(i))
self.x = x
self.y = y
self.z = z
def CalcDistance(cmpt1, cmpt2):
#cmpt means compartment
cmpt1.push()
sr1 = h.SectionRef(sec=cmpt1)
x1 = h.x3d(0.5)
y1 = h.y3d(0.5)
z1 = h.z3d(0.5)
h.pop_section()
cmpt2.push()
sr2 = h.SectionRef(sec=cmpt2)
x2 = h.x3d(0.5)
y2 = h.y3d(0.5)
z2 = h.z3d(0.5)
h.pop_section()
dx = x1 - x2
dy = y1 - y2
dz = z1 - z2
distance = dx * dx + dy * dy + dz * dz
#if(distance < 100.0):
# print "pos %f %f %f %f %f %f dist %f"%(x1, y1, z1, x2, y2, z2,distance)
return distance
def retrieve_coordinates(self, sec):
"""
Returns the 3D coordinates of all points in the currently accessed section.
Does not calculate the center of each section (see 'center_3Dcoords' above)
" """
xyzds = []
for ii in xrange(int(h.n3d(sec=sec))):
xyzds.append([
h.x3d(ii, sec=sec),
h.y3d(ii, sec=sec),
h.z3d(ii, sec=sec),
h.diam3d(ii, sec=sec)
])
return xyzds
def set_position(self, x, y, z):
"""
Set the base location in 3D and move all other
parts of the cell relative to that location.
"""
for sec in self.all:
# note: iterating like this changes the context for all NEURON
# functions that depend on a section, so no need to specify sec=
for i in range(int(h.n3d())):
h.pt3dchange(i,
x - self.x + h.x3d(i),
y - self.y + h.y3d(i),
z - self.z + h.z3d(i),
h.diam3d(i))
self.x, self.y, self.z = x, y, z
def CalcDistance(cmpt1, cmpt2):
#cmpt means compartment
cmpt1.push()
sr1 = h.SectionRef(sec=cmpt1)
x1 = h.x3d(0.5)
y1 = h.y3d(0.5)
z1 = h.z3d(0.5)
h.pop_section()
cmpt2.push()
sr2 = h.SectionRef(sec=cmpt2)
x2 = h.x3d(0.5)
y2 = h.y3d(0.5)
z2 = h.z3d(0.5)
h.pop_section()
dx = x1 - x2
dy = y1 - y2
dz = z1 - z2
distance = dx*dx + dy*dy + dz*dz
#if(distance < 100.0):
# print "pos %f %f %f %f %f %f dist %f"%(x1, y1, z1, x2, y2, z2,distance)
return distance
def find_middle_coordinates(self):
cell_list = []
self.m_coordinates = []
for n in range(self.num_neurons):
cell = []
print "Neuron ", n
for i in range(self.NSize[n]):
exec "cell.append(h.neuron" + str(n) + "_tree[" + str(i) + "])"
cell[i].push()
middle = int(h.n3d() / 2) # It has to be integer!!
self.m_coordinates.append(
(h.x3d(middle), h.y3d(middle), h.z3d(middle)))
#print "Yo(", i, ") Middle is ", middle, Coordinates[i]
h.pop_section()
cell_list.append(cell)
self.m_coordinates
def rotateZ(self, theta):
"""Rotate the cell about the Z axis."""
for sec in self.all:
for i in range(int(h.n3d(sec=sec))):
x = h.x3d(i, sec=sec)
y = h.y3d(i, sec=sec)
c = cos(theta)
s = sin(theta)
xprime = x * c - y * s
yprime = x * s + y * c
h.pt3dchange(i,
xprime,
yprime,
h.z3d(i, sec=sec),
h.diam3d(i, sec=sec),
sec=sec)
def objects_by_segment(sec):
"""
given a section, returns a dictionary whose entries are lists of objects
that should be used for distance calculations, keyed by section
.. warning::
Does not currently support non-frustum based sections (i.e. no support
for new 3d styles, like soma outlines)
.. warning::
This assumes a 3d style exists. The safest way to call this is to call
h.define_shape() first
"""
# TODO: fix the issue described in the warning
# (when this was written, these objects were only under development)
n3d = int(h.n3d(sec=sec))
length = sec.L
arc3d = [h.arc3d(i, sec=sec) for i in xrange(n3d)]
x3d = numpy.array([h.x3d(i, sec=sec) for i in xrange(n3d)])
y3d = numpy.array([h.y3d(i, sec=sec) for i in xrange(n3d)])
z3d = numpy.array([h.z3d(i, sec=sec) for i in xrange(n3d)])
diam3d = numpy.array([h.diam3d(i, sec=sec) for i in xrange(n3d)])
dx = length / sec.nseg
objs = {}
for i in xrange(sec.nseg):
x_lo = i * dx
x_hi = (i + 1) * dx
pts = [x_lo] + _values_strictly_between(x_lo, x_hi, arc3d) + [x_hi]
local_x3d = numpy.interp(pts, arc3d, x3d)
local_y3d = numpy.interp(pts, arc3d, y3d)
local_z3d = numpy.interp(pts, arc3d, z3d)
local_diam3d = numpy.interp(pts, arc3d, diam3d)
local_objs = []
for j in xrange(len(pts) - 1):
x0, y0, z0, r0 = local_x3d[j], local_y3d[j], local_z3d[j], local_diam3d[j] / 2.
x1, y1, z1, r1 = local_x3d[j + 1], local_y3d[j + 1], local_z3d[j + 1], local_diam3d[j + 1] / 2.
if r0 == r1:
local_objs.append(Cylinder(x0, y0, z0, x1, y1, z1, r0))
else:
local_objs.append(Cone(x0, y0, z0, r0, x1, y1, z1, r1))
objs[sec((i + 0.5) / sec.nseg)] = local_objs
return objs
def centroids_by_segment(sec):
"""
given a section, returns a dictionary whose entries are lists of cylinders
of radius 0 that should be used for distance calculations, keyed by section
.. warning::
Does not currently support non-frustum based sections (i.e. no support
for new 3d styles, like soma outlines)
.. warning::
This assumes a 3d style exists. The safest way to call this is to call
h.define_shape() first
"""
# TODO: fix the issue described in the warning
# (when this was written, these objects were only under development)
n3d = int(h.n3d(sec=sec))
length = sec.L
arc3d = [h.arc3d(i, sec=sec) for i in xrange(n3d)]
x3d = numpy.array([h.x3d(i, sec=sec) for i in xrange(n3d)])
y3d = numpy.array([h.y3d(i, sec=sec) for i in xrange(n3d)])
z3d = numpy.array([h.z3d(i, sec=sec) for i in xrange(n3d)])
diam3d = numpy.array([h.diam3d(i, sec=sec) for i in xrange(n3d)])
dx = length / sec.nseg
objs = {}
for i in xrange(sec.nseg):
x_lo = i * dx
x_hi = (i + 1) * dx
pts = [x_lo] + _values_strictly_between(x_lo, x_hi, arc3d) + [x_hi]
local_x3d = numpy.interp(pts, arc3d, x3d)
local_y3d = numpy.interp(pts, arc3d, y3d)
local_z3d = numpy.interp(pts, arc3d, z3d)
local_diam3d = numpy.interp(pts, arc3d, diam3d)
local_objs = []
for j in xrange(len(pts) - 1):
x0, y0, z0, r0 = local_x3d[j], local_y3d[j], local_z3d[
j], local_diam3d[j] / 2.
x1, y1, z1, r1 = local_x3d[j + 1], local_y3d[j + 1], local_z3d[
j + 1], local_diam3d[j + 1] / 2.
if x0 != x1 or y0 != y1 or z0 != z1:
local_objs.append(Cylinder(x0, y0, z0, x1, y1, z1, 0))
objs[sec((i + 0.5) / sec.nseg)] = local_objs
return objs
def move(self, xyz, move_mlab=False):
""" Move visualization and cell """
from neuron import h
if move_mlab:
if self.mlab_cell:
self.mlab_cell.mlab_source.x = self.mlab_cell.mlab_source.x + xyz[0]
self.mlab_cell.mlab_source.y = self.mlab_cell.mlab_source.y + xyz[1]
self.mlab_cell.mlab_source.z = self.mlab_cell.mlab_source.z + xyz[2]
tree = h.SectionList()
tree.wholetree(sec=self.root)
for sec in tree:
for ii in xrange(h.n3d(sec=sec).__int__()):
x=h.x3d(ii,sec=sec)
y=h.y3d(ii,sec=sec)
z=h.z3d(ii,sec=sec)
d=h.diam3d(ii,sec=sec)
h.pt3dchange(ii,x+float(xyz[0]),y+float(xyz[1]),z+float(xyz[2]),d)
def set_position(self, x, y, z):
"""
Set the base location in 3D and move all other
parts of the cell relative to that location.
"""
for sec in self.all:
sec.push()
#print('secname = %s, h.n3d = %d' % (h.secname(), h.n3d()))
for i in range(int(h.n3d())):
h.pt3dchange(i,
x - self.x + h.x3d(i),
y - self.y + h.y3d(i),
z - self.z + h.z3d(i),
h.diam3d(i), sec=sec)
h.pop_section()
#h.define_shape()
self.x, self.y, self.z = x, y, z
def tet_associate(sm):
# INPUT: Tetmesh object
# This function associates .hoc sections to the tets which contain them, and returns the association dictionary.
# It's packaged separately from the coarse() function so it can be used independently in scripts which load a Tetmesh from file
# and don't need any Tetmesh to be generated from a .hoc file.
tet_hoc = {}
for s in h.allsec():
for j in range(int(h.n3d())):
containing_tet = sm.findTetByPoint((h.x3d(j),h.y3d(j),h.z3d(j)))
if (containing_tet) not in tet_hoc.keys():
tet_hoc[containing_tet] = [s]
elif (containing_tet) in tet_hoc.keys():
if (s) not in tet_hoc[containing_tet]:
tet_hoc[containing_tet].append(s)
return tet_hoc
def z_rotation(self, theta):
"""
This method rotates the SimpleCell object in 3D space around the
z-axis by a user-specified number of degrees.
"""
theta *= (pylab.pi / 180)
for section in self.all:
for point in range(int(h.n3d(sec=section))):
xold = h.x3d(point, sec=section)
yold = h.y3d(point, sec=section)
xnew = xold * pylab.cos(theta) - yold * pylab.sin(theta)
ynew = xold * pylab.sin(theta) + yold * pylab.cos(theta)
h.pt3dchange(point,
xnew,
ynew,
h.z3d(point, sec=section),
h.diam3d(point, sec=section),
sec=section)
def set_position(self, x, y, z):
"""
Set the base location in 3D and move all other
parts of the cell relative to that location.
"""
for sec in self.all:
sec.push()
#print('secname = %s, h.n3d = %d' % (h.secname(), h.n3d()))
for i in range(int(h.n3d())):
h.pt3dchange(i,
x - self.x + h.x3d(i),
y - self.y + h.y3d(i),
z - self.z + h.z3d(i),
h.diam3d(i),
sec=sec)
h.pop_section()
#h.define_shape()
self.x, self.y, self.z = x, y, z
def cell_to_morph3d(cell):
"""Convert a neuron cell to a morphological tree.
Here we create nodes by recovering the 3d point coordinates in the
section.
Returns: g, root where g is a digraph rooted at soma, root is the
node label for the root node ({soma.name()}_0).
This will need a cleanup for nrn7.5.
"""
g = nx.DiGraph()
stack = [cell.soma]
while len(stack) > 0:
sec = stack.pop()
# This is roundabout way is required because nrn7.4 does not
# provide explicit equivalent of `access {section}`. In nrn7.5
# the 3d functions are available as Section methods.
h('access {}'.format(sec.name()))
stype = nu.sectype(sec.name())
pt3d = int(h.n3d())
# pt3d = int(sec.n3d()): # only nrn >= 7.5
for ii in range(pt3d):
name = '{}_{}'.format(sec.name(), ii)
x = h.x3d(ii)
y = h.y3d(ii)
z = h.z3d(ii)
d = h.diam3d(ii)
g.add_node(name, x=x, y=y, z=z, r=d / 2.0, s=stype, orig=sec)
for ii in range(1, pt3d):
n1 = '{}_{}'.format(sec.name(), ii - 1)
n2 = '{}_{}'.format(sec.name(), ii)
length = ng.eucd(g, n1, n2)
g.add_edge(n1, n2, length=length)
current = h.SectionRef(sec=sec)
if current.has_parent():
h('access {}'.format(current.parent.name()))
n1 = '{}_{}'.format(current.parent.name(), int(h.n3d() - 1))
g.add_edge(n1, '{}_0'.format(sec.name()), length=0)
for child in current.child:
# print('Adding', child.name())
stack.append(child)
return g, '{}_0'.format(cell.soma.name())
def get_alen_pos3d(sec):
"""Get the arclength and 3D position of the poinst in section sec.
Inspired by
http://www.neuron.yale.edu/ftp/ted/neuron/extracellular_stim_and_rec.zip:
interpxyz.hoc
Returns: length, pos where length is the list of arc3d lengths and
pos the list of 3D positions (x, y, z), of the 3D points in
section `sec`.
"""
npts = int(h.n3d(sec=sec))
pos = []
length = []
for ii in range(npts):
pos.append((h.x3d(ii, sec=sec), h.y3d(ii, sec=sec), h.z3d(ii,
sec=sec)))
length.append(h.arc3d(ii, sec=sec))
return length, pos
def swc2morph(swc_file):
"""
Generate morph sectioning data from swc file.
"""
from neuron import h
h.load_file('stdlib.hoc')
h.load_file('import3d.hoc')
cell = h.Import3d_SWC_read()
cell.input(swc_file)
i3d = h.Import3d_GUI(cell, 0)
i3d.instantiate(None)
sections = {}
for sec in h.allsec():
sections[sec.name()] = {}
sections[sec.name()]["name"] = sec.name()
sr = h.SectionRef(sec=sec)
if sr.has_parent():
parent = sr.parent.name()
else:
parent = None
sections[sec.name()]["parent"] = parent
children = []
for child in sr.child:
children.append(child.name())
sections[sec.name()]["children"] = children
x = []
y = []
z = []
d = []
n3d = int(h.n3d())
sections[sec.name()]["points"] = []
for i in range(n3d):
sections[sec.name()]["points"].append(
[h.x3d(i), h.y3d(i), h.z3d(i),
h.diam3d(i)])
return sections
def append_data(sec, xyzdv, parent_id, connections,func,segfunc):
""" Append data to xyzdv
"""
if not segfunc: v=func(sec)
n = int(h.n3d(sec=sec))
for ii in xrange(1, n):
x = h.x3d(ii,sec=sec)
y = h.y3d(ii,sec=sec)
z = h.z3d(ii,sec=sec)
d = h.diam3d(ii,sec=sec)
if segfunc:
if n==1:v=func(sec(0.5))
else:v = func(sec(ii/float(n-1)))
xyzdv.append([x,y,z,d,v])
child_id = len(xyzdv)-1
if len(xyzdv)>1:
connections.append([child_id, parent_id])
parent_id = child_id
return xyzdv, connections
def retrieve_coordinate(sec):
sec.push()
x, y, z = [], [], []
connect_next = False
for i in range(int(h.n3d())):
present = False
x_i = h.x3d(i)
y_i = h.y3d(i)
z_i = h.z3d(i)
if x_i in x:
ind = len(x) - 1 - x[::-1].index(x_i)
if y_i == y[ind]:
if z_i == z[ind]:
present = True
if not present:
x.append(x_i)
y.append(y_i)
z.append(z_i)
h.pop_section()
return (np.array(x),np.array(y),np.array(z))
def rotate(self, theta):
""" Rotate neuron coordinates.
theta = [thetax,thetay,thetaz]
"""
from neuron import h
from mytools.rotate_xyz import rotate_xyz
tree = h.SectionList()
tree.wholetree(sec=self.root)
for sec in tree:
for ii in xrange(h.n3d(sec=sec).__int__()):
x = h.x3d(ii, sec=sec)
y = h.y3d(ii, sec=sec)
z = h.z3d(ii, sec=sec)
d = h.diam3d(ii, sec=sec)
xyz_out = rotate_xyz(theta, [x, y, z])
h.pt3dchange(ii, float(xyz_out[0]), float(xyz_out[1]),
float(xyz_out[2]), d)
def printSegmentTree(rootSection, indentLevel=0):
from neuron import h
coordCount = int(h.n3d(sec=rootSection))
coords = []
for c in range(coordCount):
coords.append({
"x": h.x3d(c, sec=rootSection),
"y": h.y3d(c, sec=rootSection),
"z": h.z3d(c, sec=rootSection),
"d": h.diam3d(c, sec=rootSection)
})
sectionInfo = {
"name":
rootSection.name(),
"L":
'{:.3f}'.format(rootSection.L),
"Diam":
'{:.3f}'.format(rootSection.diam),
"Ra":
'{:.3f}'.format(rootSection.Ra),
"Branch":
'{:.3f}'.format(rootSection.rallbranch),
"Orientation":
'{:.3f}'.format(rootSection.orientation()),
"segs":
rootSection.nseg,
"locOnParent":
'{:.3f}'.format(rootSection.parentseg().x)
if rootSection.parentseg() is not None else None
}
print(" " * indentLevel + str(sectionInfo))
print("")
# for coord in coords:
# print(" " * indentLevel + str(coord))
children = rootSection.children()
children.sort(key=lambda sec: sec.name())
for child in children:
printSegmentTree(child, indentLevel + 1)
def _walk_path(sec_ref, path):
rec_pos = np.zeros([len(path), 3])
v_vec_list = []
i_vec_list = []
t_vec = h.Vector()
t_vec.record(h._ref_t)
for cnt, idx in enumerate(path):
v_vec = h.Vector()
i_vec = h.Vector()
sec = sec_ref.child[idx]
sec_pos = 0.5
# Find closest segment index to sec_pos.
idx_seg = int((h.n3d(sec=sec) - 1) * sec_pos)
rec_pos[cnt, 0] = h.x3d(idx_seg, sec=sec)
rec_pos[cnt, 1] = h.y3d(idx_seg, sec=sec)
rec_pos[cnt, 2] = h.z3d(idx_seg, sec=sec)
v_vec.record(sec(sec_pos)._ref_v)
i_vec.record(sec(sec_pos)._ref_i_membrane)
v_vec_list.append(v_vec)
i_vec_list.append(i_vec)
sec_ref = h.SectionRef(sec=sec)
return v_vec_list, i_vec_list, t_vec, rec_pos
def append_data(sec, xyzdv, parent_id, connections):
""" Append data to xyzdv """
if self.var is 'v':
v = sec.v
else:
raise AttributeError('Variable %s not implemented' % self.var)
sec.push()
for ii in xrange(1, int(nrn.n3d())):
x = nrn.x3d(ii)
y = nrn.y3d(ii)
z = nrn.z3d(ii)
d = nrn.diam3d(ii)
xyzdv.append([x,y,z,d,v])
child_id = len(xyzdv)-1
if len(xyzdv)>1:
connections.append([child_id, parent_id])
parent_id = child_id
nrn.pop_section()
return xyzdv, connections
def hoc2morph(hoc_file):
"""
Generate morph sectioning data from NEURON hoc file.
"""
import sys
from neuron import h
sections = {}
h.load_file(hoc_file)
for sec in h.allsec():
sections[sec.name()] = {}
sections[sec.name()]["name"] = sec.name()
sr = h.SectionRef(sec=sec)
if sr.has_parent():
parent = sr.parent.name()
else:
parent = None
sections[sec.name()]["parent"] = parent
children = []
for child in sr.child:
children.append(child.name())
sections[sec.name()]["children"] = children
x = []
y = []
z = []
d = []
n3d = int(h.n3d())
sections[sec.name()]["points"] = []
for i in range(n3d):
sections[sec.name()]["points"].append(
[h.x3d(i), h.y3d(i), h.z3d(i),
h.diam3d(i)])
return sections
def get_dict(self, geom_type):
"""
Create a dictionary representation of this section.
:param geom_type: 'stylized': dict with L and diam, '3d': list of [x, y, z, diam]
:type geom_type: str
:return: Dictionary containing all parameters of a section.
:rtype: dict
"""
# geometry
if geom_type == 'stylized':
geom = {'L': self.L, 'diam': self.diam}
elif geom_type == '3d':
geom = [[h.x3d(seg.x, sec=self), h.y3d(seg.x, sec=self), h.z3d(seg.x, sec=self), seg.diam]
for seg in self]
else:
raise ValueError("Invalid geometry type! Should be 'stylized' or '3d'.")
# mechanisms
mechanism_names = [mechanism_name for mechanism_name in vars(self(.5))
if isinstance(getattr(self(.5), mechanism_name), nrn.Mechanism)]
mechanisms = {name: dict() for name in mechanism_names} # saved according to name, then pos
for mechanism_name in mechanism_names:
for seg in self:
mechanisms[mechanism_name][str(seg.x)] = \
{p: getattr(seg, p) for p in vars(getattr(seg, mechanism_name))}
# parent
if h.SectionRef(sec=self).has_parent():
parent = [h.SectionRef(sec=self).parent.name, h.SectionRef(sec=self).parent.index]
else:
parent = None
return {'nseg': self.nseg, 'Ra': self.Ra, 'cm': self.cm,
'geom': geom, 'mechanisms': mechanisms, 'parent': parent,
'connection_point': self.connection_point}
def _indices_from_sec_x(self, sec, position):
# TODO: the assert is here because the diameter is not computed correctly
# unless it coincides with a 3d point, which we only know to exist at the
# endpoints and because the section does not proceed linearly between
# the endpoints (in general)... which affects the computation of the
# normal vector as well
assert (position in (0, 1))
# NOTE: some care is necessary in constructing normal vector... must be
# based on end frusta, not on vector between end points
if position == 0:
x = h.x3d(0, sec=sec)
y = h.y3d(0, sec=sec)
z = h.z3d(0, sec=sec)
nx = h.x3d(1, sec=sec) - x
ny = h.y3d(1, sec=sec) - y
nz = h.z3d(1, sec=sec) - z
elif position == 1:
n = int(h.n3d(sec=sec))
x = h.x3d(n - 1, sec=sec)
y = h.y3d(n - 1, sec=sec)
z = h.z3d(n - 1, sec=sec)
# NOTE: sign of the normal is irrelevant
nx = x - h.x3d(n - 2, sec=sec)
ny = y - h.y3d(n - 2, sec=sec)
nz = z - h.z3d(n - 2, sec=sec)
else:
raise RxDException('should never get here')
# x, y, z = x * x1 + (1 - x) * x0, x * y1 + (1 - x) * y0, x * z1 + (1 - x) * z1
r = sec(position).diam * 0.5
plane_of_disc = geometry3d.graphicsPrimitives.Plane(
x, y, z, nx, ny, nz)
potential_coordinates = []
mesh = self._mesh
xs, ys, zs = mesh._xs, mesh._ys, mesh._zs
xlo, ylo, zlo = xs[0], ys[0], zs[0]
# locate the indices of the cube containing the sphere containing the disc
# TODO: write this more efficiently
i_indices = [i for i, a in enumerate(xs) if abs(a - x) < r]
j_indices = [i for i, a in enumerate(ys) if abs(a - y) < r]
k_indices = [i for i, a in enumerate(zs) if abs(a - z) < r]
sphere_indices = [
(i, j, k)
for i, j, k in itertools.product(i_indices, j_indices, k_indices)
if (xs[i] - x)**2 + (ys[j] - y)**2 + (zs[k] - z)**2 < r**2
]
dx2 = self.dx * 0.5
dx = self.dx
disc_indices = []
for i, j, k in sphere_indices:
# a, b, c = xs[i], ys[j], zs[k]
# TODO: no need to compute all; can stop when some True and some False
# on_side1 = [plane_of_disc.distance(x, y, z) >= 0 for x, y, z in itertools.product([a - dx2, a + dx2], [b - dx2, b + dx2], [c - dx2, c + dx2])]
# NOTE: the expression is structured this way to make sure it tests the exact same corner coordinates for corners shared by multiple voxels and that there are no round-off issues (an earlier attempt had round-off issues that resulted in double-thick discs when the frustum ended exactly on a grid plane)
on_side1 = [
plane_of_disc.distance(x, y, z) >= 0
for x, y, z in itertools.product(
[(xlo + (i - 1) * dx) + dx2, (xlo + i * dx) +
dx2], [(ylo + (j - 1) * dx) + dx2, (ylo + j * dx) +
dx2], [(zlo +
(k - 1) * dx) + dx2, (zlo + k * dx) + dx2])
]
# need both sides to have at least one corner
if any(on_side1) and not all(on_side1):
# if we're here, then we've found a point on the disc.
disc_indices.append((i, j, k))
return disc_indices
def position(self, x, y, z):
self.soma.push()
for i in range(h.n3d()):
h.pt3dchange(i, x-self.x+h.x3d(i), y-self.y+h.y3d(i), z-self.z+h.z3d(i), h.diam3d(i))
self.x = x; self.y = y; self.z = z
h.pop_section()
def getCellParams(cell):
dirCell = dir(cell)
if 'all_sec' in dirCell:
secs = cell.all_sec
elif 'sec' in dirCell:
secs = [cell.sec]
elif 'allsec' in dir(h):
secs = [sec for sec in h.allsec()]
elif 'soma' in dirCell:
secs = [cell.soma]
else:
secs = []
# create dict with hname of each element in dir(cell)
dirCellHnames = {}
for dirCellName in dirCell:
try:
dirCellHnames.update(
{getattr(cell, dirCellName).hname(): dirCellName})
except:
pass
# create dict with dir(cell) name corresponding to each hname
dirCellSecNames = {}
for sec in secs:
dirCellSecNames.update({
hname: name
for hname, name in dirCellHnames.iteritems()
if hname == sec.hname()
})
secDic = {}
synMechs = []
for sec in secs:
# create new section dict with name of section
secName = getSecName(sec, dirCellSecNames)
if len(secs) == 1:
secName = 'soma' # if just one section rename to 'soma'
secDic[secName] = {
'geom': {},
'topol': {},
'mechs': {}
} # create dictionary to store sec info
# store geometry properties
standardGeomParams = ['L', 'nseg', 'diam', 'Ra', 'cm']
secDir = dir(sec)
for geomParam in standardGeomParams:
#if geomParam in secDir:
try:
secDic[secName]['geom'][geomParam] = sec.__getattribute__(
geomParam)
except:
pass
# store 3d geometry
sec.push() # access current section so ismembrane() works
numPoints = int(h.n3d())
if numPoints:
points = []
for ipoint in range(numPoints):
x = h.x3d(ipoint)
y = h.y3d(ipoint)
z = h.z3d(ipoint)
diam = h.diam3d(ipoint)
points.append((x, y, z, diam))
secDic[secName]['geom']['pt3d'] = points
# store mechanisms
varList = mechVarList(
) # list of properties for all density mechanisms and point processes
ignoreMechs = ['dist'] # dist only used during cell creation
ignoreVars = [] #
mechDic = {}
ionDic = {}
for mech in dir(sec(0.5)):
if h.ismembrane(
mech
) and mech not in ignoreMechs: # check if membrane mechanism
if not mech.endswith('_ion'): # exclude ions
mechDic[mech] = {} # create dic for mechanism properties
varNames = [
varName.replace('_' + mech, '')
for varName in varList['mechs'][mech]
]
varVals = []
for varName in varNames:
if varName not in ignoreVars:
try:
varVals = [
seg.__getattribute__(
mech).__getattribute__(varName)
for seg in sec
]
if len(set(varVals)) == 1:
varVals = varVals[0]
mechDic[mech][varName] = varVals
except:
pass
#print 'Could not read variable %s from mechanism %s'%(varName,mech)
# store ions
elif mech.endswith('_ion'):
ionName = mech.split('_ion')[0]
varNames = [
varName.replace('_' + mech, '').replace(ionName, '')
for varName in varList['mechs'][mech]
]
varNames.append('e')
varVals = []
ionDic[ionName] = {} # create dic for mechanism properties
for varName in varNames:
varNameSplit = varName
if varName not in ignoreVars:
try:
varVals = [
seg.__getattribute__(varNameSplit +
ionName)
for seg in sec
]
if len(set(varVals)) == 1:
varVals = varVals[0]
ionDic[ionName][varNameSplit] = varVals
except:
pass
#print 'Could not read variable %s from mechanism %s'%(varName,mech)
secDic[secName]['mechs'] = mechDic
if len(ionDic) > 0:
secDic[secName]['ions'] = ionDic
# add synapses and point neurons
# for now read fixed params, but need to find way to read only synapse params
pointps = {}
for seg in sec:
for ipoint, point in enumerate(seg.point_processes()):
pointpMod = point.hname().split('[')[0]
varNames = varList['pointps'][pointpMod]
if any([
s in pointpMod.lower()
for s in ['syn', 'ampa', 'gaba', 'nmda', 'glu']
]):
#if 'synMech' in pptype.lower(): # if syn in name of point process then assume synapse
synMech = {}
synMech['label'] = pointpMod + '_' + str(len(synMechs))
synMech['mod'] = pointpMod
#synMech['loc'] = seg.x
for varName in varNames:
try:
synMech[varName] = point.__getattribute__(varName)
except:
print 'Could not read variable %s from synapse %s' % (
varName, synMech['label'])
if not [
_equal_dicts(
synMech, synMech2, ignore_keys=['label'])
for synMech2 in synMechs
]:
synMechs.append(synMech)
else: # assume its a non-synapse point process
pointpName = pointpMod + '_' + str(len(pointps))
pointps[pointpName] = {}
pointps[pointpName]['mod'] = pointpMod
pointps[pointpName]['loc'] = seg.x
for varName in varNames:
try:
pointps[pointpName][
varName] = point.__getattribute__(varName)
# special condition for Izhi model, to set vinit=vr
# if varName == 'vr': secDic[secName]['vinit'] = point.__getattribute__(varName)
except:
print 'Could not read %s variable from point process %s' % (
varName, pointpName)
if pointps: secDic[secName]['pointps'] = pointps
# store topology (keep at the end since h.SectionRef messes remaining loop)
secRef = h.SectionRef(sec=sec)
if secRef.has_parent():
secDic[secName]['topol']['parentSec'] = getSecName(
secRef.parent().sec, dirCellSecNames)
secDic[secName]['topol']['parentX'] = h.parent_connection()
secDic[secName]['topol']['childX'] = h.section_orientation()
h.pop_section() # to prevent section stack overflow
# store section lists
secLists = h.List('SectionList')
if int(secLists.count()):
secListDic = {}
for i in xrange(int(secLists.count())): # loop over section lists
hname = secLists.o(i).hname()
if hname in dirCellHnames: # use python variable name
secListName = dirCellHnames[hname]
else:
secListName = hname
secListDic[secListName] = [
getSecName(sec, dirCellSecNames) for sec in secLists.o(i)
]
else:
secListDic = {}
# celsius warning
if hasattr(h, 'celsius'):
if h.celsius != 6.3: # if not default value
print "Warning: h.celsius=%.4g in imported file -- you can set this value in simConfig['hParams']['celsius']" % (
h.celsius)
# clean
h.initnrn()
del (cell) # delete cell
import gc
gc.collect()
return secDic, secListDic, synMechs
def importCell (fileName, cellName, cellArgs = None):
h.initnrn()
if cellArgs is None: cellArgs = [] # Define as empty list if not otherwise defined
''' Import cell from HOC template or python file into framework format (dict of sections, with geom, topol, mechs, syns)'''
if fileName.endswith('.hoc'):
h.load_file(fileName)
if isinstance(cellArgs, dict):
cell = getattr(h, cellName)(**cellArgs) # create cell using template, passing dict with args
else:
cell = getattr(h, cellName)(*cellArgs) # create cell using template, passing list with args
secs = list(cell.allsec())
dirCell = dir(cell)
elif fileName.endswith('.py'):
filePath,fileNameOnly = os.path.split(fileName) # split path from filename
if filePath not in sys.path: # add to path if not there (need to import module)
sys.path.insert(0, filePath)
moduleName = fileNameOnly.split('.py')[0] # remove .py to obtain module name
exec('import ' + moduleName + ' as tempModule') in globals(), locals() # import module dynamically
modulePointer = tempModule
if isinstance(cellArgs, dict):
cell = getattr(modulePointer, cellName)(**cellArgs) # create cell using template, passing dict with args
else:
cell = getattr(modulePointer, cellName)(*cellArgs) # create cell using template, passing list with args
dirCell = dir(cell)
if 'all_sec' in dirCell:
secs = cell.all_sec
elif 'sec' in dirCell:
secs = [cell.sec]
elif 'allsec' in dir(h):
secs = [sec for sec in h.allsec()]
elif 'soma' in dirCell:
secs = [cell.soma]
else:
secs = []
sys.path.remove(filePath)
else:
print "File name should be either .hoc or .py file"
return
# create dict with hname of each element in dir(cell)
dirCellHnames = {}
for dirCellName in dirCell:
try:
dirCellHnames.update({getattr(cell, dirCellName).hname(): dirCellName})
except:
pass
# create dict with dir(cell) name corresponding to each hname
dirCellSecNames = {}
for sec in secs:
dirCellSecNames.update({hname: name for hname,name in dirCellHnames.iteritems() if hname == sec.hname()})
secDic = {}
synMechs = []
for sec in secs:
# create new section dict with name of section
secName = getSecName(sec, dirCellSecNames)
if len(secs) == 1:
secName = 'soma' # if just one section rename to 'soma'
secDic[secName] = {'geom': {}, 'topol': {}, 'mechs': {}} # create dictionary to store sec info
# store geometry properties
standardGeomParams = ['L', 'nseg', 'diam', 'Ra', 'cm']
secDir = dir(sec)
for geomParam in standardGeomParams:
#if geomParam in secDir:
try:
secDic[secName]['geom'][geomParam] = sec.__getattribute__(geomParam)
except:
pass
# store 3d geometry
numPoints = int(h.n3d())
if numPoints:
points = []
for ipoint in range(numPoints):
x = h.x3d(ipoint)
y = h.y3d(ipoint)
z = h.z3d(ipoint)
diam = h.diam3d(ipoint)
points.append((x, y, z, diam))
secDic[secName]['geom']['pt3d'] = points
# store mechanisms
varList = mechVarList() # list of properties for all density mechanisms and point processes
ignoreMechs = ['dist'] # dist only used during cell creation
mechDic = {}
sec.push() # access current section so ismembrane() works
for mech in dir(sec(0.5)):
if h.ismembrane(mech) and mech not in ignoreMechs: # check if membrane mechanism
mechDic[mech] = {} # create dic for mechanism properties
varNames = [varName.replace('_'+mech, '') for varName in varList['mechs'][mech]]
varVals = []
for varName in varNames:
try:
varVals = [seg.__getattribute__(mech).__getattribute__(varName) for seg in sec]
if len(set(varVals)) == 1:
varVals = varVals[0]
mechDic[mech][varName] = varVals
except:
pass
#print 'Could not read variable %s from mechanism %s'%(varName,mech)
secDic[secName]['mechs'] = mechDic
# add synapses and point neurons
# for now read fixed params, but need to find way to read only synapse params
pointps = {}
for seg in sec:
for ipoint,point in enumerate(seg.point_processes()):
pointpMod = point.hname().split('[')[0]
varNames = varList['pointps'][pointpMod]
if any([s in pointpMod.lower() for s in ['syn', 'ampa', 'gaba', 'nmda', 'glu']]):
#if 'synMech' in pptype.lower(): # if syn in name of point process then assume synapse
synMech = {}
synMech['label'] = pointpMod + '_' + str(len(synMechs))
synMech['mod'] = pointpMod
#synMech['loc'] = seg.x
for varName in varNames:
try:
synMech[varName] = point.__getattribute__(varName)
except:
print 'Could not read variable %s from synapse %s'%(varName,synMech['label'])
if not [_equal_dicts(synMech, synMech2, ignore_keys=['label']) for synMech2 in synMechs]:
synMechs.append(synMech)
else: # assume its a non-synapse point process
pointpName = pointpMod + '_'+ str(len(pointps))
pointps[pointpName] = {}
pointps[pointpName]['mod'] = pointpMod
pointps[pointpName]['loc'] = seg.x
for varName in varNames:
try:
pointps[pointpName][varName] = point.__getattribute__(varName)
# special condition for Izhi model, to set vinit=vr
# if varName == 'vr': secDic[secName]['vinit'] = point.__getattribute__(varName)
except:
print 'Could not read %s variable from point process %s'%(varName,pointpName)
if pointps: secDic[secName]['pointps'] = pointps
# store topology (keep at the end since h.SectionRef messes remaining loop)
secRef = h.SectionRef(sec=sec)
if secRef.has_parent():
secDic[secName]['topol']['parentSec'] = getSecName(secRef.parent().sec, dirCellSecNames)
secDic[secName]['topol']['parentX'] = h.parent_connection()
secDic[secName]['topol']['childX'] = h.section_orientation()
h.pop_section() # to prevent section stack overflow
# # store synMechs in input argument
# if synMechs:
# for synMech in synMechs: synMechParams.append(synMech)
# store section lists
secLists = h.List('SectionList')
if int(secLists.count()):
secListDic = {}
for i in xrange(int(secLists.count())): # loop over section lists
hname = secLists.o(i).hname()
if hname in dirCellHnames: # use python variable name
secListName = dirCellHnames[hname]
else:
secListName = hname
secListDic[secListName] = [getSecName(sec, dirCellSecNames) for sec in secLists.o(i)]
else:
secListDic = {}
# celsius warning
if hasattr(h, 'celsius'):
if h.celsius != 6.3: # if not default value
print "Warning: h.celsius=%.4g in imported file %s -- you can set this value in simConfig['hParams']['celsius']"%(h.celsius, fileName)
# clean
h.initnrn()
del(cell) # delete cell
import gc; gc.collect()
return secDic, secListDic, synMechs
maincelldct=[]
dictcnt=0
for ij in range(len(pcpositions)):
#exec('sectdict_%d={}'%ij)
sectiondct={}
for sec in pcsecall:
segstr=str(sec)
sec.push()
listgrX=[]
listgrY=[]
listgrZ=[]
for i in range(int(h.n3d())):
listgrX.append(h.x3d(i))
listgrY.append(h.y3d(i))
listgrZ.append(h.z3d(i))
if str(sec)=="axonAIS" or str(sec)=="axonmyelin" or str(sec)=="axonmyelin4" or str(sec)=="axonNOR3" or str(sec)=="axoncoll2" or str(sec)=="axonmyelin3" or str(sec)=="axoncoll" or str(sec)=="axonNOR2" or str(sec)=="axonmyelin2" or str(sec)=="axonNOR" or str(sec)=="axonAISK" or str(sec)=="axonAIS":
segstr=str(sec)
buf=segstr
else:
segstr=segstr.split('.')
segstr=segstr[2].split('[')
if segstr[0]=='soma':
buf=segstr[0]
else:
secname=segstr[0]
segstr=segstr[1].split(']')
secid=segstr[0]
buf=secname+"_"+secid
#print 'buf contains:', buf
def getCenter(soma):
soma.push()
center = np.array((h.x3d(0), h.y3d(0), h.z3d(0)))
h.pop_section()
return center
def calcRelativeSegCoords(self):
"""Calculate segment coordinates from 3d point coordinates
Used for LFP calc (one per population cell; assumes same morphology)"""
from .. import sim
localPopGids = list(
set(sim.net.gid2lid.keys()).intersection(set(self.cellGids)))
if localPopGids:
cell = sim.net.cells[sim.net.gid2lid[localPopGids[0]]]
else:
return -1
ix = 0 # segment index
p3dsoma = cell.getSomaPos()
nseg = sum([sec['hObj'].nseg for sec in list(cell.secs.values())])
p0 = np.zeros(
(3, nseg)) # hold the coordinates of segment starting points
p1 = np.zeros((3, nseg)) # hold the coordinates of segment end points
d0 = np.zeros(nseg)
d1 = np.zeros(nseg)
for sec in list(cell.secs.values()):
hSec = sec['hObj']
hSec.push()
n3d = int(h.n3d()) # get number of n3d points in each section
p3d = np.zeros(
(3, n3d)
) # to hold locations of 3D morphology for the current section
l3d = np.zeros(
n3d
) # to hold locations of 3D morphology for the current section
diam3d = np.zeros(n3d) # to diameters
for i in range(n3d):
p3d[0, i] = h.x3d(i) - p3dsoma[0]
p3d[1, i] = h.y3d(i) - p3dsoma[
1] # shift coordinates such to place soma at the origin.
p3d[2, i] = h.z3d(i) - p3dsoma[2]
diam3d[i] = h.diam3d(i)
l3d[i] = h.arc3d(i)
l3d /= hSec.L # normalize
nseg = hSec.nseg
l0 = np.zeros(nseg) # keep range of segment starting point
l1 = np.zeros(nseg) # keep range of segment ending point
for iseg, seg in enumerate(hSec):
l0[iseg] = seg.x - 0.5 * 1 / nseg # x (normalized distance along the section) for the beginning of the segment
l1[iseg] = seg.x + 0.5 * 1 / nseg # x for the end of the segment
p0[0, ix:ix + nseg] = np.interp(l0, l3d, p3d[0, :])
p0[1, ix:ix + nseg] = np.interp(l0, l3d, p3d[1, :])
p0[2, ix:ix + nseg] = np.interp(l0, l3d, p3d[2, :])
d0[ix:ix + nseg] = np.interp(l0, l3d, diam3d[:])
p1[0, ix:ix + nseg] = np.interp(l1, l3d, p3d[0, :])
p1[1, ix:ix + nseg] = np.interp(l1, l3d, p3d[1, :])
p1[2, ix:ix + nseg] = np.interp(l1, l3d, p3d[2, :])
d1[ix:ix + nseg] = np.interp(l1, l3d, diam3d[:])
ix += nseg
h.pop_section()
self._morphSegCoords = {}
self._morphSegCoords['p0'] = p0
self._morphSegCoords['p1'] = p1
self._morphSegCoords['d0'] = d0
self._morphSegCoords['d1'] = d1
return self._morphSegCoords
def build_tree(self, func, segfunc=False):
"""
func must act on a neuron section
"""
from numpy import array
print("-" * 100)
def append_data(sec, xyzdv, parent_id, connections, func, segfunc):
""" Append data to xyzdv
"""
if not segfunc: v = func(sec)
n = int(h.n3d(sec=sec))
for ii in xrange(1, n):
x = h.x3d(ii, sec=sec)
y = h.y3d(ii, sec=sec)
z = h.z3d(ii, sec=sec)
d = h.diam3d(ii, sec=sec)
if 'node' in sec.name() or 'MYSA' in sec.name():
v = 1.0
else:
pass
if segfunc:
if n == 1: v = func(sec(0.5))
else: v = func(sec(ii / float(n - 1)))
xyzdv.append([x, y, z, d, v])
child_id = len(xyzdv) - 1
if len(xyzdv) > 1:
connections.append([child_id, parent_id])
parent_id = child_id
return xyzdv, connections
def append_children_data(parent, parent_id, xyzdv, connections, func,
segfunc):
sref = h.SectionRef(sec=parent)
if sref.child:
for child in sref.child:
xyzdv, connections = append_data(child, xyzdv, parent_id,
connections, func,
segfunc)
xyzdv, connections = append_children_data(
parent=child,
parent_id=len(xyzdv) - 1,
xyzdv=xyzdv,
connections=connections,
func=func,
segfunc=segfunc)
return xyzdv, connections
# Find data and connections
root_section = self.root_section()
if segfunc:
if root_section.nseg == 1:
v = func(root_section(0.5))
else:
v = func(root_section(0.0))
else:
v = func(root_section)
xyzdv = [[
h.x3d(0, sec=root_section),
h.y3d(0, sec=root_section),
h.z3d(0, sec=root_section),
h.diam3d(0, sec=root_section), v
]]
xyzdv, connections = append_data(root_section, xyzdv, 0, [], func,
segfunc)
xyzdv, connections = append_children_data(root_section,
len(xyzdv) - 1, xyzdv,
connections, func, segfunc)
self.xyzdv = array(xyzdv)
self.connections = array(connections)
def position(self, x, y, z):
soma.push()
for i in range(h.n3d()):
h.pt3dchange(i, x-self.x+h.x3d(i), y-self.y+h.y3d(i), z-self.z+h.z3d(i), h.diam3d(i))
self.x = x; self.y = y; self.z = z
h.pop_section()
def getCellParams(cell):
dirCell = dir(cell)
if 'all_sec' in dirCell:
secs = cell.all_sec
elif 'sec' in dirCell:
secs = [cell.sec]
elif 'allsec' in dir(h):
secs = [sec for sec in h.allsec()]
elif 'soma' in dirCell:
secs = [cell.soma]
else:
secs = []
# create dict with hname of each element in dir(cell)
dirCellHnames = {}
for dirCellName in dirCell:
try:
dirCellHnames.update({getattr(cell, dirCellName).hname(): dirCellName})
except:
pass
# create dict with dir(cell) name corresponding to each hname
dirCellSecNames = {}
for sec in secs:
dirCellSecNames.update({hname: name for hname,name in dirCellHnames.iteritems() if hname == sec.hname()})
secDic = {}
synMechs = []
for sec in secs:
# create new section dict with name of section
secName = getSecName(sec, dirCellSecNames)
if len(secs) == 1:
secName = 'soma' # if just one section rename to 'soma'
secDic[secName] = {'geom': {}, 'topol': {}, 'mechs': {}} # create dictionary to store sec info
# store geometry properties
standardGeomParams = ['L', 'nseg', 'diam', 'Ra', 'cm']
secDir = dir(sec)
for geomParam in standardGeomParams:
#if geomParam in secDir:
try:
secDic[secName]['geom'][geomParam] = sec.__getattribute__(geomParam)
except:
pass
# store 3d geometry
sec.push() # access current section so ismembrane() works
numPoints = int(h.n3d())
if numPoints:
points = []
for ipoint in range(numPoints):
x = h.x3d(ipoint)
y = h.y3d(ipoint)
z = h.z3d(ipoint)
diam = h.diam3d(ipoint)
points.append((x, y, z, diam))
secDic[secName]['geom']['pt3d'] = points
# store mechanisms
varList = mechVarList() # list of properties for all density mechanisms and point processes
ignoreMechs = ['dist'] # dist only used during cell creation
ignoreVars = [] #
mechDic = {}
ionDic = {}
for mech in dir(sec(0.5)):
if h.ismembrane(mech) and mech not in ignoreMechs: # check if membrane mechanism
if not mech.endswith('_ion'): # exclude ions
mechDic[mech] = {} # create dic for mechanism properties
varNames = [varName.replace('_'+mech, '') for varName in varList['mechs'][mech]]
varVals = []
for varName in varNames:
if varName not in ignoreVars:
try:
varVals = [seg.__getattribute__(mech).__getattribute__(varName) for seg in sec]
if len(set(varVals)) == 1:
varVals = varVals[0]
mechDic[mech][varName] = varVals
except:
pass
#print 'Could not read variable %s from mechanism %s'%(varName,mech)
# store ions
elif mech.endswith('_ion'):
ionName = mech.split('_ion')[0]
varNames = [varName.replace('_'+mech, '').replace(ionName,'') for varName in varList['mechs'][mech]]
varNames.append('e')
varVals = []
ionDic[ionName] = {} # create dic for mechanism properties
for varName in varNames:
varNameSplit = varName
if varName not in ignoreVars:
try:
varVals = [seg.__getattribute__(varNameSplit+ionName) for seg in sec]
if len(set(varVals)) == 1:
varVals = varVals[0]
ionDic[ionName][varNameSplit] = varVals
except:
pass
#print 'Could not read variable %s from mechanism %s'%(varName,mech)
secDic[secName]['mechs'] = mechDic
if len(ionDic)>0:
secDic[secName]['ions'] = ionDic
# add synapses and point neurons
# for now read fixed params, but need to find way to read only synapse params
pointps = {}
for seg in sec:
for ipoint,point in enumerate(seg.point_processes()):
pointpMod = point.hname().split('[')[0]
varNames = varList['pointps'][pointpMod]
if any([s in pointpMod.lower() for s in ['syn', 'ampa', 'gaba', 'nmda', 'glu']]):
#if 'synMech' in pptype.lower(): # if syn in name of point process then assume synapse
synMech = {}
synMech['label'] = pointpMod + '_' + str(len(synMechs))
synMech['mod'] = pointpMod
#synMech['loc'] = seg.x
for varName in varNames:
try:
synMech[varName] = point.__getattribute__(varName)
except:
print 'Could not read variable %s from synapse %s'%(varName,synMech['label'])
if not [_equal_dicts(synMech, synMech2, ignore_keys=['label']) for synMech2 in synMechs]:
synMechs.append(synMech)
else: # assume its a non-synapse point process
pointpName = pointpMod + '_'+ str(len(pointps))
pointps[pointpName] = {}
pointps[pointpName]['mod'] = pointpMod
pointps[pointpName]['loc'] = seg.x
for varName in varNames:
try:
pointps[pointpName][varName] = point.__getattribute__(varName)
# special condition for Izhi model, to set vinit=vr
# if varName == 'vr': secDic[secName]['vinit'] = point.__getattribute__(varName)
except:
print 'Could not read %s variable from point process %s'%(varName,pointpName)
if pointps: secDic[secName]['pointps'] = pointps
# store topology (keep at the end since h.SectionRef messes remaining loop)
secRef = h.SectionRef(sec=sec)
if secRef.has_parent():
secDic[secName]['topol']['parentSec'] = getSecName(secRef.parent().sec, dirCellSecNames)
secDic[secName]['topol']['parentX'] = h.parent_connection()
secDic[secName]['topol']['childX'] = h.section_orientation()
h.pop_section() # to prevent section stack overflow
# store section lists
secLists = h.List('SectionList')
if int(secLists.count()):
secListDic = {}
for i in xrange(int(secLists.count())): # loop over section lists
hname = secLists.o(i).hname()
if hname in dirCellHnames: # use python variable name
secListName = dirCellHnames[hname]
else:
secListName = hname
secListDic[secListName] = [getSecName(sec, dirCellSecNames) for sec in secLists.o(i)]
else:
secListDic = {}
# celsius warning
if hasattr(h, 'celsius'):
if h.celsius != 6.3: # if not default value
print "Warning: h.celsius=%.4g in imported file -- you can set this value in simConfig['hParams']['celsius']"%(h.celsius)
# clean
h.initnrn()
del(cell) # delete cell
import gc; gc.collect()
return secDic, secListDic, synMechs
def calc_seg_coords(self):
"""Calculate segment coordinates from 3d point coordinates"""
ix = 0 # segment index
p3dsoma = self.get_soma_pos()
self.psoma = p3dsoma
p0 = np.zeros(
(3, self.nseg)) # hold the coordinates of segment starting points
p1 = np.zeros(
(3, self.nseg)) # hold the coordinates of segment end points
d0 = np.zeros(self.nseg)
d1 = np.zeros(self.nseg)
for sec in self.hobj.all:
n3d = int(h.n3d()) # get number of n3d points in each section
p3d = np.zeros(
(3, n3d)
) # to hold locations of 3D morphology for the current section
l3d = np.zeros(
n3d
) # to hold locations of 3D morphology for the current section
diam3d = np.zeros(n3d) # to diameters
for i in range(n3d):
p3d[0, i] = h.x3d(i) - p3dsoma[0]
p3d[1, i] = h.y3d(i) - p3dsoma[
1] # shift coordinates such to place soma at the origin.
p3d[2, i] = h.z3d(i) - p3dsoma[2]
diam3d[i] = h.diam3d(i)
l3d[i] = h.arc3d(i)
l3d /= sec.L # normalize
nseg = sec.nseg
l0 = np.zeros(nseg) # keep range of segment starting point
l1 = np.zeros(nseg) # keep range of segment ending point
for iseg, seg in enumerate(sec):
l0[iseg] = seg.x - 0.5 * 1 / nseg # x (normalized distance along the section) for the beginning of the segment
l1[iseg] = seg.x + 0.5 * 1 / nseg # x for the end of the segment
p0[0, ix:ix + nseg] = np.interp(l0, l3d, p3d[0, :])
p0[1, ix:ix + nseg] = np.interp(l0, l3d, p3d[1, :])
p0[2, ix:ix + nseg] = np.interp(l0, l3d, p3d[2, :])
d0[ix:ix + nseg] = np.interp(l0, l3d, diam3d[:])
p1[0, ix:ix + nseg] = np.interp(l1, l3d, p3d[0, :])
p1[1, ix:ix + nseg] = np.interp(l1, l3d, p3d[1, :])
p1[2, ix:ix + nseg] = np.interp(l1, l3d, p3d[2, :])
d1[ix:ix + nseg] = np.interp(l1, l3d, diam3d[:])
ix += nseg
self.seg_coords = {}
self.seg_coords['p0'] = p0
self.seg_coords['p1'] = p1
self.seg_coords['d0'] = d0
self.seg_coords['d1'] = d1
return self.seg_coords
def writeNeuronToJson(filename='neuron', directory='neuron'):
"""
Create a JSON file of the morphology of the currently loaded neuron.
The position of each compartment are stored along with the diameter
at each of those positions. Each section is seperated with a row of zeros.
:param str filename: Filename.
:param str directory: Relative or full directory address.
"""
if not os.path.exists(directory):
os.makedirs(directory)
filename, ext = os.path.splitext(filename)
filename = filename + '.js'
filename = directory + '/' + filename
x = []
y = []
z = []
diam = []
arrayLength = 0
for sec in h.allsec():
arrayLength += int(h.n3d())
# Create a gap in the array to seperate sections.
arrayLength += 1
x = np.zeros(arrayLength)
y = np.zeros(arrayLength)
z = np.zeros(arrayLength)
diam = np.zeros(arrayLength)
indx = 0
for sec in h.allsec():
for i in xrange(int(h.n3d())):
x[indx] = h.x3d(i)
y[indx] = h.y3d(i)
z[indx] = h.z3d(i)
diam[indx] = h.diam3d(i)
indx += 1
indx += 1
x = np.zeros(arrayLength)
y = np.zeros(arrayLength)
z = np.zeros(arrayLength)
diam = np.zeros(arrayLength)
indx = 0
for sec in h.allsec():
for i in xrange(int(h.n3d())):
x[indx] = h.x3d(i)
y[indx] = h.y3d(i)
z[indx] = h.z3d(i)
diam[indx] = h.diam3d(i)
indx += 1
indx += 1
if len(diam) == 0:
print "No sections found."
return
data = { \
'x': x.tolist(), \
'y': y.tolist(), \
'z': z.tolist(), \
'diam': diam.tolist(), \
}
dataString = json.dumps(data)
f = open(filename, 'w')
f.write(dataString)
f.close()
def __set_3Dshape(self):
# set 3D shape of soma by calling shape_soma from class Cell
# print "WARNING: You are setting 3d shape geom. You better be doing"
# print "gui analysis and not numerical analysis!!"
self.shape_soma()
# soma proximal coords
x_prox = 0
y_prox = 0
# soma distal coords
x_distal = 0
y_distal = self.soma.L
# dend 0-3 are major axis, dend 4 is branch
# deal with distal first along major cable axis
# the way this is assigning variables is ugly/lazy right now
for i in range(0, 4):
h.pt3dclear(sec=self.list_dend[i])
# x_distal and y_distal are the starting points for each segment
# these are updated at the end of the loop
sec=self.list_dend[i]
h.pt3dadd(0, y_distal, 0, sec.diam, sec=sec)
# update x_distal and y_distal after setting them
# x_distal += dend_dx[i]
y_distal += sec.L
# add next point
h.pt3dadd(0, y_distal, 0, sec.diam, sec=sec)
# now deal with dend 4
# dend 4 will ALWAYS be positioned at the end of dend[0]
h.pt3dclear(sec=self.list_dend[4])
# activate this section with 'sec=self.list_dend[i]' notation
x_start = h.x3d(1, sec=self.list_dend[0])
y_start = h.y3d(1, sec=self.list_dend[0])
sec=self.list_dend[4]
h.pt3dadd(x_start, y_start, 0, sec.diam, sec=sec)
# self.dend_L[4] is subtracted because lengths always positive,
# and this goes to negative x
h.pt3dadd(x_start-sec.L, y_start, 0, sec.diam, sec=sec)
# now deal with proximal dends
for i in range(5, 8):
h.pt3dclear(sec=self.list_dend[i])
# deal with dend 5, ugly. sorry.
sec=self.list_dend[5]
h.pt3dadd(x_prox, y_prox, 0, sec.diam, sec=sec)
y_prox += -sec.L
h.pt3dadd(x_prox, y_prox, 0, sec.diam,sec=sec)
# x_prox, y_prox are now the starting points for BOTH of last 2 sections
# dend 6
# Calculate x-coordinate for end of dend
sec=self.list_dend[6]
dend6_x = -sec.L * np.sqrt(2) / 2.
h.pt3dadd(x_prox, y_prox, 0, sec.diam, sec=sec)
h.pt3dadd(dend6_x, y_prox-sec.L * np.sqrt(2) / 2.,
0, sec.diam, sec=sec)
# dend 7
# Calculate x-coordinate for end of dend
sec=self.list_dend[7]
dend7_x = sec.L * np.sqrt(2) / 2.
h.pt3dadd(x_prox, y_prox, 0, sec.diam, sec=sec)
h.pt3dadd(dend7_x, y_prox-sec.L * np.sqrt(2) / 2.,
0, sec.diam, sec=sec)
# set 3D position
# z grid position used as y coordinate in h.pt3dchange() to satisfy
# gui convention that y is height and z is depth. In h.pt3dchange()
# x and z components are scaled by 100 for visualization clarity
self.soma.push()
for i in range(0, int(h.n3d())):
h.pt3dchange(i, self.pos[0]*100 + h.x3d(i), -self.pos[2] + h.y3d(i),
self.pos[1] * 100 + h.z3d(i), h.diam3d(i))
h.pop_section()
def graph(self):
#Function: graph
#Input: self
#Process: create dendrite branch network
#Output: neuron
self.dendsegs = numpy.array([self.coordinates[:,0], self.coordinates[:,2], self.coordinates[:,3],self.coordinates[:,4],self.coordinates[:,5],self.coordinates[:,6]])
self.seglist = numpy.array(self.coordinates[:,0]-1,dtype=int)
self.segmap = numpy.array(self.coordinates[:,6]-1,dtype=int)
if self.seglist[0] == 1:
self.seglist = numpy.array(self.seglist-1,dtype=int)
self.segmap = numpy.array(self.segmap-1,dtype=int)
#-----------------------------------------------------------------------------------------------------------------------------------------------
self.compartmentdict = {}
segvals = []
Gcompartment = []
#-----------------------------------------------------------------------------------------------------------------------------------------------
for c in range(len(self.seglist)):
#-----------------------------------------------------------------------------------------------------------------------------------------------
if self.segmap[c] < self.seglist[c] - 1:
if len(segvals) == 0:
continue
i = c
self.compartmentdict[i] = [Gcompartment,h.Section(name='compartment',cell=self),segvals]
Gcompartment = []
segvals = []
#-----------------------------------------------------------------------------------------------------------------------------------------------
if c == len(self.seglist) - 1:
if len(segvals) == 0:
break
i = c
self.compartmentdict[i] = [Gcompartment,h.Section(name='compartment',cell=self),segvals]
Gcompartment = []
segvals = []
#-----------------------------------------------------------------------------------------------------------------------------------------------
else:
segvals.append([self.dendsegs[1,c]*1/125.0,self.dendsegs[2,c]*1/125.0,self.dendsegs[3,c]*1/125.0,self.dendsegs[4,c]*1/125.0])
Gcompartment.append(self.seglist[c])
#-----------------------------------------------------------------------------------------------------------------------------------------------
for key in self.compartmentdict.keys():
if len(self.compartmentdict[key][2]) > 0:
s = self.compartmentdict[key][2][0]
e = self.compartmentdict[key][2][-1]
if distance.euclidean(s[0:2],e[0:2]) == 0:
h.pt3dadd(s[0],s[1],s[2],s[3],sec=self.compartmentdict[key][1])
h.pt3dadd(e[0] + 1e-5,e[1] + 1e-5,e[2] + 1e-5,e[3],sec=self.compartmentdict[key][1])
else:
h.pt3dadd(s[0],s[1],s[2],s[3],sec=self.compartmentdict[key][1])
h.pt3dadd(e[0],e[1],e[2],e[3],sec=self.compartmentdict[key][1])
#-----------------------------------------------------------------------------------------------------------------------------------------------
for key in self.compartmentdict.keys():
for part in self.compartmentdict.keys():
if key in self.compartmentdict[part][0]:
self.compartmentdict[key][1].connect(self.compartmentdict[part][1])
#-----------------------------------------------------------------------------------------------------------------------------------------------
for dendID in self.compartmentdict.keys():
n3dID = int(h.n3d(sec=self.compartmentdict[dendID][1]))
for n in range(n3dID):
self.dendgraph[dendID] = numpy.array([float(h.x3d(n,sec=self.compartmentdict[dendID][1])),float(h.y3d(n,sec=self.compartmentdict[dendID][1])),float(h.z3d(n,sec=self.compartmentdict[dendID][1]))])