def loadThreeCompartmentModel(self):
# simple 3 compartment model
pnode = CompartmentNode(0, ca=1.9e-6, g_l=1.8e-3)
self.ctree = CompartmentTree(root=pnode)
cnode = CompartmentNode(1, ca=2.4e-6, g_l=0.3e-4, g_c=3.9)
self.ctree.addNodeWithParent(cnode, pnode)
lnode0 = CompartmentNode(2, ca=1.9e-6, g_l=0.3e-4, g_c=3.8e-3)
self.ctree.addNodeWithParent(lnode0, cnode)
def loadTwoCompartmentModel(self, w_locinds=True):
# simple two compartment model
pnode = CompartmentNode(0, ca=1.5e-5, g_l=2e-3)
self.ctree = CompartmentTree(root=pnode)
cnode = CompartmentNode(1, ca=2e-6, g_l=3e-4, g_c=4e-3)
self.ctree.addNodeWithParent(cnode, pnode)
if w_locinds:
self.addLocinds()
def loadMultiDendModel(self):
# simple 3 compartment model
pnode = CompartmentNode(0, ca=1.9e-6, g_l=1.8e-3)
self.ctree = CompartmentTree(root=pnode)
cnode0 = CompartmentNode(1, ca=2.4e-6, g_l=0.3e-4, g_c=3.9)
self.ctree.addNodeWithParent(cnode0, pnode)
cnode1 = CompartmentNode(2, ca=1.9e-6, g_l=0.4e-4, g_c=3.8e-3)
self.ctree.addNodeWithParent(cnode1, pnode)
cnode2 = CompartmentNode(3, ca=1.3e-6, g_l=0.5e-4, g_c=2.7e-2)
self.ctree.addNodeWithParent(cnode2, pnode)
def _initTree1(self):
# 1 2
# \ /
# 0
croot = CompartmentNode(0, loc_ind=0)
cnode1 = CompartmentNode(1, loc_ind=1)
cnode2 = CompartmentNode(2, loc_ind=2)
ctree = CompartmentTree(root=croot)
ctree.addNodeWithParent(cnode1, croot)
ctree.addNodeWithParent(cnode2, croot)
self.ctree = ctree
def loadTModel(self):
# simple T compartment model
# pnode = CompartmentNode(0, ca=1.5e-5, g_l=2e-3)
# self.ctree = CompartmentTree(root=pnode)
# cnode = CompartmentNode(1, ca=1.5e-6, g_l=2.5e-4, g_c=2e-3)
# self.ctree.addNodeWithParent(cnode, pnode)
# lnode0 = CompartmentNode(2, ca=1.5e-6, g_l=2.5e-4, g_c=2e-3)
# self.ctree.addNodeWithParent(lnode0, cnode)
# lnode1 = CompartmentNode(3, ca=1.5e-6, g_l=2.5e-4, g_c=2e-3)
# self.ctree.addNodeWithParent(lnode1, cnode)
pnode = CompartmentNode(0, ca=1.5e-5, g_l=2e-3)
self.ctree = CompartmentTree(root=pnode)
cnode = CompartmentNode(1, ca=2e-6, g_l=3e-4, g_c=4e-3)
self.ctree.addNodeWithParent(cnode, pnode)
lnode0 = CompartmentNode(2, ca=1.5e-6, g_l=2.5e-4, g_c=3e-3)
self.ctree.addNodeWithParent(lnode0, cnode)
lnode1 = CompartmentNode(3, ca=1.5e-6, g_l=2.5e-4, g_c=5e-3)
self.ctree.addNodeWithParent(lnode1, cnode)
def _initTree2(self):
# 3
# |
# 2
# |
# 1
# |
# 0
croot = CompartmentNode(0, loc_ind=0)
cnode1 = CompartmentNode(1, loc_ind=1)
cnode2 = CompartmentNode(2, loc_ind=2)
cnode3 = CompartmentNode(3, loc_ind=3)
ctree = CompartmentTree(root=croot)
ctree.addNodeWithParent(cnode1, croot)
ctree.addNodeWithParent(cnode2, cnode1)
ctree.addNodeWithParent(cnode3, cnode2)
self.ctree = ctree
def _initTree3(self):
# 4 5 6 7 8
# \|/ \ /
# 1 2 3
# \ | /
# \|/
# 0
cns = [CompartmentNode(ii, loc_ind=ii) for ii in range(9)]
ctree = CompartmentTree(root=cns[0])
# first order children
ctree.addNodeWithParent(cns[1], cns[0])
ctree.addNodeWithParent(cns[2], cns[0])
ctree.addNodeWithParent(cns[3], cns[0])
# second order children
ctree.addNodeWithParent(cns[4], cns[1])
ctree.addNodeWithParent(cns[5], cns[1])
ctree.addNodeWithParent(cns[6], cns[1])
ctree.addNodeWithParent(cns[7], cns[3])
ctree.addNodeWithParent(cns[8], cns[3])
self.ctree = ctree