def Fractal_Tree_3D(param):
"""This fuction creates the fractal tree.
Args:
param (Parameters object): this object contains all the parameters that define the tree. See the parameters module documentation for details:
Returns:
branches (dict): A dictionary that contains all the branches objects.
nodes (nodes object): the object that contains all the nodes of the tree.
"""
#Read Mesh
m=Mesh(param.meshfile)
#Define the initial direction
init_dir=(param.second_node-param.init_node)/np.linalg.norm(param.second_node-param.init_node)
#Initialize the nodes object, contains the nodes and all the distance functions
nodes=Nodes(param.init_node)
#Project the first node to the mesh.
point,tri=m.project_new_point(nodes.nodes[0])
if tri>=0:
init_tri=tri
else:
print 'initial point not in mesh'
sys.exit(0)
#Initialize the dictionary that stores the branches objects
branches={}
last_branch=0
#Compute the first branch
branches[last_branch]=Branch(m,0,init_dir,init_tri,param.init_length,0.0,0.0,nodes,[0],int(param.init_length/param.l_segment))
branches_to_grow=[]
branches_to_grow.append(last_branch)
ien=[]
for i_n in range(len(branches[last_branch].nodes)-1):
ien.append([branches[last_branch].nodes[i_n],branches[last_branch].nodes[i_n+1]])
#To grow fascicles
if param.Fascicles:
brother_nodes=[]
brother_nodes+=branches[0].nodes
for i_branch in range(len(param.fascicles_angles)):
last_branch+=1
angle=param.fascicles_angles[i_branch]
branches[last_branch]=Branch(m,branches[0].nodes[-1],branches[0].dir,branches[0].tri,param.fascicles_length[i_branch],angle,0.0,nodes,brother_nodes,int(param.fascicles_length[i_branch]/param.l_segment))
brother_nodes+=branches[last_branch].nodes
for i_n in range(len(branches[last_branch].nodes)-1):
ien.append([branches[last_branch].nodes[i_n],branches[last_branch].nodes[i_n+1]])
branches_to_grow=range(1,len(param.fascicles_angles)+1)
for i in range(param.N_it):
shuffle(branches_to_grow)
new_branches_to_grow=[]
for g in branches_to_grow:
angle=-param.branch_angle*np.random.choice([-1,1])
for j in range(2):
brother_nodes=[]
brother_nodes+=branches[g].nodes
if j>0:
brother_nodes+=branches[last_branch].nodes
#Add new branch
last_branch+=1
print last_branch
l=param.length+np.random.normal(0,param.std_length)
if l<param.min_length:
l=param.min_length
branches[last_branch]=Branch(m,branches[g].nodes[-1],branches[g].dir,branches[g].tri,l,angle,param.w,nodes,brother_nodes,int(param.length/param.l_segment))
#Add nodes to IEN
for i_n in range(len(branches[last_branch].nodes)-1):
ien.append([branches[last_branch].nodes[i_n],branches[last_branch].nodes[i_n+1]])
#Add to the new array
if branches[last_branch].growing:
new_branches_to_grow.append(last_branch)
branches[g].child[j]=last_branch
angle=-angle
branches_to_grow=new_branches_to_grow
if param.save:
if param.save_paraview:
from ParaviewWriter import write_line_VTU
print 'Finished growing, writing paraview file'
xyz=np.zeros((len(nodes.nodes),3))
for i in range(len(nodes.nodes)):
xyz[i,:]=nodes.nodes[i]
write_line_VTU(xyz, ien, param.filename + '.vtu')
np.savetxt(param.filename+'_ien.txt',ien,fmt='%d')
np.savetxt(param.filename+'_xyz.txt',xyz)
np.savetxt(param.filename+'_endnodes.txt',nodes.end_nodes,fmt='%d')
return branches,nodes
def Fractal_Tree_3D(param):
""" This fuction creates the fractal tree.
Args:
param (Parameters object): this object contains all the parameters that
define the tree. See the parameters module documentation for details:
Returns:
branches (dict): A dictionary that contains all the branches objects.
nodes (nodes object): the object that contains all the nodes of the tree.
"""
logger = logging.getLogger('fractal-tree')
# Read mesh
mesh = Mesh(param.input_file_name)
# Define the initial direction
init_dir = (param.second_node - param.init_node
) / np.linalg.norm(param.second_node - param.init_node)
#Initialize the nodes object, contains the nodes and all the distance functions
nodes = Nodes(param.init_node)
# Project the first node to the mesh.
point, tri = mesh.project_new_point(nodes.nodes[0])
if tri >= 0:
init_tri = tri
else:
logger.error('initial point not in mesh')
return None, None
#Initialize the dictionary that stores the branches objects
branches = {}
last_branch = 0
#Compute the first branch
branches[last_branch] = Branch(mesh, 0, init_dir, init_tri,
param.init_length, 0.0, 0.0, nodes, [0],
int(param.init_length / param.l_segment))
branches_to_grow = []
branches_to_grow.append(last_branch)
ien = []
for i_n in range(len(branches[last_branch].nodes) - 1):
ien.append([
branches[last_branch].nodes[i_n],
branches[last_branch].nodes[i_n + 1]
])
#To grow fascicles
if param.Fascicles:
brother_nodes = []
brother_nodes += branches[0].nodes
for i_branch in range(len(param.fascicles_angles)):
last_branch += 1
angle = param.fascicles_angles[i_branch]
branches[last_branch] = Branch(
mesh, branches[0].nodes[-1], branches[0].dir, branches[0].tri,
param.fascicles_length[i_branch], angle, 0.0, nodes,
brother_nodes,
int(param.fascicles_length[i_branch] / param.l_segment))
brother_nodes += branches[last_branch].nodes
for i_n in range(len(branches[last_branch].nodes) - 1):
ien.append([
branches[last_branch].nodes[i_n],
branches[last_branch].nodes[i_n + 1]
])
branches_to_grow = range(1, len(param.fascicles_angles) + 1)
## [DaveP] Fix xrange for python 3.5.
for i in range(param.N_it):
## [DaveP] Fix for python 3.5.
shuffle(list(branches_to_grow))
#shuffle(branches_to_grow)
new_branches_to_grow = []
for g in branches_to_grow:
angle = -param.branch_angle * np.random.choice([-1, 1])
for j in range(2):
brother_nodes = []
brother_nodes += branches[g].nodes
if j > 0:
brother_nodes += branches[last_branch].nodes
#Add new branch
last_branch += 1
#print last_branch
l = param.length + np.random.normal(0, param.std_length)
if l < param.min_length:
l = param.min_length
branches[last_branch] = Branch(
mesh, branches[g].nodes[-1], branches[g].dir,
branches[g].tri, l, angle, param.w, nodes, brother_nodes,
int(param.length / param.l_segment))
#Add nodes to IEN
for i_n in range(len(branches[last_branch].nodes) - 1):
ien.append([
branches[last_branch].nodes[i_n],
branches[last_branch].nodes[i_n + 1]
])
#Add to the new array
if branches[last_branch].growing:
new_branches_to_grow.append(last_branch)
branches[g].child[j] = last_branch
angle = -angle
branches_to_grow = new_branches_to_grow
if param.save:
if param.save_paraview:
from ParaviewWriter import write_line_VTU
logger.info('Finished growing, writing paraview file')
xyz = np.zeros((len(nodes.nodes), 3))
for i in range(len(nodes.nodes)):
xyz[i, :] = nodes.nodes[i]
write_line_VTU(xyz, ien, param.output_file_name + '.vtu')
np.savetxt(param.output_file_name + '_ien.txt', ien, fmt='%d')
np.savetxt(param.output_file_name + '_xyz.txt', xyz)
np.savetxt(param.output_file_name + '_endnodes.txt',
nodes.end_nodes,
fmt='%d')
return branches, nodes, ien
