def additional_nodes(connecting_points):
#Create pointset
extra_nodes = Pointset(3)
for i in range(len(connecting_points)):
for j in range(len(connecting_points)):
if 0 < connecting_points[i].Distance(connecting_points[j]) < 4:
#Merge points
extra_nodes.Append(
(connecting_points[i] + connecting_points[j]) / 2)
for i in range(len(connecting_points)):
#Create copy
connecting_points_copy = connecting_points.Copy()
#Remove all from copy to avoid distance = 0.
connecting_points_copy.RemoveAll(connecting_points[i])
if np.sum(
(connecting_points[i].Distance(connecting_points_copy)) < 4) == 0:
extra_nodes.Append(connecting_points[i])
new_nodes = extra_nodes
return new_nodes
def convert_2d_point_to_3d_point(center_point, vec1, vec2, pointset_2d_points):
"""
Given a pointset containing 2D points (y,x), a center point (z,y,x), and two vectors which
describe the orientation of the slice inside the 3D volume, the algorithm
will convert the 2D points to 3D points.
"""
if pointset_2d_points.__class__ == Point:
temp = Pointset(2)
temp.Append(pointset_2d_points)
pointset_2d_points = temp
#Pointset to store 3D points
pointset_3d_points = Pointset(3)
for i in range(len(pointset_2d_points)):
#Shift from point 127.5,127.5 which is the rotation point
y_shift = pointset_2d_points[i][1] - 127.5
x_shift = pointset_2d_points[i][0] - 127.5
center = Point(center_point[2], center_point[1], center_point[0])
point_3d = center + y_shift * vec1 + x_shift * vec2
point_3d = Point(point_3d[2], point_3d[1], point_3d[0])
pointset_3d_points.Append(point_3d)
return pointset_3d_points
def check_for_possible_bifurcation(average_radius, center_point_3d_with_radius,\
rotation_point ,found_bifurcation, global_direction):
"""
This function tracks the radius of the stent. If the radius drops to less
than 75%, the bifurcation might have been found. If so, two new starting points will be
calculated.
"""
#Initially no new starting positions.
new_starting_positions = []
#Easier notation in rotation matrix
gd = global_direction
#To avoid wrong predictions on an early error in radius
if len(average_radius) > 10:
if 0.75*np.mean(average_radius) > center_point_3d_with_radius.r \
and not found_bifurcation:
if center_point_3d_with_radius.Distance(
rotation_point) > 0.25 * np.mean(average_radius):
#found bifurcation
found_bifurcation = True
#calculate new starting points.
new_starting_positions = Pointset(3)
#vector of first branch
fb_vector = np.mat(
[[center_point_3d_with_radius[2] - rotation_point[2]],
[center_point_3d_with_radius[1] - rotation_point[1]],
[center_point_3d_with_radius[0] - rotation_point[0]]])
#Create rotation matrix to rotate vector
rotation_matrix = np.mat(
[[2 * gd[0]**2 - 1, 2 * gd[0] * gd[1], 2 * gd[0] * gd[2]],
[2 * gd[1] * gd[2], 2 * gd[1]**2 - 1, 2 * gd[1] * gd[2]],
[2 * gd[2] * gd[0], 2 * gd[1] * gd[2], 2 * gd[2]**2 - 1]])
#second branch
sb = rotation_matrix * fb_vector
sb_center_point = rotation_point + Point(sb[2], sb[1], sb[0])
#Return new starting positions
new_starting_positions.Append(center_point_3d_with_radius)
new_starting_positions.Append(sb_center_point)
#Add radius to list with radia
if not center_point_3d_with_radius.r == []:
average_radius.append(center_point_3d_with_radius.r)
return average_radius, found_bifurcation, new_starting_positions
def check_for_nodes(connecting_points, slice_i_plus_1):
"""
Given a set of stent points, the algorithm checks whether there are any
duplicates. A duplicate would mean that that point was found by two stent
points and could therefore be a node. An additional check is done to check
whether there are no connecting points above the potential node. If this is
the case, than the point is not a node.
"""
#Pointset to store 2D nodes
point_nodes = Pointset(2)
#Pointset to store point which need to be removed
point_remove = Pointset(2)
#points in slice_i_plus_1
points_check = stentPoints2d.detect_points(slice_i_plus_1)
#For every connecting point
for i in range(len(connecting_points)):
for j in range(len(connecting_points)):
#if points are the same
if connecting_points[i].Distance(
connecting_points[j]) <= 3 and i != j:
#check if this point would find a connecting point
point = Pointset(2)
point.Append(connecting_points[i])
node_check, unused = find_connecting_points(
point, points_check)
#Only add node once.
if not node_check:
if not point_nodes:
point_nodes.Append(
(connecting_points[i] + connecting_points[j]) / 2)
elif point_nodes.Contains(connecting_points[i]) == False:
point_nodes.Append(
(connecting_points[i] + connecting_points[j]) / 2)
#The connecting points need to be removed later
point_remove.append(connecting_points[i])
point_remove.append(connecting_points[i])
return point_nodes, point_remove
def find_connecting_points(pointset_slice_i, pointset_slice_i_plus_1):
"""
Given a set of points in slice i, the algorithm will calculate distances
between these points and the points in slice i+1. If this distance is less
than a certain distance, the point in slice i+1 is returned as connecting
point. If there is no connecting point found, a virtual point is created.
"""
#Maximum distance for which a point is seen as connecting
max_distance = ssdf._stent_tracking_params.max_dist
#Pointsets to store points
connecting_points = Pointset(2)
virtual_points = Pointset(2)
#for each point in slice i
for i in range(len(pointset_slice_i)):
distances = pointset_slice_i[i, :] - pointset_slice_i_plus_1[:, :]
#for all distances from this point
for j in range(len(distances)):
#if distance is smaller or equal to the max distance
if abs(distances[j, 0]) + abs(distances[j, 1]) <= max_distance:
#make the point a connecting point
connecting_points.Append(pointset_slice_i_plus_1[j])
#if the point from slice i has no connecting point
if len(
np.where(
abs(distances[:, 0]) +
abs(distances[:, 1]) <= max_distance)[0]) == 0:
#change the point from slice i into a virtual point
virtual_points.Append(pointset_slice_i[i])
return connecting_points, virtual_points
def select_stent(volnr, params=None):
"""
This functions calls the stent extration function. It contains seed points
for each dataset
"""
if params is None:
params = getDefaultParams()
ssdf._stent_tracking_params = params
if volnr == 1:
#vol 1
vol, sampling, origin = load_volume(1)
seed_points = Pointset(3)
seed_points.Append(60, 110, 133)
seed_points.Append(100, 75, 150)
seed_points.Append(160, 70, 148)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 2:
#vol 2
vol, sampling, origin = load_volume(2)
seed_points = Pointset(3)
seed_points.Append(60, 175, 155)
seed_points.Append(100, 150, 170)
seed_points.Append(165, 140, 167)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 3:
#vol 3
vol, sampling, origin = load_volume(3)
seed_points = Pointset(3)
seed_points.Append(47, 160, 140)
seed_points.Append(80, 145, 130)
seed_points.Append(130, 130, 128)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 4:
#vol 4
vol, sampling, origin = load_volume(4)
seed_points = Pointset(3)
seed_points.Append(40, 160, 160)
seed_points.Append(140, 145, 135)
seed_points.Append(150, 150, 150)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 5:
#vol 5
vol, sampling, origin = load_volume(5)
seed_points = Pointset(3)
seed_points.Append(34, 150, 170)
seed_points.Append(60, 135, 180)
seed_points.Append(130, 140, 180)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 6:
#vol 6
vol, sampling, origin = load_volume(6)
seed_points = Pointset(3)
seed_points.Append(40, 170, 175)
seed_points.Append(70, 160, 180)
seed_points.Append(140, 142, 168)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 7:
#vol 7
vol, sampling, origin = load_volume(7)
seed_points = Pointset(3)
seed_points.Append(40, 180, 160)
seed_points.Append(110, 160, 160)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 8:
#vol 8
vol, sampling, origin = load_volume(8)
seed_points = Pointset(3)
seed_points.Append(60, 130, 190)
seed_points.Append(80, 110, 180)
seed_points.Append(120, 112, 140)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
elif volnr == 18:
#vol 18
vol, sampling, origin = load_volume(18)
seed_points = Pointset(3)
seed_points.Append(70, 170, 140)
seed_points.Append(135, 150, 160)
node_points_stent, center_points_stent, stent_points_stent = stent_detection(
vol, sampling, origin, seed_points)
else:
raise ValueError('Invalid volnr')
plot = True
if plot:
points = Pointset(3)
for i in range(len(node_points_stent)):
points.Append(node_points_stent[i][2], node_points_stent[i][1],
node_points_stent[i][0])
points_2 = Pointset(3)
for i in range(len(stent_points_stent)):
points_2.Append(stent_points_stent[i][2], stent_points_stent[i][1],
stent_points_stent[i][0])
vv.closeAll()
vv.volshow(vol)
vv.plot(points_2, ls='', ms='.', mc='g', mw=4, alpha=0.5)
vv.plot(points, ls='', ms='.', mc='b', mw=4, alpha=0.9)
graph = from_nodes_to_graph(node_points_stent)
return graph
def stent_detection(vol, sampling, origin, seed_points):
"""
This is the function that will be called in order to extract the stent
from the CT data.
"""
#Point set where the final points will be stored. In node, the 4th number
#indicates the ring number, the 5th indicates the direction where it is found
node_points_stent = Pointset(5)
center_points_stent = Pointset(3)
stent_points_stent = Pointset(3)
#Initially, the bifurcation is not found
found_bifurcation = False
average_radius = []
#start with ring 1
ring = 1
#Weighting factor alpha
alpha = ssdf._stent_tracking_params.weighting_factor
distance = ssdf._stent_tracking_params.distance
#From seed point to seed point except for the last seed point, where the
#bifurcation needs to be found.
for i in range(len(seed_points) - 2):
round = 0
#Don't look for the bifurcation when not connecting points in the last
#part of the stent
look_for_bifurcation = False
#Get initial center point and direction using the seed points
center_point, global_direction = initial_center_point(
vol, seed_points[i], seed_points[i + 1], sampling, origin, alpha)
#While the center point has not passed the seed point
while center_point[0] < seed_points[i + 1][0] and round < 10:
#Find stent, node and center points for a certain stent ring
node_points_ring, stent_points_ring, center_points_ring, \
jump_location, jump_direction, found_bifurcation, new_starting_positions, \
ring = searching_for_ring(vol, sampling, center_point, global_direction,\
look_for_bifurcation, average_radius, alpha, ring)
#Set new starting center point inside the new ring
center_point = jump_location + distance * Point(
jump_direction[2], jump_direction[1], jump_direction[0])
global_direction = jump_direction
#Add points to point sets
node_points_stent.Extend(node_points_ring)
center_points_stent.Extend(center_points_ring)
stent_points_stent.Extend(stent_points_ring)
round = round + 1
#For the last part of the stent where the bifurcation needs to be found
for i in range(len(seed_points) - 2, len(seed_points) - 1):
#Reset round to zero
round = 0
look_for_bifurcation = True
center_point, global_direction = initial_center_point(vol, seed_points[i],\
seed_points[i+1], sampling, origin, alpha)
#While the bifurcation is not found
while found_bifurcation == False and round < 10:
node_points_ring, stent_points_ring, center_points_ring, \
jump_location, jump_direction, found_bifurcation, new_starting_positions, \
ring = searching_for_ring(vol, sampling, center_point, global_direction, \
look_for_bifurcation, average_radius, alpha, ring)
center_point = jump_location + distance * Point(
jump_direction[2], jump_direction[1], jump_direction[0])
global_direction = jump_direction
#Add points to point sets
node_points_stent.Extend(node_points_ring)
center_points_stent.Extend(center_points_ring)
stent_points_stent.Extend(stent_points_ring)
round = round + 1
#Store new starting positions in another poitset, because algorithm will
#return [] as new_starting_positions.
starting_positions = Pointset(3)
#For the case where there is no bifurcation present
try:
starting_positions.Append(
new_starting_positions[0]
) # + distance * Point(jump_direction[2],jump_direction[1],jump_direction[0]))
starting_positions.Append(
new_starting_positions[1]
) # + distance * Point(jump_direction[2],jump_direction[1],jump_direction[0]))
except IndexError:
[]
alpha = ssdf._stent_tracking_params.weighting_factor_bif
#Now points after the bifurcation will be found
for i in range(len(starting_positions)):
center_point = starting_positions[i]
look_for_bifurcation = False
round = 0
while round < 4:
node_points_ring, stent_points_ring, center_points_ring, \
jump_location, jump_direction, found_bifurcation, new_starting_positions, \
ring = searching_for_ring(vol, sampling, center_point, global_direction, \
look_for_bifurcation, average_radius, alpha, ring)
center_point = jump_location + distance * Point(
jump_direction[2], jump_direction[1], jump_direction[0])
global_direction = jump_direction
if 255 < center_point[0]:
break
#Add points to point sets
node_points_stent.Extend(node_points_ring)
center_points_stent.Extend(center_points_ring)
stent_points_stent.Extend(stent_points_ring)
round = round + 1
return node_points_stent, center_points_stent, stent_points_stent
def connecting_stent_points(vol, sampling, center_point, global_direction, look_for_bifurcation, \
average_radius, direction, expected_amount_of_nodes, points_in_slice, found_bifurcation, alpha, ring):
"""
This algorithm uses the earlier stated functions in order to connect points
and define nodes.
"""
#Nodes that are found for the current direction
node_points_direction = Pointset(3)
#Other pointsets to store points
center_points = Pointset(3)
stent_points = Pointset(3)
node_points = Pointset(5)
#Set round to 0 for the case that the amount of nodes criterion is not met.
round = 0
#Initial
new_starting_positions = []
#connecting points
while len(node_points_direction) < expected_amount_of_nodes and round < 12:
#Get slice
slice, center_point, global_direction, rotation_point, vec1, vec2, \
center_point_3d_with_radius = centerline_tracking.get_slice(vol, sampling, \
center_point, global_direction, look_for_bifurcation, alpha)
#If looking for the bifurcation, check radius
if look_for_bifurcation and direction == 1:
if not found_bifurcation:
average_radius, found_bifurcation, new_starting_positions \
= check_for_possible_bifurcation(average_radius, center_point_3d_with_radius, \
rotation_point, found_bifurcation, global_direction)
else:
new_starting_positions = []
#Find points
points_in_next_slice = stentPoints2d.detect_points(slice)
#Find connecting points. Change not connecting points into virtual points
connecting_points, virtual_points = find_connecting_points(points_in_slice, \
points_in_next_slice)
#Check if virtual points should be converted into connecting points
connecting_points, temp_slice = check_virtual_points(virtual_points, \
connecting_points, center_point, vol, sampling, global_direction, alpha)
#Check for nodes
point_nodes_2d, point_remove = check_for_nodes(connecting_points,
temp_slice)
#If nodes are found, these points should be deleted from the connecting points list
connecting_points = delete_nodes_from_list(connecting_points,
point_remove)
#Convert 2d points into 3d points
connecting_points_3d = convert_2d_point_to_3d_point(center_point, vec1,\
vec2, connecting_points)
point_nodes_3d = convert_2d_point_to_3d_point(center_point, vec1, vec2,\
point_nodes_2d)
#Add 3d points to their list
center_points.Append(rotation_point)
stent_points.Extend(connecting_points_3d)
node_points_direction.Extend(point_nodes_3d)
for i in range(len(point_nodes_3d)):
node_points.Append(
Point(point_nodes_3d[i][0], point_nodes_3d[i][1],
point_nodes_3d[i][2], ring, direction))
#Set connecting points as new base points
points_in_slice = connecting_points
#Next round
round = round + 1
#If there are three nodes found, do first one more run.
if len(node_points_direction) > 2:
diff = 10 - round
if diff > 0:
round = round + diff
if round == 12:
new_nodes = additional_nodes(connecting_points_3d)
for i in range(len(new_nodes)):
node_points.Append(
Point(new_nodes[i][0], new_nodes[i][1], new_nodes[i][2],
ring, direction))
return center_points, stent_points, node_points, global_direction, found_bifurcation, new_starting_positions, ring
def from_nodes_to_graph(node_points_stent):
"""
Given a set of nodes it creates a graph. The node set contains a ring number
(4th dimension) and direction (5th dimension)
"""
graph = Graph()
#Min and maximum distance when connecting nodes
min = 10
max = 18
for i in range(len(node_points_stent)):
#Take point
point = Point(node_points_stent[i][2], node_points_stent[i][1],
node_points_stent[i][0])
#Add node to graph
graph.AppendNode(point)
#Pointset to store possible matches
possible_match = Pointset(3)
for j in range(len(node_points_stent)):
if node_points_stent[j][3] == node_points_stent[i][
3] and node_points_stent[j][4] != node_points_stent[i][4]:
if min < point.Distance(
Point(node_points_stent[j][2], node_points_stent[j][1],
node_points_stent[j][0])) < max:
possible_match.Append(
Point(node_points_stent[j][2], node_points_stent[j][1],
node_points_stent[j][0]))
if len(possible_match) == 0:
continue
elif len(possible_match) == 1:
graph.AppendNode(possible_match[0])
graph.CreateEdge(graph[np.size(graph) - 2],
graph[np.size(graph) - 1])
elif len(possible_match) == 2:
graph.AppendNode(possible_match[0])
graph.AppendNode(possible_match[1])
graph.CreateEdge(graph[np.size(graph) - 1],
graph[np.size(graph) - 3])
graph.CreateEdge(graph[np.size(graph) - 2],
graph[np.size(graph) - 3])
else:
while True:
sorted = False
for j in range(len(possible_match) - 1):
if point.Distance(possible_match[j]) > point.Distance(
possible_match[j + 1]):
possible_match[j], possible_match[
j + 1] = possible_match[j + 1], possible_match[j]
sorted = True
if not sorted:
break
graph.AppendNode(possible_match[0])
graph.AppendNode(possible_match[1])
graph.CreateEdge(graph[np.size(graph) - 1],
graph[np.size(graph) - 3])
graph.CreateEdge(graph[np.size(graph) - 2],
graph[np.size(graph) - 3])
return graph