def findCenterOfSoma(self):
'''
Method find start point for work main algorithm
first point should be in soma. Soma is the
biggest segment of cell.
'''
iter = 0
temp_points = []
slices = []
for p in range(len(self.vertices)):
temp_points.append(HelpPoint(p,0))
slice = Slice(temp_points,self.faces)
slices.append(slice)
while len(slice) != 0:
temp_points = filter(lambda p: not slice.__contains__(p), temp_points)
slice = None
slice = Slice(temp_points,self.faces)
if len(slice) != 0:
slices.append(slice)
print len(temp_points)
#slice.printSlice()
#print slice.getPerimetr(self.vertices)
perimiter_coll = sorted(slices,key=lambda slice:slice.getPerimetr(self.vertices), reverse=True)
startSlice = Slice(perimiter_coll[0],self.faces)
self.start_center_point = self.__getCenterPoint(startSlice)
self.start_center_point.diametr = 2 * self.start_center_point.len_between_point(self.vertices[perimiter_coll[0][0].point])
def __more4AdjacentPointCase(self, adjacentPoints, slice, isBrunch,iteration, current_point, center_point):
'''
Work when algorithm find more that 4 adjacent points
'''
branchesCollection = self.__fillUpBrachesCollection(adjacentPoints, slice)
if len(branchesCollection) >= 2 :
center_points = {}
thirdBrunchCollection = []
for branch in branchesCollection:
branch_center_point = self.__getCenterPoint(branch)
center_points[branch_center_point] = branch
for branch_center_point,branch in center_points.items():
self.find_point(branch_center_point,iteration,current_point,True,True, _slice=branch)
if len(adjacentPoints) > 6:
thirdBrunchCollection.extend(branch)
thirdBrunchPoints = [HelpPoint(p.point,self.vertices[p.point].len_between_point(center_point)) \
for p in thirdBrunchCollection if not slice.__contains__(p)]
slice_t = Slice(thirdBrunchPoints, self.faces)
if len(slice_t) == 4:
third_brunch_center_point = self.__getCenterPoint(slice_t)
self.find_point(third_brunch_center_point,iteration, current_point,True,True, _slice=slice_t)
return True
elif len(branchesCollection) == 0 or (len(branchesCollection) == 1 and not isBrunch):
sortedadjacentPoints = sorted(adjacentPoints,key=lambda p:p.lenght)
first_slice = Slice(sortedadjacentPoints,self.faces)
second_slice = Slice(filter(lambda p: first_slice.__contains__(p) == False, sortedadjacentPoints),self.faces)
perimeter_1 = first_slice.getPerimetr(self.vertices)
perimeter_2 = second_slice.getPerimetr(self.vertices)
if perimeter_1 > perimeter_2 and perimeter_2 != 0:
new_center_point = self.__getCenterPoint(second_slice)
self.find_point(new_center_point,iteration, current_point,False,False, _slice=second_slice)
return True
elif perimeter_1 < perimeter_2 or perimeter_2 == 0:
if perimeter_1 == 0:
if len(branchesCollection) == 1:
first_slice = branchesCollection[0]
else:
first_slice.getFaceFromColl(adjacentPoints,self.faces)
new_center_point = self.__getCenterPoint(first_slice)
self.find_point(new_center_point,iteration, current_point,isBrunch,False, _slice=first_slice)
else:
new_center_point = self.__getCenterPoint(first_slice)
self.find_point(new_center_point,iteration, current_point,False,False, _slice=first_slice)
return True
elif len(branchesCollection) == 1 and isBrunch:
slice = branchesCollection[0]
if len(slice) == 0:
slice = slice.getFaceFromColl(adjacentPoints,self.faces)
new_center_point = self.__getCenterPoint(slice)
self.find_point(new_center_point,iteration, parentPoint=current_point,isNeurite=True,isBrunchStart=False, _slice=slice)
return True
return False
def __checkDendrite(self, slice, center_point, vector_len, current_point):
'''
Private Method.
Check if soma has other output processes
if it's contain than run find_point for it.
'''
iteration = 1
vector_len = filter(lambda p: slice.__contains__(p) == False
and self.checked_points.__contains__(p.point) == False, vector_len)
vector_len = sorted(vector_len,key=lambda p:p.lenght)
for i in range(5):
slice2 = Slice(vector_len,self.faces)
if (len(slice2) == 4 and
int(slice.getPerimetr(self.vertices) / slice2.getPerimetr(self.vertices)) <= 1 and
int(slice2.getPerimetr(self.vertices) / slice.getPerimetr(self.vertices)) <= 1):
new_center_point = self.__getCenterPoint(slice2)
iteration += 1
self.find_point(new_center_point,iteration,parentPoint=current_point,isNeurite=False,isBrunchStart=False, _slice=slice2)
vector_len = filter(lambda p: slice2.__contains__(p) == False
and self.checked_points.__contains__(p.point) == False, vector_len)
vector_len = sorted(vector_len, key=lambda p:p.lenght)
