/
fibers.py
executable file
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fibers.py
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""" fibers.py
This module contains code for representation of tractography using a
fixed-length parameterization.
class FiberArray
"""
import numpy
import vtk
import time
import whitematteranalysis as wma
class Fiber:
"""A class for fiber tractography data, represented with a fixed length"""
def __init__(self):
self.r = None
self.a = None
self.s = None
self.points_per_fiber = None
self.hemisphere_percent_threshold = 0.95
def get_equivalent_fiber(self):
""" Get the reverse order of current line (trajectory), as the
fiber can be equivalently represented in either order."""
fiber = Fiber()
fiber.r = self.r[::-1]
fiber.a = self.a[::-1]
fiber.s = self.s[::-1]
fiber.points_per_fiber = self.points_per_fiber
return fiber
def get_reflected_fiber(self):
""" Returns reflected version of current fiber by reflecting
fiber across midsagittal plane. Just sets output R coordinate to -R."""
fiber = Fiber()
fiber.r = - self.r
fiber.a = self.a
fiber.s = self.s
fiber.points_per_fiber = self.points_per_fiber
return fiber
def match_order(self, other):
""" Reverse order of fiber to match this one if needed """
# compute correlation
corr = numpy.multiply(self.r, other.r) + \
numpy.multiply(self.a, other.a) + \
numpy.multiply(self.s, other.s)
other2 = other.get_equivalent_fiber()
corr2 = numpy.multiply(self.r, other2.r) + \
numpy.multiply(self.a, other2.a) + \
numpy.multiply(self.s, other2.s)
if numpy.sum(corr) > numpy.sum(corr2):
return other
else:
return other2
def __add__(self, other):
"""This is the + operator for fibers"""
other_matched = self.match_order(other)
fiber = Fiber()
fiber.r = self.r + other_matched.r
fiber.a = self.a + other_matched.a
fiber.s = self.s + other_matched.s
return fiber
def __div__(self, other):
""" This is to divide a fiber by a number"""
fiber = Fiber()
fiber.r = numpy.divide(self.r, other)
fiber.a = numpy.divide(self.a, other)
fiber.s = numpy.divide(self.s, other)
return fiber
def __mul__(self, other):
""" This is to multiply a fiber by a number"""
fiber = Fiber()
fiber.r = numpy.multiply(self.r, other)
fiber.a = numpy.multiply(self.a, other)
fiber.s = numpy.multiply(self.s, other)
return fiber
def __subtract__(self, other):
"""This is the - operator for fibers"""
other_matched = self.match_order(other)
fiber = Fiber()
fiber.r = self.r - other_matched.r
fiber.a = self.a - other_matched.a
fiber.s = self.s - other_matched.s
#fiber.r = self.r + other_matched.r
#fiber.a = self.a + other_matched.a
#fiber.s = self.s + other_matched.s
return fiber
class FiberArray:
"""A class for arrays of fiber tractography data, represented with
a fixed length"""
def __init__(self):
# parameters
self.points_per_fiber = 10
self.verbose = 0
# fiber data
self.fiber_array_r = None
self.fiber_array_a = None
self.fiber_array_s = None
# output arrays indicating hemisphere/callosal (L,C,R= -1, 0, 1)
self.fiber_hemisphere = None
self.hemispheres = False
# output boolean arrays for each hemisphere and callosal fibers
self.is_left_hem = None
self.is_right_hem = None
self.is_commissure = None
# output indices of each type above
self.index_left_hem = None
self.index_right_hem = None
self.index_commissure = None
self.index_hem = None
# output totals of each type also
self.number_of_fibers = 0
self.number_left_hem = None
self.number_right_hem = None
self.number_commissure = None
def __str__(self):
output = "\n points_per_fiber\t" + str(self.points_per_fiber) \
+ "\n number_of_fibers\t\t" + str(self.number_of_fibers) \
+ "\n fiber_hemisphere\t\t" + str(self.fiber_hemisphere) \
+ "\n verbose\t" + str(self.verbose)
return output
def _calculate_line_indices(self, input_line_length, output_line_length):
""" Figure out indices for downsampling of polyline data.
The indices include the first and last points on the line,
plus evenly spaced points along the line. This code figures
out which indices we actually want from a line based on its
length (in number of points) and the desired length.
"""
# this is the increment between output points
step = (input_line_length - 1.0) / (output_line_length - 1.0)
# these are the output point indices (0-based)
ptlist = []
for ptidx in range(0, output_line_length):
#print(ptidx*step)
ptlist.append(ptidx * step)
# test
if __debug__:
# this tests we output the last point on the line
#test = ((output_line_length - 1) * step == input_line_length - 1)
test = (round(ptidx*step) == input_line_length-1)
if not test:
print("<fibers.py> ERROR: fiber numbers don't add up.")
print(step)
print(input_line_length)
print(output_line_length)
print(test)
raise AssertionError
return ptlist
def get_fiber(self, fiber_index):
""" Return fiber number fiber_index. Return value is class
Fiber."""
fiber = Fiber()
fiber.r = self.fiber_array_r[fiber_index, :]
fiber.a = self.fiber_array_a[fiber_index, :]
fiber.s = self.fiber_array_s[fiber_index, :]
fiber.points_per_fiber = self.points_per_fiber
return fiber
def get_equivalent_fiber(self, fiber_index):
""" Return equivalent version of fiber number
fiber_index. Return value is class Fiber. Gets the reverse
order of line (trajectory), as the fiber can be equivalently
represented in either order."""
fiber = self.get_fiber(fiber_index)
return fiber.get_equivalent_fiber()
def get_fibers(self, fiber_indices):
""" Return FiberArray containing subset of data corresponding
to fiber_indices"""
fibers = FiberArray()
fibers.number_of_fibers = len(fiber_indices)
# parameters
fibers.points_per_fiber = self.points_per_fiber
fibers.verbose = self.verbose
# fiber data
fibers.fiber_array_r = self.fiber_array_r[fiber_indices]
fibers.fiber_array_a = self.fiber_array_a[fiber_indices]
fibers.fiber_array_s = self.fiber_array_s[fiber_indices]
if self.fiber_hemisphere is not None:
# Output arrays indicating hemisphere/callosal (L,C,R= -1, 0, 1)
fibers.fiber_hemisphere = self.fiber_hemisphere[fiber_indices]
# output boolean arrays for each hemisphere and callosal fibers
fibers.is_left_hem = self.is_left_hem[fiber_indices]
fibers.is_right_hem = self.is_right_hem[fiber_indices]
fibers.is_commissure = self.is_commissure[fiber_indices]
# calculate indices of each type above
fibers.index_left_hem = numpy.nonzero(fibers.is_left_hem)[0]
fibers.index_right_hem = numpy.nonzero(fibers.is_right_hem)[0]
fibers.index_commissure = numpy.nonzero(fibers.is_commissure)[0]
fibers.index_hem = \
numpy.nonzero(fibers.is_left_hem | fibers.is_right_hem)[0]
# output totals of each type also
fibers.number_left_hem = len(fibers.index_left_hem)
fibers.number_right_hem = len(fibers.index_right_hem)
fibers.number_commissure = len(fibers.index_commissure)
# test
if __debug__:
test = fibers.number_of_fibers == \
(fibers.number_left_hem + fibers.number_right_hem \
+ fibers.number_commissure)
if not test:
print("<fibers.py> ERROR: fiber numbers don't add up.")
raise AssertionError
return fibers
def get_oriented_fibers(self, fiber_indices, order):
"""Return FiberArray containing subset of data corresponding to
fiber_indices. Order fibers according to the array (where 0 is no
change, and 1 means to reverse the order and return the
equivalent fiber)
"""
fibers = FiberArray()
fibers.number_of_fibers = len(fiber_indices)
# parameters
fibers.points_per_fiber = self.points_per_fiber
fibers.verbose = self.verbose
# fiber data
fibers.fiber_array_r = self.fiber_array_r[fiber_indices]
fibers.fiber_array_a = self.fiber_array_a[fiber_indices]
fibers.fiber_array_s = self.fiber_array_s[fiber_indices]
# swap orientation as requested
for (ord, fidx) in zip(order, range(fibers.number_of_fibers)):
if ord == 1:
f2 = fibers.get_equivalent_fiber(fidx)
# replace it in the array
fibers.fiber_array_r[fidx,:] = f2.r
fibers.fiber_array_a[fidx,:] = f2.a
fibers.fiber_array_s[fidx,:] = f2.s
if self.fiber_hemisphere is not None:
# Output arrays indicating hemisphere/callosal (L,C,R= -1, 0, 1)
fibers.fiber_hemisphere = self.fiber_hemisphere[fiber_indices]
# output boolean arrays for each hemisphere and callosal fibers
fibers.is_left_hem = self.is_left_hem[fiber_indices]
fibers.is_right_hem = self.is_right_hem[fiber_indices]
fibers.is_commissure = self.is_commissure[fiber_indices]
# calculate indices of each type above
fibers.index_left_hem = numpy.nonzero(fibers.is_left_hem)[0]
fibers.index_right_hem = numpy.nonzero(fibers.is_right_hem)[0]
fibers.index_commissure = numpy.nonzero(fibers.is_commissure)[0]
fibers.index_hem = \
numpy.nonzero(fibers.is_left_hem | fibers.is_right_hem)[0]
# output totals of each type also
fibers.number_left_hem = len(fibers.index_left_hem)
fibers.number_right_hem = len(fibers.index_right_hem)
fibers.number_commissure = len(fibers.index_commissure)
# test
if __debug__:
test = fibers.number_of_fibers == \
(fibers.number_left_hem + fibers.number_right_hem \
+ fibers.number_commissure)
if not test:
print("<fibers.py> ERROR: fiber numbers don't add up.")
raise AssertionError
return fibers
def convert_from_polydata(self, input_vtk_polydata, points_per_fiber=None,gifti=None,cifti=None,dir_flag=False,data='HCP'):
"""Convert input vtkPolyData to the fixed length fiber
representation of this class.
The polydata should contain the output of tractography.
The output is downsampled fibers in array format and
hemisphere info is also calculated.
"""
# points used in discretization of each trajectory
if points_per_fiber is not None:
self.points_per_fiber = points_per_fiber
# line count. Assume all input lines are from tractography.
self.number_of_fibers = input_vtk_polydata.GetNumberOfLines()
if self.verbose:
print("<fibers.py> Converting polydata to array representation. Lines:", \
self.number_of_fibers)
# allocate array number of lines by line length
self.fiber_array_r = numpy.zeros((self.number_of_fibers,
self.points_per_fiber))
self.fiber_array_a = numpy.zeros((self.number_of_fibers,
self.points_per_fiber))
self.fiber_array_s = numpy.zeros((self.number_of_fibers,
self.points_per_fiber))
self.fiber_array_p = numpy.zeros((self.number_of_fibers,
self.points_per_fiber))
self.fiber_dir_r = numpy.zeros((self.number_of_fibers,
self.points_per_fiber))
self.fiber_dir_a = numpy.zeros((self.number_of_fibers,
self.points_per_fiber))
self.fiber_dir_s = numpy.zeros((self.number_of_fibers,
self.points_per_fiber))
self.fiber_length = numpy.zeros(self.number_of_fibers)
self.fiber_surface_ve = numpy.zeros((self.number_of_fibers,2))
self.fiber_surface_dk = numpy.zeros((self.number_of_fibers, 2))
self.fiber_surface_des = numpy.zeros((self.number_of_fibers, 2))
self.fiber_roi= numpy.zeros((self.number_of_fibers,
self.points_per_fiber))
inpointdata = input_vtk_polydata.GetPointData()
point_data_array_indices = list(range(inpointdata.GetNumberOfArrays()))
roi_list = []
roi_list1 = []
roi_list2 = []
roi_list3 = []
roi_list4 = []
roi_list5 = []
roi_list6 = []
for idx in point_data_array_indices:
array = inpointdata.GetArray(idx)
if array.GetName() == 'ROI_label':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
#print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
roi_list.append(roi_line)
self.roi_list = roi_list
elif array.GetName() == 'ROI_nei1':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
#print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
roi_list1.append(roi_line)
self.roi_list1 = roi_list1
elif array.GetName() == 'ROI_nei2':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
#print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
roi_list2.append(roi_line)
self.roi_list2 = roi_list2
elif array.GetName() == 'ROI_nei3':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
#print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
roi_list3.append(roi_line)
self.roi_list3 = roi_list3
elif array.GetName() == 'ROI_nei4':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
# print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
roi_list4.append(roi_line)
self.roi_list4 = roi_list4
elif array.GetName() == 'ROI_nei5':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
# print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
roi_list5.append(roi_line)
self.roi_list5 = roi_list5
elif array.GetName() == 'ROI_nei6':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
# print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
roi_list6.append(roi_line)
self.roi_list6 = roi_list6
elif array.GetName() == 'surf_label_ve':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
#print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
#print(roi_line)
self.fiber_surface_ve[lidx,0]=roi_line[0]
self.fiber_surface_ve[lidx, 1] = roi_line[-1]
elif array.GetName() == 'surf_label_dk':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
#print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
#print(roi_line)
#print(data)
if not data=='HCP':
surf_map = numpy.load('/home/annabelchen/PycharmProjects/torch_DFC/surf_map.npy')
range_ctx = numpy.concatenate((numpy.array(range(1000, 1036)), numpy.array(range(2000, 2036))))
range_wm = numpy.concatenate((numpy.array(range(3000, 3036)), numpy.array(range(4000, 4036))))
range_cw = numpy.concatenate((range_ctx, range_wm))
if roi_line[0] in range_cw:
surf_label=roi_line[0]%100
else:
surf_label = surf_map[1, surf_map[0] == roi_line[0]]
self.fiber_surface_dk[lidx,0]=surf_label
if roi_line[-1] in range_cw:
surf_label=roi_line[-1]%100
else:
surf_label = surf_map[1, surf_map[0] == roi_line[-1]]
self.fiber_surface_dk[lidx,1]=surf_label
else:
self.fiber_surface_dk[lidx,0]=roi_line[0]
self.fiber_surface_dk[lidx, 1] = roi_line[-1]
elif array.GetName() == 'surf_label_des':
input_vtk_polydata.GetLines().InitTraversal()
for lidx in range(0, input_vtk_polydata.GetNumberOfLines()):
#print(lidx)
ptids = vtk.vtkIdList()
input_vtk_polydata.GetLines().GetNextCell(ptids)
roi_line = -numpy.ones(ptids.GetNumberOfIds())
for pidx in range(0, ptids.GetNumberOfIds()):
roi_line[pidx] = array.GetTuple(ptids.GetId(pidx))[0]
#print(roi_line)
self.fiber_surface_des[lidx,0]=roi_line[0]
self.fiber_surface_des[lidx, 1] = roi_line[-1]
# loop over lines
input_vtk_polydata.GetLines().InitTraversal()
line_ptids = vtk.vtkIdList()
inpoints = input_vtk_polydata.GetPoints()
vtk_array = vtk.vtkDoubleArray()
vtk_array.SetName('Point_Seq')
# inpd=input_vtk_polydata
# roi = numpy.zeros((inpd.GetNumberOfLines(), 300)) - 1
# inpointdata = inpd.GetPointData()
# if inpointdata.GetNumberOfArrays() > 0:
# point_data_array_indices = list(range(inpointdata.GetNumberOfArrays()))
# for idx in point_data_array_indices:
# array = inpointdata.GetArray(idx)
# if array.GetName() == 'Point_ROI':
# inpd.GetLines().InitTraversal()
# for lidx in range(0, inpd.GetNumberOfLines()):
# ptids = vtk.vtkIdList()
# inpd.GetLines().GetNextCell(ptids)
# for pidx in range(0, ptids.GetNumberOfIds()):
# roi[lidx, pidx] = array.GetTuple(ptids.GetId(pidx))[0]
for lidx in range(0, self.number_of_fibers):
input_vtk_polydata.GetLines().GetNextCell(line_ptids)
line_length = line_ptids.GetNumberOfIds()
self.fiber_length[lidx]=line_length
if self.verbose:
if lidx % 100 == 0:
print("<fibers.py> Line:", lidx, "/", self.number_of_fibers)
print("<fibers.py> number of points:", line_length)
for pidx in range(0, line_ptids.GetNumberOfIds()):
vtk_array.InsertNextTuple1(pidx)
# loop over the indices that we want and get those points
pidx = 0
for ind,line_index in enumerate(self._calculate_line_indices(line_length,
self.points_per_fiber)):
# do nearest neighbor interpolation: round index
ptidx = line_ptids.GetId(int(round(line_index)))
#print(lidx,line_index,ptidx,line_length)
roi=roi_list[lidx][int(round(line_index))]
#point = inpoints.GetPoint(ptidx)
point = list(inpoints.GetPoint(ptidx))
point[0]=abs(point[0])
self.fiber_array_p[lidx, pidx]=array.GetTuple(ptidx)[0]
self.fiber_array_r[lidx, pidx] = point[0]
self.fiber_array_a[lidx, pidx] = point[1]
self.fiber_array_s[lidx, pidx] = point[2]
self.fiber_roi[lidx,pidx]=roi
if gifti is not None:
if ind==0 or ind==points_per_fiber-1:
dx = gifti[:,0] - point[0]
dy = gifti[:,1] - point[1]
dz = gifti[:,2] - point[2]
dx = numpy.square(dx)
dy = numpy.square(dy)
dz = numpy.square(dz)
distance = dx + dy + dz
# now compute minimum of the two endpoint distances
min_distance = numpy.amin(distance, 0)
index_min=numpy.where(distance==min_distance)
if ind==0:
self.fiber_surface[lidx, 0] = cifti[index_min]
else:
self.fiber_surface[lidx, 1] = cifti[index_min]
if dir_flag:
if pidx==0:
#pointa = inpoints.GetPoint(ptidx + 1)
pointa=list(inpoints.GetPoint(ptidx+1))
pointa[0] = abs(pointa[0])
norm_diff = numpy.sqrt(numpy.sum(numpy.square(numpy.array(pointa)-numpy.array(point))))
self.fiber_dir_r[lidx, pidx] = (pointa[0] - point[0])/norm_diff
self.fiber_dir_a[lidx, pidx] = (pointa[1] - point[1])/norm_diff
self.fiber_dir_s[lidx, pidx] = (pointa[2] - point[2])/norm_diff
elif round(line_index) ==line_length-1:
#pointb = inpoints.GetPoint(ptidx - 1)
pointb = list(inpoints.GetPoint(ptidx - 1))
pointb[0] = abs(pointb[0])
norm_diff = numpy.sqrt(numpy.sum(numpy.square(numpy.array(point) - numpy.array(pointb))))
self.fiber_dir_r[lidx, pidx] = (point[0] - pointb[0])/norm_diff
self.fiber_dir_a[lidx, pidx] = (point[1] - pointb[1])/norm_diff
self.fiber_dir_s[lidx, pidx] = (point[2] - pointb[2])/norm_diff
else:
# pointa = inpoints.GetPoint(ptidx + 1)
# pointb = inpoints.GetPoint(ptidx - 1)
pointa = list(inpoints.GetPoint(ptidx + 1))
pointb = list(inpoints.GetPoint(ptidx - 1))
pointa[0] = abs(pointa[0])
pointb[0] = abs(pointb[0])
norm_diffa = numpy.sqrt(numpy.sum(numpy.square(numpy.array(pointa) - numpy.array(point))))
norm_diffb = numpy.sqrt(numpy.sum(numpy.square(numpy.array(point) - numpy.array(pointb))))
self.fiber_dir_r[lidx, pidx] = ((pointa[0] - point[0])/norm_diffa+(point[0] - pointb[0])/norm_diffb)/2
self.fiber_dir_a[lidx, pidx] = ((pointa[1] - point[1])/norm_diffa+(point[1] - pointb[1])/norm_diffb)/2
self.fiber_dir_s[lidx, pidx] = ((pointa[2] - point[2])/norm_diffa+(point[2] - pointb[2])/norm_diffb)/2
pidx = pidx + 1
input_vtk_polydata.GetPointData().AddArray(vtk_array)
# initialize hemisphere info
if self.hemispheres:
self.calculate_hemispheres()
def calculate_hemispheres(self):
""" For each fiber assign a hemisphere using the first (R)
coordinates.
This part assumes we are in RAS so the first coordinate is
positive to the RIGHT and negative to the LEFT. The fiber
must be more than 95% within 1 hemisphere. This excludes
corpus but can retain errant cingulum. We also want to
identify likely commissural fibers.
"""
# Figure out hemisphere of each line
self.fiber_hemisphere = numpy.zeros(self.number_of_fibers)
# percentage in left hemisphere
test = sum(self.fiber_array_r.T < 0) / float(self.points_per_fiber)
thresh = self.hemisphere_percent_threshold
self.fiber_hemisphere[numpy.nonzero(test > thresh)] = -1
self.fiber_hemisphere[numpy.nonzero(test < 1 - thresh)] = 1
# previous code left for clarity below, concrete example of threshold:
#self.fiber_hemisphere[numpy.nonzero(test > 0.95)] = -1
#self.fiber_hemisphere[numpy.nonzero(test < 0.05)] = 1
# otherwise hem stays 0 for commissural
# output boolean arrays for each hemisphere and callosal fibers
self.is_left_hem = (self.fiber_hemisphere == -1)
self.is_right_hem = (self.fiber_hemisphere == 1)
self.is_commissure = (self.fiber_hemisphere == 0)
# output indices of each type above
self.index_left_hem = numpy.nonzero(self.is_left_hem)[0]
self.index_right_hem = numpy.nonzero(self.is_right_hem)[0]
self.index_commissure = numpy.nonzero(self.is_commissure)[0]
self.index_hem = \
numpy.nonzero(self.is_left_hem | self.is_right_hem)[0]
# output totals of each type also
self.number_left_hem = len(self.index_left_hem)
self.number_right_hem = len(self.index_right_hem)
self.number_commissure = len(self.index_commissure)
# test
if __debug__:
test = self.number_of_fibers == \
(self.number_left_hem + self.number_right_hem \
+ self.number_commissure)
if not test:
print("<fibers.py> ERROR: fiber numbers don't add up.")
raise AssertionError
def convert_to_polydata(self):
"""Convert fiber array to vtkPolyData object."""
outpd = vtk.vtkPolyData()
outpoints = vtk.vtkPoints()
outlines = vtk.vtkCellArray()
outlines.InitTraversal()
for lidx in range(0, self.number_of_fibers):
cellptids = vtk.vtkIdList()
for pidx in range(0, self.points_per_fiber):
idx = outpoints.InsertNextPoint(self.fiber_array_r[lidx, pidx],
self.fiber_array_a[lidx, pidx],
self.fiber_array_s[lidx, pidx])
cellptids.InsertNextId(idx)
outlines.InsertNextCell(cellptids)
# put data into output polydata
outpd.SetLines(outlines)
outpd.SetPoints(outpoints)
return outpd