def __init__(self):
# parameters
# medium sigma
self.sigma = 20.0
# stricter and more accurate than 5 points
self.points_per_fiber = 20
# aid in matching across hemispheres with threshold
self.threshold = 5.0
# same number of fibers measured from each hemisphere
# avoid biasing due just to number of fibers
self.use_equal_fibers = True
# If using equal fibers, can set how many to use same number across subjects
self.fibers_per_hemisphere = None
# performance options
self.verbose = True
# set parallel_jobs to 0 to turn off multiprocessing
self.parallel_jobs = 2
self.parallel_verbose = 0
# internal data storage
self.fibers = FiberArray()
def __init__(self):
# parameters
self.sigma = 10
self.points_per_fiber = 5
self.threshold = 5
# same number of fibers measured from each hemisphere
self.equal_fiber_num = True
# performance options
self.verbose = True
# set parallel_jobs to 0 to turn off multiprocessing
self.parallel_jobs = 2
self.parallel_verbose = 0
# internal data storage
self.fibers = FiberArray()
def __init__(self):
# parameters
# medium sigma
self.sigma = 20.0
# stricter and more accurate than 5 points
self.points_per_fiber = 20
# aid in matching across hemispheres with threshold
self.threshold = 5.0
# same number of fibers measured from each hemisphere
# avoid biasing due just to number of fibers
self.use_equal_fibers = True
# If using equal fibers, can set how many to use same number across subjects
self.fibers_per_hemisphere = None
# performance options
self.verbose = True
# set parallel_jobs to 0 to turn off multiprocessing
self.parallel_jobs = 2
self.parallel_verbose = 0
# internal data storage
self.fibers = FiberArray()
class WhiteMatterLaterality:
"""Laterality computation from fiber tracts."""
def __init__(self):
# parameters
self.sigma = 10
self.points_per_fiber = 5
self.threshold = 5
# same number of fibers measured from each hemisphere
self.equal_fiber_num = True
# performance options
self.verbose = True
# set parallel_jobs to 0 to turn off multiprocessing
self.parallel_jobs = 2
self.parallel_verbose = 0
# internal data storage
self.fibers = FiberArray()
def __str__(self):
output = " sigma\t\t\t" + str(self.sigma) \
+ "\n points_per_fiber\t" + str(self.points_per_fiber) \
+ "\n threshold\t\t" + str(self.threshold) \
+ "\n verbose\t\t" + str(self.verbose) \
+ "\n parallel_jobs\t\t" + str(self.parallel_jobs) \
+ "\n parallel_verbose\t" + str(self.parallel_verbose) \
+ "\n fibers\n\t\t\t" \
+ str(self.fibers)
return output
def compute(self, input_vtk_polydata):
""" Actually calculate the laterality index for every input
fiber.
Input polydata is required. This polydata is modified by
adding a cell data array containing laterality indices.
Output from this class is a struct: <io.py> class
LateralityResults
Parameters in the class can also be modified for experiments:
sigma (in Gaussian on inter-fiber-point distance),
points_per_fiber (for parameterization), threshold (below
which inter-fiber-point distance is set to 0).
Performance options are the number of parallel_jobs, and
verbose (whether to print progress).
"""
# internal representation for fast similarity computation
# this also detects which hemisphere fibers are in
self.fibers.points_per_fiber = self.points_per_fiber
# must request hemisphere computation from object
self.fibers.hemispheres = True
# Now convert to array with points and hemispheres as above
self.fibers.convert_from_polydata(input_vtk_polydata)
# square sigma for later Gaussian
sigmasq = self.sigma * self.sigma
# allocate outputs
nf = self.fibers.number_of_fibers
laterality_index = numpy.zeros(nf)
right_hem_total = numpy.zeros(nf)
left_hem_total = numpy.zeros(nf)
#right_hem_distance = numpy.zeros([nf, nf])
#left_hem_distance = numpy.zeros([nf, nf])
# get the same number from each hemisphere if requested
# -------------------------
if self.equal_fiber_num:
num_fibers = min(self.fibers.number_left_hem, self.fibers.number_right_hem)
# grab num_fibers fibers from each hemisphere.
# use the first n since they were randomly sampled from the whole dataset
fiber_array_right = self.fibers.get_fibers(self.fibers.index_right_hem[0:num_fibers])
fiber_array_left = self.fibers.get_fibers(self.fibers.index_left_hem[0:num_fibers])
if self.verbose:
print "<laterality.py> Using ", num_fibers , " fibers per hemisphere."
else:
# grab all fibers from each hemisphere
fiber_array_right = self.fibers.get_fibers(self.fibers.index_right_hem)
fiber_array_left = self.fibers.get_fibers(self.fibers.index_left_hem)
# tell user we are doing something
if self.verbose:
print "<laterality.py> Fibers in each hemisphere.", \
"L:", self.fibers.number_left_hem, \
"R:", self.fibers.number_right_hem, \
"/ Total:", self.fibers.number_of_fibers
print "<laterality.py> Starting to compute laterality indices"
# run the computation, either in parallel or not
if (USE_PARALLEL & (self.parallel_jobs > 1)):
if self.verbose:
print "<laterality.py> Starting parallel code. Processes:", \
self.parallel_jobs
# compare to right hemisphere (reflect fiber first if in left hem)
ret = Parallel(
n_jobs=self.parallel_jobs, verbose=self.parallel_verbose)(
delayed(similarity.total_similarity_and_distances)(
self.fibers.get_fiber(lidx),
fiber_array_right,
self.fibers.is_left_hem[lidx],
self.threshold,
sigmasq)
for lidx in self.fibers.index_hem)
ret = zip(*ret)
right_hem_total[self.fibers.index_hem] = ret[0]
right_hem_distance = ret[1]
# compare to left hemisphere (reflect fiber first if in right hem)
ret = Parallel(
n_jobs=self.parallel_jobs, verbose=self.parallel_verbose)(
delayed(similarity.total_similarity_and_distances)(
self.fibers.get_fiber(lidx),
fiber_array_left,
self.fibers.is_right_hem[lidx],
self.threshold,
sigmasq)
for lidx in self.fibers.index_hem)
ret = zip(*ret)
left_hem_total[self.fibers.index_hem] = ret[0]
left_hem_distance = ret[1]
else:
right_hem_distance = numpy.zeros([nf, len(self.fibers.index_right_hem)])
left_hem_distance = numpy.zeros([nf, len(self.fibers.index_left_hem)])
# compare to right hemisphere (reflect fiber first if in left hem)
for lidx in self.fibers.index_hem:
ret = similarity.total_similarity_and_distances(
self.fibers.get_fiber(lidx),
fiber_array_right,
self.fibers.is_left_hem[lidx],
self.threshold,
sigmasq)
right_hem_total[lidx] = ret[0]
right_hem_distance[lidx,:] = ret[1]
# compare to left hemisphere (reflect fiber first if in right hem)
for lidx in self.fibers.index_hem:
ret = similarity.total_similarity_and_distances(
self.fibers.get_fiber(lidx),
fiber_array_left,
self.fibers.is_right_hem[lidx],
self.threshold,
sigmasq)
left_hem_total[lidx] = ret[0]
left_hem_distance[lidx,:] = ret[1]
laterality_index = compute_laterality_index(left_hem_total,
right_hem_total,
self.fibers.index_hem)
# output the LI as cell data in the polydata
# for visualization and/or further analyses
cell_data = vtk.vtkFloatArray()
cell_data.SetName('Laterality')
for lidx in range(0, self.fibers.number_of_fibers):
cell_data.InsertNextTuple1(laterality_index[lidx])
input_vtk_polydata.GetCellData().SetScalars(cell_data)
# output everything
results = LateralityResults()
results.laterality_index = laterality_index
results.polydata = input_vtk_polydata
#results.right_hem_distance = right_hem_distance
#results.left_hem_distance = left_hem_distance
results.sigma = self.sigma
results.points_per_fiber = self.points_per_fiber
results.threshold = self.threshold
results.left_hem_similarity = left_hem_total
results.right_hem_similarity = right_hem_total
results.hemisphere = self.fibers.fiber_hemisphere
return results
class WhiteMatterLaterality:
"""Laterality computation from fiber tracts."""
def __init__(self):
# parameters
# medium sigma
self.sigma = 20.0
# stricter and more accurate than 5 points
self.points_per_fiber = 20
# aid in matching across hemispheres with threshold
self.threshold = 5.0
# same number of fibers measured from each hemisphere
# avoid biasing due just to number of fibers
self.use_equal_fibers = True
# If using equal fibers, can set how many to use same number across subjects
self.fibers_per_hemisphere = None
# performance options
self.verbose = True
# set parallel_jobs to 0 to turn off multiprocessing
self.parallel_jobs = 2
self.parallel_verbose = 0
# internal data storage
self.fibers = FiberArray()
def __str__(self):
output = " sigma\t\t\t" + str(self.sigma) \
+ "\n points_per_fiber\t" + str(self.points_per_fiber) \
+ "\n threshold\t\t" + str(self.threshold) \
+ "\n verbose\t\t" + str(self.verbose) \
+ "\n parallel_jobs\t\t" + str(self.parallel_jobs) \
+ "\n parallel_verbose\t" + str(self.parallel_verbose) \
+ "\n fibers\n\t\t\t" \
+ str(self.fibers)
return output
def compute(self, input_vtk_polydata):
""" Actually calculate the laterality index for every input
fiber.
Input polydata is required. This polydata is modified by
adding a cell data array containing laterality indices.
Output from this class is a struct: <io.py> class
LateralityResults
Parameters in the class can also be modified for experiments:
sigma (in Gaussian on inter-fiber-point distance),
points_per_fiber (for parameterization), threshold (below
which inter-fiber-point distance is set to 0).
Performance options are the number of parallel_jobs, and
verbose (whether to print progress).
"""
# internal representation for fast similarity computation
# this also detects which hemisphere fibers are in
self.fibers.points_per_fiber = self.points_per_fiber
# must request hemisphere computation from object
self.fibers.hemispheres = True
# Now convert to array with points and hemispheres as above
self.fibers.convert_from_polydata(input_vtk_polydata)
# get the same number from each hemisphere if requested
# -------------------------
if self.use_equal_fibers:
num_fibers = min(self.fibers.number_left_hem,
self.fibers.number_right_hem)
if self.fibers_per_hemisphere is not None:
if self.fibers_per_hemisphere <= num_fibers:
num_fibers = self.fibers_per_hemisphere
else:
raise Exception(
"Fibers per hemisphere is set too high for the dataset. Current subject maximum is"
+ str(num_fibers))
# grab num_fibers fibers from each hemisphere.
# use the first n since they were randomly sampled from the whole dataset
selected_right = self.fibers.index_right_hem[0:num_fibers]
selected_left = self.fibers.index_left_hem[0:num_fibers]
mask = numpy.zeros(input_vtk_polydata.GetNumberOfLines())
mask[selected_right] = 1
mask[selected_left] = 1
# go back to the input data and use just those fibers
input_vtk_polydata = filter.mask(input_vtk_polydata, mask)
# Now convert to array with points and hemispheres as above
self.fibers.convert_from_polydata(input_vtk_polydata)
if self.verbose:
print "<laterality.py> Using ", num_fibers, " fibers per hemisphere."
# square sigma for later Gaussian
sigmasq = self.sigma * self.sigma
# allocate outputs
nf = self.fibers.number_of_fibers
laterality_index = numpy.zeros(nf)
right_hem_total = numpy.zeros(nf)
left_hem_total = numpy.zeros(nf)
#right_hem_distance = numpy.zeros([nf, nf])
#left_hem_distance = numpy.zeros([nf, nf])
# grab all fibers from each hemisphere
fiber_array_right = self.fibers.get_fibers(self.fibers.index_right_hem)
fiber_array_left = self.fibers.get_fibers(self.fibers.index_left_hem)
# tell user we are doing something
if self.verbose:
print "<laterality.py> Fibers in each hemisphere.", \
"L:", self.fibers.number_left_hem, \
"R:", self.fibers.number_right_hem, \
"/ Total:", self.fibers.number_of_fibers
print "<laterality.py> Starting to compute laterality indices"
# run the computation, either in parallel or not
if (USE_PARALLEL & (self.parallel_jobs > 1)):
if self.verbose:
print "<laterality.py> Starting parallel code. Processes:", \
self.parallel_jobs
# compare to right hemisphere (reflect fiber first if in left hem)
ret = Parallel(
n_jobs=self.parallel_jobs, verbose=self.parallel_verbose)(
delayed(similarity.total_similarity_for_laterality)(
self.fibers.get_fiber(lidx), fiber_array_right,
self.fibers.is_left_hem[lidx], self.threshold, sigmasq)
for lidx in self.fibers.index_hem)
#ret = zip(*ret)
right_hem_total[self.fibers.index_hem] = ret
#right_hem_distance = ret[1]
# compare to left hemisphere (reflect fiber first if in right hem)
ret = Parallel(
n_jobs=self.parallel_jobs, verbose=self.parallel_verbose)(
delayed(similarity.total_similarity_for_laterality)
(self.fibers.get_fiber(lidx), fiber_array_left,
self.fibers.is_right_hem[lidx], self.threshold, sigmasq)
for lidx in self.fibers.index_hem)
#ret = zip(*ret)
left_hem_total[self.fibers.index_hem] = ret
#left_hem_distance = ret[1]
else:
right_hem_distance = numpy.zeros(
[nf, len(self.fibers.index_right_hem)])
left_hem_distance = numpy.zeros(
[nf, len(self.fibers.index_left_hem)])
# compare to right hemisphere (reflect fiber first if in left hem)
for lidx in self.fibers.index_hem:
ret = similarity.total_similarity_for_laterality(
self.fibers.get_fiber(lidx), fiber_array_right,
self.fibers.is_left_hem[lidx], self.threshold, sigmasq)
right_hem_total[lidx] = ret
#right_hem_total[lidx] = ret[0]
#right_hem_distance[lidx,:] = ret[1]
# compare to left hemisphere (reflect fiber first if in right hem)
for lidx in self.fibers.index_hem:
ret = similarity.total_similarity_for_laterality(
self.fibers.get_fiber(lidx), fiber_array_left,
self.fibers.is_right_hem[lidx], self.threshold, sigmasq)
left_hem_total[lidx] = ret
#left_hem_distance[lidx,:] = ret[1]
laterality_index = compute_laterality_index(left_hem_total,
right_hem_total,
self.fibers.index_hem)
# output the LI as cell data in the polydata
# for visualization and/or further analyses
cell_data = vtk.vtkFloatArray()
cell_data.SetName('Laterality')
for lidx in range(0, self.fibers.number_of_fibers):
cell_data.InsertNextTuple1(laterality_index[lidx])
input_vtk_polydata.GetCellData().SetScalars(cell_data)
# output everything
results = LateralityResults()
results.laterality_index = laterality_index
results.polydata = input_vtk_polydata
#results.right_hem_distance = right_hem_distance
#results.left_hem_distance = left_hem_distance
results.sigma = self.sigma
results.points_per_fiber = self.points_per_fiber
results.threshold = self.threshold
results.left_hem_similarity = left_hem_total
results.right_hem_similarity = right_hem_total
results.hemisphere = self.fibers.fiber_hemisphere
return results