def anisotropic_smooth(inpd, fiber_distance_threshold, points_per_fiber=30, n_jobs=2, cluster_max = 10):
""" Average nearby fibers.
The pairwise fiber distance matrix is computed, then fibers
are averaged with their neighbors until an edge (>max_fiber_distance) is encountered.
"""
# polydata to array conversion, fixed-length fiber representation
current_fiber_array = fibers.FiberArray()
current_fiber_array.points_per_fiber = points_per_fiber
current_fiber_array.convert_from_polydata(inpd)
original_number_of_fibers = current_fiber_array.number_of_fibers
# fiber list data structure initialization for easy fiber averaging
curr_count = list()
curr_fibers = list()
curr_indices = list()
for lidx in range(0, current_fiber_array.number_of_fibers):
curr_fibers.append(current_fiber_array.get_fiber(lidx))
curr_count.append(1)
curr_indices.append(list([lidx]))
converged = False
iteration_count = 0
while not converged:
print "<filter.py> ITERATION:", iteration_count, "SUM FIBER COUNTS:", numpy.sum(numpy.array(curr_count))
print "<filter.py> number indices", len(curr_indices)
# fiber data structures for output of this iteration
next_fibers = list()
next_count = list()
next_indices = list()
# information for this iteration
done = numpy.zeros(current_fiber_array.number_of_fibers)
fiber_indices = range(0, current_fiber_array.number_of_fibers)
# if the maximum number of fibers have been combined, stop averaging this fiber
done[numpy.nonzero(numpy.array(curr_count) >= cluster_max)] = 1
# pairwise distance matrix
if USE_PARALLEL:
distances = Parallel(n_jobs=n_jobs, verbose=1)(
delayed(similarity.fiber_distance)(
current_fiber_array.get_fiber(lidx),
current_fiber_array,
0, 'Hausdorff')
for lidx in fiber_indices)
distances = numpy.array(distances)
else:
distances = \
numpy.zeros(
(current_fiber_array.number_of_fibers,
current_fiber_array.number_of_fibers))
for lidx in fiber_indices:
distances[lidx, :] = \
similarity.fiber_distance(
current_fiber_array.get_fiber(lidx),
current_fiber_array, 0, 'Hausdorff')
# distances to self are not of interest
for lidx in fiber_indices:
distances[lidx,lidx] = numpy.inf
# sort the pairwise distances.
distances_flat = distances.flatten()
pair_order = numpy.argsort(distances_flat)
print "<filter.py> DISTANCE MIN:", distances_flat[pair_order[0]], \
"DISTANCE COUNT:", distances.shape
# if the smallest distance is greater or equal to the
# threshold, we have converged
if distances_flat[pair_order[0]] >= fiber_distance_threshold:
converged = True
print "<filter.py> CONVERGED"
break
else:
print "<filter.py> NOT CONVERGED"
# loop variables
idx = 0
pair_idx = pair_order[idx]
number_of_fibers = distances.shape[0]
number_averages = 0
# combine nearest neighbors unless done, until hit threshold
while distances_flat[pair_idx] < fiber_distance_threshold:
# find the fiber indices corresponding to this pairwise distance
# use div and mod
f_row = pair_idx / number_of_fibers
f_col = pair_idx % number_of_fibers
# check if this neighbor pair can be combined
combine = (not done[f_row]) and (not done[f_col])
if combine :
done[f_row] += 1
done[f_col] += 1
# weighted average of the fibers (depending on how many each one represents)
next_fibers.append(
(curr_fibers[f_row] * curr_count[f_row] + \
curr_fibers[f_col] *curr_count[f_col]) / \
(curr_count[f_row] + curr_count[f_col]))
# this was the regular average
#next_fibers.append((curr_fibers[f_row] + curr_fibers[f_col])/2)
next_count.append(curr_count[f_row] + curr_count[f_col])
number_averages += 1
#next_indices.append(list([curr_indices[f_row], curr_indices[f_col]]))
next_indices.append(list(curr_indices[f_row] + curr_indices[f_col]))
# increment for the loop
idx += 1
pair_idx = pair_order[idx]
# copy through any unvisited (already converged) fibers
unvisited = numpy.nonzero(done==0)[0]
for fidx in unvisited:
next_fibers.append(curr_fibers[fidx])
next_count.append(curr_count[fidx])
next_indices.append(curr_indices[fidx])
# set up for next iteration
curr_fibers = next_fibers
curr_count = next_count
curr_indices = next_indices
iteration_count += 1
# set up array for next iteration distance computation
current_fiber_array = fibers.FiberArray()
current_fiber_array.number_of_fibers = len(curr_fibers)
current_fiber_array.points_per_fiber = points_per_fiber
dims = [current_fiber_array.number_of_fibers, current_fiber_array.points_per_fiber]
# fiber data
current_fiber_array.fiber_array_r = numpy.zeros(dims)
current_fiber_array.fiber_array_a = numpy.zeros(dims)
current_fiber_array.fiber_array_s = numpy.zeros(dims)
curr_fidx = 0
for curr_fib in curr_fibers:
current_fiber_array.fiber_array_r[curr_fidx] = curr_fib.r
current_fiber_array.fiber_array_a[curr_fidx] = curr_fib.a
current_fiber_array.fiber_array_s[curr_fidx] = curr_fib.s
curr_fidx += 1
print "<filter.py> SUM FIBER COUNTS:", numpy.sum(numpy.array(curr_count)), "SUM DONE FIBERS:", numpy.sum(done)
print "<filter.py> MAX COUNT:" , numpy.max(numpy.array(curr_count)), "AVGS THIS ITER:", number_averages
# when converged, convert output to polydata
outpd = current_fiber_array.convert_to_polydata()
# color output by the number of fibers that each output fiber corresponds to
outcolors = vtk.vtkFloatArray()
outcolors.SetName('FiberTotal')
for count in curr_count:
outcolors.InsertNextTuple1(count)
outpd.GetCellData().SetScalars(outcolors)
# also color the input pd by output cluster number
cluster_numbers = numpy.zeros(original_number_of_fibers)
cluster_count = numpy.zeros(original_number_of_fibers)
cluster_idx = 0
for index_list in curr_indices:
indices = numpy.array(index_list).astype(int)
cluster_numbers[indices] = cluster_idx
cluster_count[indices] = curr_count[cluster_idx]
cluster_idx += 1
outclusters = vtk.vtkFloatArray()
outclusters.SetName('ClusterNumber')
for cluster in cluster_numbers:
outclusters.InsertNextTuple1(cluster)
inpd.GetCellData().AddArray(outclusters)
inpd.GetCellData().SetActiveScalars('ClusterNumber')
return outpd, numpy.array(curr_count), inpd, cluster_numbers, cluster_count
def anisotropic_smooth(inpd,
fiber_distance_threshold,
points_per_fiber=30,
n_jobs=2,
cluster_max=10):
""" Average nearby fibers.
The pairwise fiber distance matrix is computed, then fibers
are averaged with their neighbors until an edge (>max_fiber_distance) is encountered.
"""
# polydata to array conversion, fixed-length fiber representation
current_fiber_array = fibers.FiberArray()
current_fiber_array.points_per_fiber = points_per_fiber
current_fiber_array.convert_from_polydata(inpd)
original_number_of_fibers = current_fiber_array.number_of_fibers
# fiber list data structure initialization for easy fiber averaging
curr_count = list()
curr_fibers = list()
curr_indices = list()
for lidx in range(0, current_fiber_array.number_of_fibers):
curr_fibers.append(current_fiber_array.get_fiber(lidx))
curr_count.append(1)
curr_indices.append(list([lidx]))
converged = False
iteration_count = 0
while not converged:
print("<filter.py> ITERATION:", iteration_count, "SUM FIBER COUNTS:",
numpy.sum(numpy.array(curr_count)))
print("<filter.py> number indices", len(curr_indices))
# fiber data structures for output of this iteration
next_fibers = list()
next_count = list()
next_indices = list()
# information for this iteration
done = numpy.zeros(current_fiber_array.number_of_fibers)
fiber_indices = list(range(0, current_fiber_array.number_of_fibers))
# if the maximum number of fibers have been combined, stop averaging this fiber
done[numpy.nonzero(numpy.array(curr_count) >= cluster_max)] = 1
# pairwise distance matrix
if USE_PARALLEL:
distances = Parallel(n_jobs=n_jobs,
verbose=1)(delayed(similarity.fiber_distance)(
current_fiber_array.get_fiber(lidx),
current_fiber_array, 0, 'Hausdorff')
for lidx in fiber_indices)
distances = numpy.array(distances)
else:
distances = \
numpy.zeros(
(current_fiber_array.number_of_fibers,
current_fiber_array.number_of_fibers))
for lidx in fiber_indices:
distances[lidx, :] = \
similarity.fiber_distance(
current_fiber_array.get_fiber(lidx),
current_fiber_array, 0, 'Hausdorff')
# distances to self are not of interest
for lidx in fiber_indices:
distances[lidx, lidx] = numpy.inf
# sort the pairwise distances.
distances_flat = distances.flatten()
pair_order = numpy.argsort(distances_flat)
print("<filter.py> DISTANCE MIN:", distances_flat[pair_order[0]], \
"DISTANCE COUNT:", distances.shape)
# if the smallest distance is greater or equal to the
# threshold, we have converged
if distances_flat[pair_order[0]] >= fiber_distance_threshold:
converged = True
print("<filter.py> CONVERGED")
break
else:
print("<filter.py> NOT CONVERGED")
# loop variables
idx = 0
pair_idx = pair_order[idx]
number_of_fibers = distances.shape[0]
number_averages = 0
# combine nearest neighbors unless done, until hit threshold
while distances_flat[pair_idx] < fiber_distance_threshold:
# find the fiber indices corresponding to this pairwise distance
# use div and mod
f_row = pair_idx / number_of_fibers
f_col = pair_idx % number_of_fibers
# check if this neighbor pair can be combined
combine = (not done[f_row]) and (not done[f_col])
if combine:
done[f_row] += 1
done[f_col] += 1
# weighted average of the fibers (depending on how many each one represents)
next_fibers.append(
(curr_fibers[f_row] * curr_count[f_row] + \
curr_fibers[f_col] *curr_count[f_col]) / \
(curr_count[f_row] + curr_count[f_col]))
# this was the regular average
#next_fibers.append((curr_fibers[f_row] + curr_fibers[f_col])/2)
next_count.append(curr_count[f_row] + curr_count[f_col])
number_averages += 1
#next_indices.append(list([curr_indices[f_row], curr_indices[f_col]]))
next_indices.append(
list(curr_indices[f_row] + curr_indices[f_col]))
# increment for the loop
idx += 1
pair_idx = pair_order[idx]
# copy through any unvisited (already converged) fibers
unvisited = numpy.nonzero(done == 0)[0]
for fidx in unvisited:
next_fibers.append(curr_fibers[fidx])
next_count.append(curr_count[fidx])
next_indices.append(curr_indices[fidx])
# set up for next iteration
curr_fibers = next_fibers
curr_count = next_count
curr_indices = next_indices
iteration_count += 1
# set up array for next iteration distance computation
current_fiber_array = fibers.FiberArray()
current_fiber_array.number_of_fibers = len(curr_fibers)
current_fiber_array.points_per_fiber = points_per_fiber
dims = [
current_fiber_array.number_of_fibers,
current_fiber_array.points_per_fiber
]
# fiber data
current_fiber_array.fiber_array_r = numpy.zeros(dims)
current_fiber_array.fiber_array_a = numpy.zeros(dims)
current_fiber_array.fiber_array_s = numpy.zeros(dims)
curr_fidx = 0
for curr_fib in curr_fibers:
current_fiber_array.fiber_array_r[curr_fidx] = curr_fib.r
current_fiber_array.fiber_array_a[curr_fidx] = curr_fib.a
current_fiber_array.fiber_array_s[curr_fidx] = curr_fib.s
curr_fidx += 1
print("<filter.py> SUM FIBER COUNTS:",
numpy.sum(numpy.array(curr_count)), "SUM DONE FIBERS:",
numpy.sum(done))
print("<filter.py> MAX COUNT:", numpy.max(numpy.array(curr_count)),
"AVGS THIS ITER:", number_averages)
# when converged, convert output to polydata
outpd = current_fiber_array.convert_to_polydata()
# color output by the number of fibers that each output fiber corresponds to
outcolors = vtk.vtkFloatArray()
outcolors.SetName('FiberTotal')
for count in curr_count:
outcolors.InsertNextTuple1(count)
outpd.GetCellData().SetScalars(outcolors)
# also color the input pd by output cluster number
cluster_numbers = numpy.zeros(original_number_of_fibers)
cluster_count = numpy.zeros(original_number_of_fibers)
cluster_idx = 0
for index_list in curr_indices:
indices = numpy.array(index_list).astype(int)
cluster_numbers[indices] = cluster_idx
cluster_count[indices] = curr_count[cluster_idx]
cluster_idx += 1
outclusters = vtk.vtkFloatArray()
outclusters.SetName('ClusterNumber')
for cluster in cluster_numbers:
outclusters.InsertNextTuple1(cluster)
inpd.GetCellData().AddArray(outclusters)
inpd.GetCellData().SetActiveScalars('ClusterNumber')
return outpd, numpy.array(curr_count), inpd, cluster_numbers, cluster_count
TOTAL_PREDS = y_test_event_label_array.shape[0]
y_test_event_label_array = y_test_event_label_array.reshape(
(TOTAL_PREDS // OUTPUT_EVENT_NUM, OUTPUT_EVENT_NUM))
y_regression_pred1_event_labels = y_regression_pred1_event_labels.reshape(
(TOTAL_PREDS // OUTPUT_EVENT_NUM, OUTPUT_EVENT_NUM))
# y_regression_pred1_event_labels = np.asarray(y_regression_pred1_event_labels)
print(y_regression_pred1_event_labels)
print("y_regression_pred1_event_labels shape")
print(y_regression_pred1_event_labels.shape)
#let's save the predictions
pred_data = {
"prediction":
list(y_regression_pred1_event_labels.flatten()),
"actual": list(y_test_event_label_array.flatten())
}
#make pred df
pred_df = pd.DataFrame(data=pred_data)
print(pred_df)
# sys.exit(0)
#save data
output_fp = main_output_dir + "predictions-vs-ground-truth.csv"
pred_df.to_csv(output_fp, index=False)
print(output_fp)
for TAG in TAGS:
rnn = Parallel(n_jobs=num_cores)(
delayed(spir.build_cov)(data, [event], lag, fs)
for event in events)
rnns += rnn
# Limit to 2000 events
if total_events > 2000:
break
# -
# ## Compress Rnns
# +
tmp = list()
for rnn in rnns:
tmp.append(rnn.flatten() / np.sum(np.diag(rnn))) # Normalize
pca = PCA(0.99)
pca.fit(tmp)
compressed = pca.fit_transform(tmp)
print('Number of compressed components: {}'.format(compressed.shape[1]))
# -
# ## Perform K-means clustering
# +
## Find n-clusters
def calculate_WSS(points, kmax):
sse = []
for k in range(1, kmax + 1):
kmeans = KMeans(n_clusters=k).fit(points)
centroids = kmeans.cluster_centers_