def vb_index_internal_loop(i0, iN, surf_faces, data, norm, print_progress=False):
"""Computes the Voigt-Bailey index of vertices in a given range
Parameters
----------
i0: integer
Index of first vertex to be analysed
iN: integer
Index of last vertex to be analysed
surf_faces: (M, 3) numpy array
Faces of the mesh. Used to find the neighborhood of a given vertice
data: (M, N) numpy array
Data to use the to calculate the VB index. M must math the number of vertices in the mesh
norm: string
Method of reordering. Possibilities are 'geig', 'unnorm', 'rw' and 'sym'
print_progress: boolean
Print the current progress of the system
Returns
-------
loc_result: (N) numpy array
Resulting VB index of the indices in range. Will have length iN - i0
"""
# Calculate how many vertices we will compute
diff = iN - i0
loc_result = np.zeros(diff)
for idx in range(diff):
#Calculate the real index
i = idx + i0
# Get neighborhood and its data
# TODO: Make this elegant
neighbour_idx = np.array(np.sum(surf_faces == i, 1), np.bool)
I = np.unique(surf_faces[neighbour_idx, :])
neighborhood = data[I]
if len(neighborhood) == 0:
print("Warning: no neighborhood")
# Calculate the eigenvalues
affinity = m.create_affinity_matrix(neighborhood)
_, _, _, eigenvalues, _ = m.spectral_reorder(affinity, norm)
normalisation_factor = np.average(eigenvalues[1:])
# Store the result of this run
loc_result[idx] = eigenvalues[1]/normalisation_factor
if print_progress:
global counter
global n
with counter.get_lock():
counter.value += 1
print("{}/{}".format(counter.value, n))
return loc_result
def vb_cluster_internal_loop(idx_cluster_0,
idx_cluster_N,
surf_faces,
data,
cluster_index,
norm,
print_progress=False):
"""Computes the Vogt-Bailey index of vertices of given clusters
Parameters
----------
idx_cluster_0: integer
Number of first cluster to be analysed
idx_cluster_N: integer
Number of last cluster to be analysed
surf_faces: (M, 3) numpy array
Faces of the mesh. Used to find the neighborhood of a given vertice
data: (M, N) numpy array
Data to use the to calculate the VB index. M must math the number of vertices in the mesh
cluster_index: (M) numpy array
Array containing the cluster which each vertex belongs
norm: string
Method of reordering. Possibilities are 'geig', 'unnorm', 'rw' and 'sym'
print_progress: boolean
Print the current progress of the system
Returns
-------
loc_result: list of pairs of (float, (N) numpy array)
Resulting VB index and eigenvectors of the clusters in range.
"""
# Calculate how many vertices we will compute
diff = idx_cluster_N - idx_cluster_0
loc_result = []
cluster_labels = np.unique(cluster_index)
for idx in range(diff):
#Calculate the real index
i = idx + idx_cluster_0
if (cluster_labels[i] == 0):
loc_result.append(([], []))
continue
# Get neighborhood and its data
neighborhood = data[cluster_index == cluster_labels[i]]
# Calculate the eigenvalues
affinity = m.create_affinity_matrix(neighborhood)
_, _, _, eigenvalues, eigenvectors = m.spectral_reorder(affinity, norm)
normalisation_factor = sum(eigenvalues) / len(eigenvalues - 1)
# Store the result of this run
# Warning: It is not true that the eigenvectors will be all the same
# size, as the clusters might be of different sizes
val = eigenvalues[1] / normalisation_factor
vel = eigenvectors[:, 1]
loc_result.append((val, vel))
if print_progress:
global counter
global n
with counter.get_lock():
counter.value += 1
if counter.value % 1000 == 0:
print("{}/{}".format(counter.value, n))
return loc_result
def vb_hybrid_internal_loop(i0,
iN,
surf_vertices,
brain_mask,
data,
norm,
print_progress=False):
"""Computes the Vogt-Bailey index of vertices in a given range
Parameters
----------
i0: integer
Index of first vertex to be analysed
iN: integer
iN - 1 is the index of the last vertex to be analysed
surf_vertices: (M, 3) numpy array
Coordinates of vertices of the mesh in voxel space
brain_mask: (nRows, nCols, nSlices) numpy array
Whole brain mask. Used to mask volumetric data
data: (nRows, nCols, nSlices, N) numpy array
Volumetric data used to calculate the VB index. N is the number of maps
norm: string
Method of reordering. Possibilities are 'geig', 'unnorm', 'rw' and 'sym'
print_progress: boolean
Print the current progress of the system
Returns
-------
loc_result: (N) numpy array
Resulting VB index of the indices in range. Will have length iN - i0
"""
# Calculate how many vertices we will compute
diff = iN - i0
loc_result = np.zeros(diff)
for idx in range(diff):
#Calculate the real index
i = idx + i0
# Get neighborhood and its data
# print(data.shape)
try:
neighborhood = get_neighborhood(data, surf_vertices[i, :],
brain_mask)
if len(neighborhood) == 0:
print("Warning: no neighborhood")
loc_result[idx] = np.nan
continue
affinity = m.create_affinity_matrix(neighborhood)
if affinity.shape[0] > 3:
#tr_row, tr_col = np.triu_indices(affinity.shape[0], k=1)
# Calculate the second smallest eigenvalue
_, _, eigenvalue, _ = m.spectral_reorder(affinity, norm)
# return [0]
# Store the result of this run
loc_result[idx] = eigenvalue
#loc_result[idx] = np.mean(affinity[tr_row, tr_col])
else:
loc_result[idx] = np.nan
except m.TimeSeriesTooShortError as error:
raise error
except Exception:
traceback.print_exc()
loc_result[idx] = np.nan
if print_progress:
global counter
global n
with counter.get_lock():
counter.value += 1
if counter.value % 1000 == 0:
print("{}/{}".format(counter.value, n))
return loc_result