def zernike_moments_per_label(vtk_file, order=10, exclude_labels=[-1],
scale_input=True,
decimate_fraction=0, decimate_smooth=25):
"""
Compute the Zernike moments per labeled region in a file.
Optionally decimate the input mesh.
Parameters
----------
vtk_file : string
name of VTK surface mesh file containing index scalars (labels)
order : integer
number of moments to compute
exclude_labels : list of integers
labels to be excluded
scale_input : Boolean
translate and scale each object so it is bounded by a unit sphere?
(this is the expected input to zernike_moments())
decimate_fraction : float
fraction of mesh faces to remove for decimation (1 for no decimation)
decimate_smooth : integer
number of smoothing steps for decimation
Returns
-------
descriptors_lists : list of lists of floats
Zernike descriptors per label
label_list : list of integers
list of unique labels for which moments are computed
Examples
--------
>>> # Uncomment "if label==22:" below to run example:
>>> # Twins-2-1 left postcentral (22) pial surface:
>>> import os
>>> from mindboggle.shapes.zernike.zernike import zernike_moments_per_label
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> order = 3
>>> exclude_labels = [0]
>>> scale_input = True
>>> zernike_moments_per_label(vtk_file, order, exclude_labels, scale_input)
([[0.00528486237819844,
0.009571754617699853,
0.0033489494903015944,
0.00875603468268444,
0.0015879536633349918,
0.0008080165707033097]],
[22])
([[0.0018758013185778298,
0.001757973693050823,
0.002352403177686726,
0.0032281044369938286,
0.002215900343702539,
0.0019646380916703856]],
[14.0])
Arthur Mikhno's result:
1.0e+07 *
0.0000
0.0179
0.0008
4.2547
0.0534
4.4043
"""
import numpy as np
from mindboggle.utils.io_vtk import read_vtk
from mindboggle.utils.mesh import remove_faces
from mindboggle.shapes.zernike.zernike import zernike_moments
min_points_faces = 4
#-------------------------------------------------------------------------
# Read VTK surface mesh file:
#-------------------------------------------------------------------------
faces, u1,u2, points, u3, labels, u4,u5 = read_vtk(vtk_file)
#-------------------------------------------------------------------------
# Loop through labeled regions:
#-------------------------------------------------------------------------
ulabels = [x for x in np.unique(labels) if x not in exclude_labels]
label_list = []
descriptors_lists = []
for label in ulabels:
#if label == 22:
# print("DEBUG: COMPUTE FOR ONLY ONE LABEL")
if label == 14:
#---------------------------------------------------------------------
# Determine the indices per label:
#---------------------------------------------------------------------
Ilabel = [i for i,x in enumerate(labels) if x == label]
print(' {0} vertices for label {1}'.format(len(Ilabel), label))
if len(Ilabel) > min_points_faces:
#-----------------------------------------------------------------
# Remove background faces:
#-----------------------------------------------------------------
pick_faces = remove_faces(faces, Ilabel)
if len(pick_faces) > min_points_faces:
#-------------------------------------------------------------
# Compute Zernike moments for the label:
#-------------------------------------------------------------
descriptors = zernike_moments(points, pick_faces,
order, scale_input,
decimate_fraction,
decimate_smooth)
#-------------------------------------------------------------
# Append to a list of lists of spectra:
#-------------------------------------------------------------
descriptors_lists.append(descriptors)
label_list.append(label)
return descriptors_lists, label_list
def spectrum_per_label(vtk_file, spectrum_size=10, exclude_labels=[-1],
normalization='area', area_file='',
largest_segment=True):
"""
Compute Laplace-Beltrami spectrum per labeled region in a file.
Parameters
----------
vtk_file : string
name of VTK surface mesh file containing index scalars (labels)
spectrum_size : integer
number of eigenvalues to be computed (the length of the spectrum)
exclude_labels : list of integers
labels to be excluded
normalization : string
the method used to normalize eigenvalues ('area' or None)
if "area", use area of the 2D structure as in Reuter et al. 2006
area_file : string
name of VTK file with surface area scalar values
largest_segment : Boolean
compute spectrum only for largest segment with a given label?
Returns
-------
spectrum_lists : list of lists
first eigenvalues for each label's Laplace-Beltrami spectrum
label_list : list of integers
list of unique labels for which spectra are obtained
Examples
--------
>>> # Uncomment "if label==22:" below to run example:
>>> # Spectrum for Twins-2-1 left postcentral (22) pial surface:
>>> import os
>>> from mindboggle.shapes.laplace_beltrami import spectrum_per_label
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT31.manual.vtk')
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> spectrum_size = 6
>>> exclude_labels = [0] #[-1]
>>> largest_segment = True
>>> spectrum_per_label(vtk_file, spectrum_size, exclude_labels, None,
>>> area_file, largest_segment)
([[6.3469513010430304e-18,
0.0005178862383467463,
0.0017434911095630772,
0.003667561767487686,
0.005429017880363784,
0.006309346984678924]],
[22])
"""
from mindboggle.utils.io_vtk import read_vtk, read_scalars
from mindboggle.utils.mesh import remove_faces, reindex_faces_points
from mindboggle.shapes.laplace_beltrami import fem_laplacian,\
spectrum_of_largest
# Read VTK surface mesh file:
faces, u1, u2, points, u4, labels, u5, u6 = read_vtk(vtk_file)
# Area file:
if area_file:
areas, u1 = read_scalars(area_file)
else:
areas = None
# Loop through labeled regions:
ulabels = []
[ulabels.append(int(x)) for x in labels if x not in ulabels
if x not in exclude_labels]
label_list = []
spectrum_lists = []
for label in ulabels:
#if label == 22:
# print("DEBUG: COMPUTE FOR ONLY ONE LABEL")
# Determine the indices per label:
Ilabel = [i for i,x in enumerate(labels) if x == label]
print('{0} vertices for label {1}'.format(len(Ilabel), label))
# Remove background faces:
pick_faces = remove_faces(faces, Ilabel)
pick_faces, pick_points, o1 = reindex_faces_points(pick_faces, points)
# Compute Laplace-Beltrami spectrum for the label:
if largest_segment:
exclude_labels_inner = [-1]
spectrum = spectrum_of_largest(pick_points, pick_faces,
spectrum_size,
exclude_labels_inner,
normalization, areas)
else:
spectrum = fem_laplacian(pick_points, pick_faces,
spectrum_size, normalization)
# Append to a list of lists of spectra:
spectrum_lists.append(spectrum)
label_list.append(label)
return spectrum_lists, label_list
def close_surface_pair(faces, points1, points2, scalars, background_value=-1):
"""
Close a surface patch by connecting its border vertices with
corresponding vertices in a second surface file.
Assumes no lines or indices when reading VTK files in.
Note ::
Scalar values different than background define the surface patch.
The two sets of points have a 1-to-1 mapping; they are from
two surfaces whose corresponding vertices are shifted in position.
For pial vs. gray-white matter, the two surfaces are not parallel,
so connecting the vertices leads to intersecting faces.
Parameters
----------
faces : list of lists of integers
each sublist contains 3 indices of vertices that form a face
on a surface mesh
points1 : list of lists of floats
each sublist contains 3-D coordinates of a vertex on a surface mesh
points2 : list of lists of floats
points from second surface with 1-to-1 correspondence with points1
scalars : numpy array of integers
labels used to find foreground vertices
background_value : integer
scalar value for background vertices
Returns
-------
closed_faces : list of lists of integers
indices of vertices that form a face on the closed surface mesh
closed_points : list of lists of floats
3-D coordinates from points1 and points2
closed_scalars : list of integers
scalar values for points1 and points2
Examples
--------
>>> # Example 1: build a cube by closing two parallel planes:
>>> import os
>>> from mindboggle.utils.morph import close_surface_pair
>>> from mindboggle.utils.plots import plot_surfaces
>>> from mindboggle.utils.io_vtk import write_vtk
>>> # Build plane:
>>> background_value = -1
>>> n = 10 # plane edge length
>>> points1 = []
>>> for x in range(n):
>>> for y in range(n):
>>> points1.append([x,y,0])
>>> points2 = [[x[0],x[1],1] for x in points1]
>>> scalars = [background_value for x in range(len(points1))]
>>> p = n*(n-1)/2 - 1
>>> for i in [p, p+1, p+n, p+n+1]:
>>> scalars[i] = 1
>>> faces = []
>>> for x in range(n-1):
>>> for y in range(n-1):
>>> faces.append([x+y*n,x+n+y*n,x+n+1+y*n])
>>> faces.append([x+y*n,x+1+y*n,x+n+1+y*n])
>>> #write_vtk('plane.vtk', points1, [], [], faces, scalars)
>>> #plot_surfaces('plane.vtk') # doctest: +SKIP
>>> closed_faces, closed_points, closed_scalars = close_surface_pair(faces, points1, points2, scalars, background_value)
>>> # View:
>>> write_vtk('cube.vtk', closed_points, [], [], closed_faces, closed_scalars, 'int')
>>> plot_surfaces('cube.vtk') # doctest: +SKIP
>>> #
>>> # Example 2: Gray and white cortical brain surfaces:
>>> import os
>>> from mindboggle.utils.morph import close_surface_pair
>>> from mindboggle.utils.plots import plot_surfaces
>>> from mindboggle.utils.io_vtk import read_scalars, read_vtk, read_points, write_vtk
>>> path = os.environ['MINDBOGGLE_DATA']
>>> patch_surface1 = 'fold.pial.vtk'
>>> whole_surface2 = 'fold.white.vtk'
>>> # Select a single fold:
>>> folds_file = os.path.join(path, 'arno', 'features', 'folds.vtk')
>>> points1 = read_points(folds_file)
>>> scalars, name = read_scalars(folds_file, True, True)
>>> fold_number = 11
>>> scalars[scalars != fold_number] = -1
>>> white_surface = os.path.join(path, 'arno', 'freesurfer', 'lh.white.vtk')
>>> faces, u1, u2, points2, N, u3, u4, u5 = read_vtk(white_surface)
>>> background_value = -1
>>> closed_faces, closed_points, closed_scalars = close_surface_pair(faces, points1, points2, scalars, background_value)
>>> # View:
>>> write_vtk('closed.vtk', closed_points, [], [], closed_faces, closed_scalars, name, 'int')
>>> plot_surfaces('closed.vtk') # doctest: +SKIP
"""
import sys
import numpy as np
from mindboggle.utils.mesh import find_neighbors, remove_faces
from mindboggle.utils.segment import extract_borders
if isinstance(scalars, list):
scalars = np.array(scalars)
N = len(points1)
closed_points = points1 + points2
# Find all vertex neighbors and surface patch border vertices:
neighbor_lists = find_neighbors(faces, N)
I = np.where(scalars != background_value)[0]
scalars[scalars == background_value] = background_value + 1
scalars[I] = background_value + 2
scalars = scalars.tolist()
borders, u1, u2 = extract_borders(range(N), scalars, neighbor_lists)
if not len(borders):
sys.exit('There are no border vertices!')
borders = [x for x in borders if x in I]
# Reindex copy of faces and combine with original (both zero-index):
indices = range(N)
indices2 = range(N, 2 * N)
reindex = dict([(index, indices2[i]) for i, index in enumerate(indices)])
faces = remove_faces(faces, I)
faces2 = [[reindex[i] for i in face] for face in faces]
closed_faces = faces + faces2
# Connect border vertices between surface patches and add new faces:
add_faces = []
taken_already = []
for index in borders:
if index not in taken_already:
neighbors = list(set(neighbor_lists[index]).intersection(borders))
taken_already.append(index)
#taken_already.extend([index] + neighbors)
for neighbor in neighbors:
add_faces.append([index, index + N, neighbor])
add_faces.append([index + N, neighbor, neighbor + N])
closed_faces = closed_faces + add_faces
closed_scalars = scalars * 2
return closed_faces, closed_points, closed_scalars
def write_average_face_values_per_label(
input_indices_vtk, input_values_vtk="", area_file="", output_stem="", exclude_values=[-1], background_value=-1
):
"""
Write out a separate VTK file for each integer (>-1)
in (the first) scalar list of an input VTK file.
Optionally write the values drawn from a second VTK file.
Parameters
----------
input_indices_vtk : string
path of the input VTK file that contains indices as scalars
input_values_vtk : string
path of the input VTK file that contains values as scalars
output_stem : string
path and stem of the output VTK file
exclude_values : list or array
values to exclude
background_value : integer or float
background value in output VTK files
scalar_name : string
name of a lookup table of scalars values
Examples
--------
>>> import os
>>> from mindboggle.utils.io_table import write_average_face_values_per_label
>>> path = os.environ['MINDBOGGLE_DATA']
>>> input_indices_vtk = os.path.join(path, 'allen', 'labels', 'lh.DKTatlas100.gcs.vtk')
>>> input_values_vtk = os.path.join(path, 'allen', 'shapes', 'lh.thickness.vtk')
>>> area_file = os.path.join(path, 'allen', 'shapes', 'lh.pial.area.vtk')
>>> output_stem = 'labels_thickness'
>>> exclude_values = [-1]
>>> background_value = -1
>>> #
>>> write_average_face_values_per_label(input_indices_vtk,
>>> input_values_vtk, area_file, output_stem, exclude_values, background_value)
>>> #
>>> # View:
>>> #example_vtk = os.path.join(os.getcwd(), output_stem + '0.vtk')
>>> #from mindboggle.utils.plots import plot_vtk
>>> #plot_vtk(example_vtk)
"""
import os
import numpy as np
from mindboggle.utils.io_vtk import read_scalars, read_vtk, write_vtk
from mindboggle.utils.io_table import write_columns
from mindboggle.utils.mesh import remove_faces
# Load VTK file:
faces, lines, indices, points, npoints, scalars, scalar_names, foo1 = read_vtk(input_indices_vtk, True, True)
if area_file:
area_scalars, name = read_scalars(area_file, True, True)
print("Explode the scalar list in {0}".format(os.path.basename(input_indices_vtk)))
if input_values_vtk != input_indices_vtk:
values, name = read_scalars(input_values_vtk, True, True)
print(
"Explode the scalar list of values in {0} "
"with the scalar list of indices in {1}".format(
os.path.basename(input_values_vtk), os.path.basename(input_indices_vtk)
)
)
else:
values = np.copy(scalars)
# Loop through unique (non-excluded) scalar values:
unique_scalars = [int(x) for x in np.unique(scalars) if x not in exclude_values]
for scalar in unique_scalars:
keep_indices = [x for sublst in faces for x in sublst]
new_faces = remove_faces(faces, keep_indices)
# Create array and indices for scalar value:
select_scalars = np.copy(scalars)
select_scalars[scalars != scalar] = background_value
scalar_indices = [i for i, x in enumerate(select_scalars) if x == scalar]
print(" Scalar {0}: {1} vertices".format(scalar, len(scalar_indices)))
# ---------------------------------------------------------------------
# For each face, average vertex values:
# ---------------------------------------------------------------------
output_table = os.path.join(os.getcwd(), output_stem + str(scalar) + ".csv")
columns = []
for face in new_faces:
values = []
for index in face:
if area_file:
values.append(scalars[index] / area_scalars[index])
else:
values.append(scalars[index])
columns.append(np.mean(values))
# -----------------------------------------------------------------
# Write to table:
# -----------------------------------------------------------------
write_columns(columns, "", output_table, delimiter=",", quote=False)
return W, Path, Degree, TreeNbr
# Example use of the minimum spanning tree algorithm
if __name__ == "__main__" :
import os
import networkx as nx
from mindboggle.utils.io_vtk import read_vtk, rewrite_scalars
from mindboggle.utils.mesh import find_neighbors, remove_faces
from mindboggle.utils.mesh import min_span_tree
from mindboggle.utils.plots import plot_vtk
data_path = os.environ['MINDBOGGLE_DATA']
sulci_file = os.path.join(data_path, 'arno', 'features', 'sulci.vtk')
faces, lines, indices, points, npoints, sulci, name, input_vtk = read_vtk(sulci_file)
sulcus_ID = 1
sulcus_indices = [i for i,x in enumerate(sulci) if x == sulcus_ID]
sulcus_faces = remove_faces(faces, sulcus_indices)
sulcus_neighbor_lists = find_neighbors(sulcus_faces, len(points))
G=nx.Graph()
G.add_nodes_from(sulcus_indices)
for i, sulcus_neighbor_list in enumerate(sulcus_neighbor_lists):
G.add_edges_from([[i,x] for x in sulcus_neighbor_list])
adjacency_matrix = nx.adjacency_matrix(G, nodelist=None, weight='weight')
indices_to_connect = [0, len(sulcus_indices)-1]
adjacency_matrix2, W, Path, Degree, TreeNbr = min_span_tree(adjacency_matrix,
indices_to_connect)
# Write results to vtk file and view:
MST = np.zeros(len(points))
MST[W] = 1
rewrite_scalars(sulci_file, 'test_min_span_tree.vtk', MST, 'MST', MST)
def zernike_moments_per_label(vtk_file, order=20, exclude_labels=[-1], area_file="", largest_segment=True):
"""
Compute the Zernike moments per labeled region in a file.
Parameters
----------
vtk_file : string
name of VTK surface mesh file containing index scalars (labels)
order : integer
number of moments to compute
exclude_labels : list of integers
labels to be excluded
area_file : string
name of VTK file with surface area scalar values
largest_segment : Boolean
compute moments only for largest segment with a given label?
Returns
-------
descriptors_lists : list of lists of floats
Zernike descriptors per label
label_list : list of integers
list of unique labels for which moments are computed
Examples
--------
>>> # Moments for label 22 (postcentral) in Twins-2-1:
>>> import os
>>> from mindboggle.shapes.zernike.zernike import zernike_moments_per_label
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> order = 3
>>> exclude_labels = [0]
>>> largest_segment = True
>>> zernike_moments_per_label(vtk_file, order, exclude_labels, area_file,
>>> largest_segment)
([[7562.751480397972,
143262239.5171249,
1107670.7893994227,
28487908892.820065,
112922387.17238183,
10250734140.30357]],
[22])
>>> order = 10
>>> zernike_moments_per_label(vtk_file, order, exclude_labels, area_file,
>>> largest_segment)
([[7562.751480397972,
143262239.5171249,
3308874674202.293,
8.485211965384958e+16,
2.3330162566631947e+21,
6.743205749389719e+25,
1107670.7893994227,
28487908892.820065,
750581458956752.5,
2.08268406178679e+19,
6.041241636463012e+23,
112922387.17238183,
3771094165018.0186,
1.1436534456761454e+17,
3.475222918728238e+21,
1.0745294340540639e+26,
10250734140.30357,
429344737184365.75,
1.4944306620454633e+19,
4.98685998888202e+23,
889109957039.494,
4.5419095219797416e+16,
1.798809048329269e+21,
6.5720455808877056e+25,
76646448525991.2,
4.648745223427816e+18,
2.067942924550439e+23,
6705825311489244.0,
4.701251187236028e+20,
2.3147665646780795e+25,
5.969381989053711e+17,
4.728007168783364e+22,
5.360784767352255e+19,
4.7214146910478664e+24,
4.813773883638603e+21,
4.3049570618844856e+23]],
[22])
"""
from mindboggle.utils.io_vtk import read_vtk, read_scalars
from mindboggle.utils.mesh import remove_faces
from mindboggle.shapes.zernike.zernike import zernike_moments, zernike_moments_of_largest
# Read VTK surface mesh file:
faces, u1, u2, points, u4, labels, u5, u6 = read_vtk(vtk_file)
# Area file:
if area_file:
areas, u1 = read_scalars(area_file)
else:
areas = None
# Loop through labeled regions:
ulabels = []
[ulabels.append(int(x)) for x in labels if x not in ulabels if x not in exclude_labels]
label_list = []
descriptors_lists = []
for label in ulabels:
# if label==22:
# print("DEBUG: COMPUTE FOR ONLY ONE LABEL")
# Determine the indices per label:
label_indices = [i for i, x in enumerate(labels) if x == label]
print("{0} vertices for label {1}".format(len(label_indices), label))
# Remove background faces:
select_faces = remove_faces(faces, label_indices)
# Compute Zernike moments for the label:
if largest_segment:
exclude_labels_inner = [-1]
descriptors = zernike_moments_of_largest(points, select_faces, order, exclude_labels_inner, areas)
else:
descriptors = zernike_moments(points, select_faces, order)
# Append to a list of lists of spectra:
descriptors_lists.append(descriptors)
label_list.append(label)
return descriptors_lists, label_list
def spectrum_per_label(vtk_file, n_eigenvalues=3, exclude_labels=[-1],
normalization='area', area_file=''):
"""
Compute Laplace-Beltrami spectrum per labeled region in a file.
Parameters
----------
vtk_file : string
name of VTK surface mesh file containing index scalars (labels)
n_eigenvalues : integer
number of eigenvalues to be computed (the length of the spectrum)
exclude_labels : list of integers
labels to be excluded
normalization : string
the method used to normalize eigenvalues ('area' or None)
if "area", use area of the 2D structure as in Reuter et al. 2006
area_file : string
name of VTK file with surface area scalar values
Returns
-------
spectrum_lists : list of lists
first eigenvalues for each label's Laplace-Beltrami spectrum
label_list : list of integers
list of unique labels for which spectra are obtained
Examples
--------
>>> # Spectrum for label 22 (postcentral) in Twins-2-1:
>>> import os
>>> from mindboggle.shapes.laplace_beltrami import laplacian_per_label
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> n_eigenvalues = 6
>>> exclude_labels = [0] #[-1]
>>> laplacian_per_label(vtk_file, n_eigenvalues, exclude_labels,
>>> normalization=None, area_file=area_file)
Load "Labels" scalars from lh.labels.DKT25.manual.vtk
Load "scalars" scalars from lh.pial.area.vtk
7819 vertices for label 22
Reduced 290134 to 15230 triangular faces
Linear FEM Laplace-Beltrami spectrum:
([[6.3469513010430304e-18,
0.0005178862383467463,
0.0017434911095630772,
0.003667561767487686,
0.005429017880363784,
0.006309346984678924]],
[22])
"""
from mindboggle.utils.io_vtk import read_vtk, read_scalars
from mindboggle.utils.mesh import remove_faces
from mindboggle.shapes.laplace_beltrami import spectrum_of_largest
# Read VTK surface mesh file:
faces, u1, u2, points, u4, labels, u5, u6 = read_vtk(vtk_file)
# Area file:
if area_file:
areas, u1 = read_scalars(area_file)
else:
areas = None
# Loop through labeled regions:
ulabels = []
[ulabels.append(int(x)) for x in labels if x not in ulabels
if x not in exclude_labels]
label_list = []
spectrum_lists = []
for label in ulabels:
#if label==22:
# Determine the indices per label:
label_indices = [i for i,x in enumerate(labels) if x == label]
print('{0} vertices for label {1}'.format(len(label_indices), label))
# Remove background faces:
select_faces = remove_faces(faces, label_indices)
# Compute Laplace-Beltrami spectrum for the label:
spectrum = spectrum_of_largest(points, select_faces, n_eigenvalues,
exclude_labels, normalization, areas)
# Append to a list of lists of spectra:
spectrum_lists.append(spectrum)
label_list.append(label)
return spectrum_lists, label_list
def propagate(points, faces, region, seeds, labels,
max_iters=500, tol=0.001, sigma=10):
"""
Propagate labels to segment surface into contiguous regions,
starting from seed vertices.
Imports : mindboggle.labels.rebound
Parameters
----------
points : array (or list) of lists of three integers
coordinates for all vertices
faces : list of lists of three integers
indices to three vertices per face (indices start from zero)
region : list (or array) of integers
values > -1 indicate inclusion in a region for all vertices
seeds : numpy array of integers
seed numbers for all vertices (default -1 for not a seed)
labels : numpy array of integers
label numbers for all vertices, with -1s for unlabeled vertices
max_iters : integer
maximum number of iterations to run graph-based learning algorithm
tol: float
threshold to assess convergence of the algorithm
sigma: float
gaussian kernel parameter
Returns
-------
segments : numpy array of integers
region numbers for all vertices (default -1)
Examples
--------
>>> # Propagate labels between label boundary segments in a single fold:
>>> import os
>>> import numpy as np
>>> import mindboggle.labels.rebound as rb
>>> from mindboggle.utils.mesh import find_neighbors
>>> from mindboggle.labels.labels import extract_borders
>>> from mindboggle.utils.segment import propagate
>>> from mindboggle.utils.io_vtk import read_scalars, read_vtk, rewrite_scalars
>>> from mindboggle.labels.protocol import dkt_protocol
>>> protocol = 'DKT25'
>>> sulcus_names, sulcus_label_pair_lists, unique_sulcus_label_pairs,
... label_names, label_numbers, cortex_names, cortex_numbers,
... noncortex_names, noncortex_numbers = dkt_protocol(protocol)
>>> path = os.environ['MINDBOGGLE_DATA']
>>> folds_file = os.path.join(path, 'arno', 'features', 'folds.vtk')
>>> labels_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> folds, name = read_scalars(folds_file, return_first=True, return_array=True)
>>> faces, lines, indices, points, npoints, labels, name, input_vtk = read_vtk(labels_file,
>>> return_first=True, return_array=True)
>>> neighbor_lists = find_neighbors(faces, npoints)
>>> indices_borders, label_pairs, foo = extract_borders(range(npoints),
>>> labels, neighbor_lists)
>>> # Select a single fold
>>> fold_ID = 2
>>> indices_fold = [i for i,x in enumerate(folds) if x == fold_ID]
>>> fold_array = -1 * np.ones(npoints)
>>> fold_array[indices_fold] = 1
>>> # Extract the boundary for this fold
>>> indices_borders, label_pairs, foo = extract_borders(indices_fold,
>>> labels, neighbor_lists)
>>> # Select boundary segments in the sulcus labeling protocol
>>> seeds = -1 * np.ones(npoints)
>>> for ilist,label_pair_list in enumerate(sulcus_label_pair_lists):
>>> I = [x for i,x in enumerate(indices_borders)
>>> if np.sort(label_pairs[i]).tolist() in label_pair_list]
>>> seeds[I] = ilist
>>> #
>>> segments = propagate(points, faces, fold_array, seeds, labels)
>>> #
>>> # Write results to vtk file and view:
>>> rewrite_scalars(labels_file, 'propagate.vtk',
>>> segments, 'segments', segments)
>>> from mindboggle.utils.plots import plot_vtk
>>> plot_vtk('propagate.vtk')
"""
import numpy as np
from mindboggle.utils.mesh import remove_faces
import mindboggle.utils.kernels as kernels
import mindboggle.labels.rebound as rb
# Make sure arguments are numpy arrays
if not isinstance(seeds, np.ndarray):
seeds = np.array(seeds)
if not isinstance(labels, np.ndarray):
labels = np.array(labels)
if not isinstance(points, np.ndarray):
points = np.array(points)
indices_region = [i for i,x in enumerate(region) if x > -1]
if indices_region and faces:
local_indices_region = -1 * np.ones(labels.shape)
local_indices_region[indices_region] = range(len(indices_region))
if points.size:
n_sets = len(np.unique([x for x in seeds if x > -1]))
if n_sets == 1:
print('Segment {0} vertices from 1 set of seed vertices'.
format(len(indices_region)))
else:
print('Segment {0} vertices from {1} sets of seed vertices'.
format(len(indices_region), n_sets))
# Remove faces whose three vertices are not among specified indices:
refaces = remove_faces(faces, indices_region)
# Set up rebound Bounds class instance
B = rb.Bounds()
if refaces:
B.Faces = np.array(refaces)
B.Indices = local_indices_region
B.Points = points[indices_region]
B.Labels = labels[indices_region]
B.seed_labels = seeds[indices_region]
B.num_points = len(B.Points)
# Propagate seed IDs from seeds
B.graph_based_learning(method='propagate_labels', realign=False,
kernel=kernels.rbf_kernel, sigma=sigma,
max_iters=max_iters, tol=tol, vis=False)
else:
print(" No faces")
# Assign maximum probability seed IDs to each point of region
max_prob_labels = B.assign_max_prob_label()
# Return segment IDs in original vertex array
segments = -1 * np.ones(len(points))
segments[indices_region] = max_prob_labels
else:
segments = -1 * np.ones(len(points))
return segments
def spectrum_per_label(vtk_file, spectrum_size=10, exclude_labels=[-1],
normalization='area', area_file='',
largest_segment=True):
"""
Compute Laplace-Beltrami spectrum per labeled region in a file.
Parameters
----------
vtk_file : string
name of VTK surface mesh file containing index scalars (labels)
spectrum_size : integer
number of eigenvalues to be computed (the length of the spectrum)
exclude_labels : list of integers
labels to be excluded
normalization : string
the method used to normalize eigenvalues ('area' or None)
if "area", use area of the 2D structure as in Reuter et al. 2006
area_file : string
name of VTK file with surface area scalar values
largest_segment : Boolean
compute spectrum only for largest segment with a given label?
Returns
-------
spectrum_lists : list of lists
first eigenvalues for each label's Laplace-Beltrami spectrum
label_list : list of integers
list of unique labels for which spectra are obtained
Examples
--------
>>> # Uncomment "if label==22:" below to run example:
>>> # Spectrum for Twins-2-1 left postcentral (22) pial surface:
>>> import os
>>> from mindboggle.shapes.laplace_beltrami import spectrum_per_label
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT31.manual.vtk')
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> spectrum_size = 6
>>> exclude_labels = [0] #[-1]
>>> largest_segment = True
>>> spectrum_per_label(vtk_file, spectrum_size, exclude_labels, None,
>>> area_file, largest_segment)
([[6.3469513010430304e-18,
0.0005178862383467463,
0.0017434911095630772,
0.003667561767487686,
0.005429017880363784,
0.006309346984678924]],
[22])
"""
from mindboggle.utils.io_vtk import read_vtk, read_scalars
from mindboggle.utils.mesh import remove_faces, reindex_faces_points
from mindboggle.shapes.laplace_beltrami import fem_laplacian,\
spectrum_of_largest
# Read VTK surface mesh file:
faces, u1, u2, points, u4, labels, u5, u6 = read_vtk(vtk_file)
# Area file:
if area_file:
areas, u1 = read_scalars(area_file)
else:
areas = None
# Loop through labeled regions:
ulabels = []
[ulabels.append(int(x)) for x in labels if x not in ulabels
if x not in exclude_labels]
label_list = []
spectrum_lists = []
for label in ulabels:
#if label == 22:
# print("DEBUG: COMPUTE FOR ONLY ONE LABEL")
# Determine the indices per label:
Ilabel = [i for i,x in enumerate(labels) if x == label]
print('{0} vertices for label {1}'.format(len(Ilabel), label))
# Remove background faces:
pick_faces = remove_faces(faces, Ilabel)
pick_faces, pick_points, o1 = reindex_faces_points(pick_faces, points)
# Compute Laplace-Beltrami spectrum for the label:
if largest_segment:
exclude_labels_inner = [-1]
spectrum = spectrum_of_largest(pick_points, pick_faces,
spectrum_size,
exclude_labels_inner,
normalization, areas)
else:
spectrum = fem_laplacian(pick_points, pick_faces,
spectrum_size, normalization)
# Append to a list of lists of spectra:
spectrum_lists.append(spectrum)
label_list.append(label)
return spectrum_lists, label_list
def spectrum_of_largest(points, faces, n_eigenvalues=6, exclude_labels=[-1],
normalization=None, areas=None):
"""
Compute Laplace-Beltrami spectrum on largest connected segment.
In case a surface patch is fragmented, we select the largest fragment,
remove extraneous triangular faces, and reindex indices.
Parameters
----------
points : list of lists of 3 floats
x,y,z coordinates for each vertex of the structure
faces : list of lists of 3 integers
3 indices to vertices that form a triangle on the mesh
n_eigenvalues : integer
number of eigenvalues to be computed (the length of the spectrum)
exclude_labels : list of integers
background values to exclude
normalization : string
the method used to normalize eigenvalues ('area' or None)
if "area", use area of the 2D structure as in Reuter et al. 2006
areas : numpy array or list of floats (or None)
surface area scalar values for all vertices
Returns
-------
spectrum : list
first n_eigenvalues eigenvalues for Laplace-Beltrami spectrum
Examples
--------
>>> # Spectrum for one label (artificial composite), two fragments:
>>> import os
>>> import numpy as np
>>> from mindboggle.utils.io_vtk import read_scalars, read_vtk, write_vtk
>>> from mindboggle.utils.mesh import remove_faces
>>> from mindboggle.shapes.laplace_beltrami import spectrum_of_largest
>>> path = os.environ['MINDBOGGLE_DATA']
>>> label_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> n_eigenvalues = 6
>>> exclude_labels = [0] #[-1]
>>> normalization = None
>>> faces, lines, indices, points, foo1, labels, foo2, foo3 = read_vtk(label_file,
>>> return_first=True, return_array=True)
>>> I2 = [i for i,x in enumerate(labels) if x==2] # cingulate
>>> I22 = [i for i,x in enumerate(labels) if x==22] # postcentral
>>> I2.extend(I22)
>>> faces = remove_faces(faces, I2)
>>> areas, u1 = read_scalars(area_file, True, True)
>>> #
>>> spectrum_of_largest(points, faces, n_eigenvalues, exclude_labels,
>>> normalization, areas)
>>> #
>>> # View:
>>> from mindboggle.utils.plots import plot_vtk
>>> scalars = np.zeros(np.shape(labels))
>>> scalars[I2] = 1
>>> vtk_file = 'test_two_labels.vtk'
>>> write_vtk(vtk_file, points, indices, lines, faces,
>>> scalars, scalar_names='scalars')
>>> plot_vtk(vtk_file)
Load "Labels" scalars from lh.labels.DKT25.manual.vtk
Reduced 290134 to 29728 triangular faces
Load "scalars" scalars from lh.pial.area.vtk
2 segments
Reduced 29728 to 14498 triangular faces
Compute linear FEM Laplace-Beltrami spectrum
[-8.764053090852845e-18,
0.00028121452203987146,
0.0010941205613292243,
0.0017301461686759188,
0.0034244633555606295,
0.004280982704174599]
"""
from scipy.sparse.linalg import eigsh, lobpcg
import numpy as np
from mindboggle.utils.mesh import find_neighbors, remove_faces, \
reindex_faces_points
from mindboggle.utils.segment import segment
from mindboggle.shapes.laplace_beltrami import fem_laplacian
# Areas:
use_area = False
if isinstance(areas, np.ndarray) and np.shape(areas):
use_area = True
elif isinstance(areas, list) and len(areas):
areas = np.array(areas)
use_area = True
# Check to see if there are enough points:
min_npoints = n_eigenvalues
npoints = len(points)
if npoints < min_npoints or len(faces) < min_npoints:
print("The input size {0} ({1} faces) should be much larger "
"than n_eigenvalues {2}".
format(npoints, len(faces), n_eigenvalues))
return None
else:
#---------------------------------------------------------------------
# Segment the indices into connected sets of indices:
#---------------------------------------------------------------------
# Construct neighbor lists:
neighbor_lists = find_neighbors(faces, npoints)
# Determine the indices:
indices = [x for sublst in faces for x in sublst]
# Segment:
segments = segment(indices, neighbor_lists, min_region_size=1,
seed_lists=[], keep_seeding=False, spread_within_labels=False,
labels=[], label_lists=[], values=[], max_steps='', verbose=False)
#---------------------------------------------------------------------
# Select the largest segment (connected set of indices):
#---------------------------------------------------------------------
unique_segments = [x for x in np.unique(segments)
if x not in exclude_labels]
if len(unique_segments) > 1:
select_indices = []
max_segment_area = 0
for segment_number in unique_segments:
segment_indices = [i for i,x in enumerate(segments)
if x == segment_number]
if use_area:
segment_area = np.sum(areas[segment_indices])
else:
segment_area = len(segment_indices)
if segment_area > max_segment_area:
select_indices = segment_indices
max_segment_area = len(select_indices)
print('Maximum size of {0} segments: {1} vertices'.
format(len(unique_segments), len(select_indices)))
#-----------------------------------------------------------------
# Extract points and renumber faces for the selected indices:
#-----------------------------------------------------------------
faces = remove_faces(faces, select_indices)
else:
select_indices = indices
# Alert if the number of indices is small:
if len(select_indices) < min_npoints:
print("The input size {0} is too small.".format(len(select_indices)))
return None
elif faces:
#-----------------------------------------------------------------
# Reindex indices in faces:
#-----------------------------------------------------------------
faces, points = reindex_faces_points(faces, points)
#-----------------------------------------------------------------
# Compute spectrum:
#-----------------------------------------------------------------
spectrum = fem_laplacian(points, faces, n_eigenvalues,
normalization)
return spectrum
else:
return None
def rewrite_scalars(input_vtk, output_vtk, new_scalars,
new_scalar_names=['scalars'], filter_scalars=[]):
"""
Load VTK format file and save a subset of scalars into a new file.
Parameters
----------
input_vtk : string
input VTK file name
output_vtk : string
output VTK file name
new_scalars : list of lists of floats (or single list or array of floats)
each list (lookup table) contains new values to assign to the vertices
new_scalar_names : string or list of strings
each element is the new name for a lookup table
filter_scalars : list or numpy array (optional)
scalar values used to filter faces (values > -1 retained)
Returns
-------
output_vtk : string
output VTK file name
Examples
--------
>>> # Write vtk file with curvature values on sulci
>>> import os
>>> from mindboggle.utils.io_vtk import read_scalars, rewrite_scalars
>>> path = os.environ['MINDBOGGLE_DATA']
>>> curv_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.mean_curvature.vtk')
>>> curvs, name = read_scalars(curv_file, True,True)
>>> sulci_file = os.path.join(path, 'arno', 'features', 'sulci.vtk')
>>> sulci, name = read_scalars(sulci_file)
>>> #
>>> rewrite_scalars(curv_file, 'rewrite_scalars.vtk',
>>> [curvs, sulci], ['curvs', 'sulci'], sulci)
>>> #
>>> # View:
>>> from mindboggle.utils.plots import plot_vtk
>>> plot_vtk('rewrite_scalars.vtk')
"""
import os
import numpy as np
from mindboggle.utils.mesh import remove_faces
from mindboggle.utils.io_vtk import write_header, write_points, \
write_vertices, write_faces, write_scalars, read_vtk, \
scalars_checker
# Convert numpy arrays to lists
if isinstance(new_scalars, np.ndarray):
new_scalars = new_scalars.tolist()
if isinstance(filter_scalars, np.ndarray):
filter_scalars = filter_scalars.tolist()
# Output VTK file to current working directory
output_vtk = os.path.join(os.getcwd(), output_vtk)
# Load VTK file
faces, lines, indices, points, npoints, scalars, name, input_vtk = read_vtk(input_vtk)
# Find indices to nonzero values
indices = range(npoints)
if filter_scalars:
indices_filter = [i for i,x in enumerate(filter_scalars) if x > -1]
indices_remove = [i for i,x in enumerate(filter_scalars) if x == -1]
# Remove surface mesh faces whose three vertices are not all in indices
faces = remove_faces(faces, indices_filter)
# Write VTK file
Fp = open(output_vtk,'w')
write_header(Fp)
write_points(Fp, points)
if indices:
write_vertices(Fp, indices)
if faces:
write_faces(Fp, faces)
if new_scalars:
new_scalars, new_scalar_names = scalars_checker(new_scalars, new_scalar_names)
for i, new_scalar_list in enumerate(new_scalars):
if filter_scalars:
for iremove in indices_remove:
new_scalar_list[iremove] = -1
if i == 0:
new_scalar_name = new_scalar_names[0]
write_scalars(Fp, new_scalar_list, new_scalar_name)
else:
if len(new_scalar_names) < i + 1:
new_scalar_name = new_scalar_names[0]
else:
new_scalar_name = new_scalar_names[i]
write_scalars(Fp, new_scalar_list, new_scalar_name, begin_scalars=False)
else:
print('Error: new_scalars is empty')
exit()
Fp.close()
return output_vtk
def evaluate_deep_features(features_file, labels_file, sulci_file='', hemi='',
excludeIDs=[-1], output_vtk_name='', verbose=True):
"""
Evaluate deep surface features by computing the minimum distance from each
label boundary vertex to all of the feature vertices in the same sulcus,
and from each feature vertex to all of the label boundary vertices in the
same sulcus. The label boundaries run along the deepest parts of sulci
and correspond to fundi in the DKT cortical labeling protocol.
Parameters
----------
features_file : string
VTK surface file with feature numbers for vertex scalars
labels_file : string
VTK surface file with label numbers for vertex scalars
sulci_file : string
VTK surface file with sulcus numbers for vertex scalars
excludeIDs : list of integers
feature/sulcus/label IDs to exclude (background set to -1)
output_vtk_name : Boolean
if not empty, output a VTK file beginning with output_vtk_name that
contains a surface with mean distances as scalars
verbose : Boolean
print mean distances to standard output?
Returns
-------
feature_to_fundus_mean_distances : numpy array [number of features x 1]
mean distance from each feature to sulcus label boundary ("fundus")
feature_to_fundus_sd_distances : numpy array [number of features x 1]
standard deviations of feature-to-fundus distances
feature_to_fundus_mean_distances_vtk : string
VTK surface file containing feature_to_fundus_mean_distances
fundus_to_feature_mean_distances : numpy array [number of features x 1]
mean distances from each sulcus label boundary ("fundus") to feature
fundus_to_feature_sd_distances : numpy array [number of features x 1]
standard deviations of fundus-to-feature distances
fundus_to_feature_mean_distances_vtk : string
VTK surface file containing fundus_to_feature_mean_distances
"""
import os
import sys
import numpy as np
from mindboggle.utils.io_vtk import read_vtk, read_scalars, write_vtk
from mindboggle.utils.mesh import find_neighbors, remove_faces
from mindboggle.utils.segment import extract_borders
from mindboggle.utils.compute import source_to_target_distances
from mindboggle.LABELS import DKTprotocol
dkt = DKTprotocol()
#-------------------------------------------------------------------------
# Load labels, features, and sulci:
#-------------------------------------------------------------------------
faces, lines, indices, points, npoints, labels, scalar_names, \
input_vtk = read_vtk(labels_file, True, True)
features, name = read_scalars(features_file, True, True)
if sulci_file:
sulci, name = read_scalars(sulci_file, True, True)
# List of indices to sulcus vertices:
sulcus_indices = [i for i,x in enumerate(sulci) if x != -1]
segmentIDs = sulci
sulcus_faces = remove_faces(faces, sulcus_indices)
else:
sulcus_indices = range(len(labels))
segmentIDs = []
sulcus_faces = faces
#-------------------------------------------------------------------------
# Prepare neighbors, label pairs, fundus IDs, and outputs:
#-------------------------------------------------------------------------
# Calculate neighbor lists for all points:
print('Find neighbors to all vertices...')
neighbor_lists = find_neighbors(faces, npoints)
# Find label boundary points in any of the sulci:
print('Find label boundary points in any of the sulci...')
border_indices, border_label_tuples, unique_border_label_tuples = \
extract_borders(sulcus_indices, labels, neighbor_lists,
ignore_values=[], return_label_pairs=True)
if not len(border_indices):
sys.exit('There are no label boundary points!')
# Initialize an array of label boundaries fundus IDs
# (label boundary vertices that define sulci in the labeling protocol):
print('Build an array of label boundary fundus IDs...')
label_boundary_fundi = -1 * np.ones(npoints)
if hemi == 'lh':
nsulcus_lists = len(dkt.left_sulcus_label_pair_lists)
else:
nsulcus_lists = len(dkt.right_sulcus_label_pair_lists)
feature_to_fundus_mean_distances = -1 * np.ones(nsulcus_lists)
feature_to_fundus_sd_distances = -1 * np.ones(nsulcus_lists)
fundus_to_feature_mean_distances = -1 * np.ones(nsulcus_lists)
fundus_to_feature_sd_distances = -1 * np.ones(nsulcus_lists)
feature_to_fundus_mean_distances_vtk = ''
fundus_to_feature_mean_distances_vtk = ''
#-------------------------------------------------------------------------
# Loop through sulci:
#-------------------------------------------------------------------------
# For each list of sorted label pairs (corresponding to a sulcus):
for isulcus, label_pairs in enumerate(dkt.sulcus_label_pair_lists):
# Keep the boundary points with label pair labels:
fundus_indices = [x for i,x in enumerate(border_indices)
if np.unique(border_label_tuples[i]).tolist()
in label_pairs]
# Store the points as sulcus IDs in the fundus IDs array:
if fundus_indices:
label_boundary_fundi[fundus_indices] = isulcus
if len(np.unique(label_boundary_fundi)) > 1:
#---------------------------------------------------------------------
# Construct a feature-to-fundus distance matrix and VTK file:
#---------------------------------------------------------------------
# Construct a distance matrix:
print('Construct a feature-to-fundus distance matrix...')
sourceIDs = features
targetIDs = label_boundary_fundi
distances, distance_matrix = source_to_target_distances(
sourceIDs, targetIDs, points, segmentIDs, excludeIDs)
# Compute mean distances for each feature:
nfeatures = min(np.shape(distance_matrix)[1], nsulcus_lists)
for ifeature in range(nfeatures):
feature_distances = [x for x in distance_matrix[:, ifeature]
if x != -1]
feature_to_fundus_mean_distances[ifeature] = \
np.mean(feature_distances)
feature_to_fundus_sd_distances[ifeature] = \
np.std(feature_distances)
if verbose:
print('Feature-to-fundus mean distances:')
print(feature_to_fundus_mean_distances)
print('Feature-to-fundus standard deviations of distances:')
print(feature_to_fundus_sd_distances)
# Write resulting feature-label boundary distances to VTK file:
if output_vtk_name:
feature_to_fundus_mean_distances_vtk = os.path.join(os.getcwd(),
output_vtk_name + '_feature_to_fundus_mean_distances.vtk')
print('Write feature-to-fundus distances to {0}...'.
format(feature_to_fundus_mean_distances_vtk))
write_vtk(feature_to_fundus_mean_distances_vtk, points,
[], [], sulcus_faces, [distances],
['feature-to-fundus_distances'], 'float')
#---------------------------------------------------------------------
# Construct a fundus-to-feature distance matrix and VTK file:
#---------------------------------------------------------------------
# Construct a distance matrix:
print('Construct a fundus-to-feature distance matrix...')
sourceIDs = label_boundary_fundi
targetIDs = features
distances, distance_matrix = source_to_target_distances(
sourceIDs, targetIDs, points, segmentIDs, excludeIDs)
# Compute mean distances for each feature:
nfeatures = min(np.shape(distance_matrix)[1], nsulcus_lists)
for ifeature in range(nfeatures):
fundus_distances = [x for x in distance_matrix[:, ifeature]
if x != -1]
fundus_to_feature_mean_distances[ifeature] = \
np.mean(fundus_distances)
fundus_to_feature_sd_distances[ifeature] = \
np.std(fundus_distances)
if verbose:
print('Fundus-to-feature mean distances:')
print(fundus_to_feature_mean_distances)
print('Fundus-to-feature standard deviations of distances:')
print(fundus_to_feature_sd_distances)
# Write resulting feature-label boundary distances to VTK file:
if output_vtk_name:
fundus_to_feature_mean_distances_vtk = os.path.join(os.getcwd(),
output_vtk_name + '_fundus_to_feature_mean_distances.vtk')
print('Write fundus-to-feature distances to {0}...'.
format(fundus_to_feature_mean_distances_vtk))
write_vtk(fundus_to_feature_mean_distances_vtk, points,
[], [], sulcus_faces, [distances],
['fundus-to-feature_distances'], 'float')
#-------------------------------------------------------------------------
# Return outputs:
#-------------------------------------------------------------------------
return feature_to_fundus_mean_distances, feature_to_fundus_sd_distances,\
feature_to_fundus_mean_distances_vtk,\
fundus_to_feature_mean_distances, fundus_to_feature_sd_distances,\
fundus_to_feature_mean_distances_vtk
def zernike_moments_per_label(vtk_file, n_moments, exclude_labels=[-1]):
"""
Compute the Zernike moments per labeled region in a file.
Parameters
----------
vtk_file : string
name of VTK surface mesh file containing index scalars (labels)
n_moments : integer
number of moments to compute
exclude_labels : list of integers
labels to be excluded
Returns
-------
moments : numpy matrix
Zernike moments
label_list : list of integers
list of unique labels for which moments are obtained
Examples
--------
>>> import os
>>> from mindboggle.shapes.laplace_beltrami import laplacian_per_label
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT25.manual.vtk')
>>> n_moments = 20
>>> zernike_moments_per_label(vtk_file, n_moments, exclude_labels=[-1]
"""
from mindboggle.utils.io_vtk import read_vtk
from mindboggle.utils.mesh import remove_faces
from mindboggle.shapes.zernike.zernike import zernike_moments
# Read VTK surface mesh file:
faces, u1,u2, points, u4, labels, u5,u6 = read_vtk(vtk_file)
# Loop through labeled regions:
ulabels = []
[ulabels.append(int(x)) for x in labels if x not in ulabels
if x not in exclude_labels]
label_list = []
moments_lists = []
for label in ulabels:
#if label==22:
# Determine the indices per label:
label_indices = [i for i,x in enumerate(labels) if x == label]
print('{0} vertices for label {1}'.format(len(label_indices), label))
# Remove background faces:
select_faces = remove_faces(faces, label_indices)
# Compute Zernike moments for the label:
moments = zernike_moments(points, select_faces, n_moments)
# Append to a list of lists of spectra:
moments_lists.append(moments)
label_list.append(label)
return moments_lists, label_list
def close_surface_pair(faces, points1, points2, scalars, background_value=-1):
"""
Close a surface patch by connecting its border vertices with
corresponding vertices in a second surface file.
Assumes no lines or indices when reading VTK files in.
Note ::
Scalar values different than background define the surface patch.
The two sets of points have a 1-to-1 mapping; they are from
two surfaces whose corresponding vertices are shifted in position.
For pial vs. gray-white matter, the two surfaces are not parallel,
so connecting the vertices leads to intersecting faces.
Parameters
----------
faces : list of lists of integers
each sublist contains 3 indices of vertices that form a face
on a surface mesh
points1 : list of lists of floats
each sublist contains 3-D coordinates of a vertex on a surface mesh
points2 : list of lists of floats
points from second surface with 1-to-1 correspondence with points1
scalars : numpy array of integers
labels used to find foreground vertices
background_value : integer
scalar value for background vertices
Returns
-------
closed_faces : list of lists of integers
indices of vertices that form a face on the closed surface mesh
closed_points : list of lists of floats
3-D coordinates from points1 and points2
closed_scalars : list of integers
scalar values for points1 and points2
Examples
--------
>>> # Example 1: build a cube by closing two parallel planes:
>>> import os
>>> from mindboggle.utils.morph import close_surface_pair
>>> from mindboggle.utils.plots import plot_surfaces
>>> from mindboggle.utils.io_vtk import write_vtk
>>> # Build plane:
>>> background_value = -1
>>> n = 10 # plane edge length
>>> points1 = []
>>> for x in range(n):
>>> for y in range(n):
>>> points1.append([x,y,0])
>>> points2 = [[x[0],x[1],1] for x in points1]
>>> scalars = [background_value for x in range(len(points1))]
>>> p = n*(n-1)/2 - 1
>>> for i in [p, p+1, p+n, p+n+1]:
>>> scalars[i] = 1
>>> faces = []
>>> for x in range(n-1):
>>> for y in range(n-1):
>>> faces.append([x+y*n,x+n+y*n,x+n+1+y*n])
>>> faces.append([x+y*n,x+1+y*n,x+n+1+y*n])
>>> #write_vtk('plane.vtk', points1, [], [], faces, scalars)
>>> #plot_surfaces('plane.vtk') # doctest: +SKIP
>>> closed_faces, closed_points, closed_scalars = close_surface_pair(faces, points1, points2, scalars, background_value)
>>> # View:
>>> write_vtk('cube.vtk', closed_points, [], [], closed_faces, closed_scalars, 'int')
>>> plot_surfaces('cube.vtk') # doctest: +SKIP
>>> #
>>> # Example 2: Gray and white cortical brain surfaces:
>>> import os
>>> from mindboggle.utils.morph import close_surface_pair
>>> from mindboggle.utils.plots import plot_surfaces
>>> from mindboggle.utils.io_vtk import read_scalars, read_vtk, read_points, write_vtk
>>> path = os.environ['MINDBOGGLE_DATA']
>>> patch_surface1 = 'fold.pial.vtk'
>>> whole_surface2 = 'fold.white.vtk'
>>> # Select a single fold:
>>> folds_file = os.path.join(path, 'arno', 'features', 'folds.vtk')
>>> points1 = read_points(folds_file)
>>> scalars, name = read_scalars(folds_file, True, True)
>>> fold_number = 11
>>> scalars[scalars != fold_number] = -1
>>> white_surface = os.path.join(path, 'arno', 'freesurfer', 'lh.white.vtk')
>>> faces, u1, u2, points2, N, u3, u4, u5 = read_vtk(white_surface)
>>> background_value = -1
>>> closed_faces, closed_points, closed_scalars = close_surface_pair(faces, points1, points2, scalars, background_value)
>>> # View:
>>> write_vtk('closed.vtk', closed_points, [], [], closed_faces, closed_scalars, name, 'int')
>>> plot_surfaces('closed.vtk') # doctest: +SKIP
"""
import sys
import numpy as np
from mindboggle.utils.mesh import find_neighbors, remove_faces
from mindboggle.utils.segment import extract_borders
if isinstance(scalars, list):
scalars = np.array(scalars)
N = len(points1)
closed_points = points1 + points2
# Find all vertex neighbors and surface patch border vertices:
neighbor_lists = find_neighbors(faces, N)
I = np.where(scalars != background_value)[0]
scalars[scalars == background_value] = background_value + 1
scalars[I] = background_value + 2
scalars = scalars.tolist()
borders, u1, u2 = extract_borders(range(N), scalars, neighbor_lists)
if not len(borders):
sys.exit('There are no border vertices!')
borders = [x for x in borders if x in I]
# Reindex copy of faces and combine with original (both zero-index):
indices = range(N)
indices2 = range(N, 2 * N)
reindex = dict([(index, indices2[i]) for i, index in enumerate(indices)])
faces = remove_faces(faces, I)
faces2 = [[reindex[i] for i in face] for face in faces]
closed_faces = faces + faces2
# Connect border vertices between surface patches and add new faces:
add_faces = []
taken_already = []
for index in borders:
if index not in taken_already:
neighbors = list(set(neighbor_lists[index]).intersection(borders))
taken_already.append(index)
#taken_already.extend([index] + neighbors)
for neighbor in neighbors:
add_faces.append([index, index + N, neighbor])
add_faces.append([index + N, neighbor, neighbor + N])
closed_faces = closed_faces + add_faces
closed_scalars = scalars * 2
return closed_faces, closed_points, closed_scalars
def plot_mask_surface(vtk_file, mask_file='', nonmask_value=-1,
masked_output='', remove_nonmask=False,
program='vtkviewer',
use_colormap=False, colormap_file=''):
"""
Use vtkviewer or mayavi2 to visualize VTK surface mesh data.
If a mask_file is provided, a temporary masked file is saved,
and it is this file that is viewed.
If using vtkviewer, can optionally provide colormap file
or set $COLORMAP environment variable.
Parameters
----------
vtk_file : string
name of VTK surface mesh file
mask_file : string
name of VTK surface mesh file to mask vtk_file vertices
nonmask_value : integer
nonmask (usually background) value
masked_output : string
temporary masked output file name
remove_nonmask : Boolean
remove vertices that are not in mask? (otherwise assign nonmask_value)
program : string {'vtkviewer', 'mayavi2'}
program to visualize VTK file
use_colormap : Boolean
use Paraview-style XML colormap file set by $COLORMAP env variable?
colormap_file : string
use colormap in given file if use_colormap==True? if empty and
use_colormap==True, use file set by $COLORMAP environment variable
Examples
--------
>>> import os
>>> from mindboggle.utils.plots import plot_mask_surface
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT31.manual.vtk')
>>> mask_file = os.path.join(path, 'test_one_label.vtk')
>>> nonmask_value = 0 #-1
>>> masked_output = ''
>>> remove_nonmask = True
>>> program = 'vtkviewer'
>>> use_colormap = True
>>> colormap_file = '' #'/software/mindboggle_tools/colormap.xml'
>>> plot_mask_surface(vtk_file, mask_file, nonmask_value, masked_output, remove_nonmask, program, use_colormap, colormap_file)
"""
import os
import numpy as np
from mindboggle.utils.mesh import remove_faces, reindex_faces_points
from mindboggle.utils.utils import execute
from mindboggle.utils.plots import plot_surfaces
from mindboggle.utils.io_vtk import read_scalars, rewrite_scalars, \
read_vtk, write_vtk
#-------------------------------------------------------------------------
# Filter mesh with non-background values from a second (same-size) mesh:
#-------------------------------------------------------------------------
if mask_file:
mask, name = read_scalars(mask_file, True, True)
if not masked_output:
masked_output = os.path.join(os.getcwd(), 'temp.vtk')
file_to_plot = masked_output
#---------------------------------------------------------------------
# Remove nonmask-valued vertices:
#---------------------------------------------------------------------
if remove_nonmask:
#-----------------------------------------------------------------
# Load VTK files:
#-----------------------------------------------------------------
faces, lines, indices, points, npoints, scalars, scalar_names, \
o1 = read_vtk(vtk_file, True, True)
#-----------------------------------------------------------------
# Find mask indices, remove nonmask faces, and reindex:
#-----------------------------------------------------------------
Imask = [i for i,x in enumerate(mask) if x != nonmask_value]
mask_faces = remove_faces(faces, Imask)
mask_faces, points, \
original_indices = reindex_faces_points(mask_faces, points)
#-----------------------------------------------------------------
# Write VTK file with scalar values:
#-----------------------------------------------------------------
if np.ndim(scalars) == 1:
scalar_type = type(scalars[0]).__name__
elif np.ndim(scalars) == 2:
scalar_type = type(scalars[0][0]).__name__
else:
print("Undefined scalar type!")
write_vtk(file_to_plot, points, [], [], mask_faces,
scalars[original_indices].tolist(), scalar_names,
scalar_type=scalar_type)
else:
scalars, name = read_scalars(vtk_file, True, True)
scalars[mask == nonmask_value] = nonmask_value
rewrite_scalars(vtk_file, file_to_plot, scalars)
else:
file_to_plot = vtk_file
#-------------------------------------------------------------------------
# Display with vtkviewer.py:
#-------------------------------------------------------------------------
if program == 'vtkviewer':
plot_surfaces(file_to_plot, use_colormap=use_colormap,
colormap_file=colormap_file)
#-------------------------------------------------------------------------
# Display with mayavi2:
#-------------------------------------------------------------------------
elif program == 'mayavi2':
cmd = ["mayavi2", "-d", file_to_plot, "-m", "Surface", "&"]
execute(cmd, 'os')
def select_largest(points, faces, exclude_labels=[-1], areas=None,
reindex=True):
"""
Select the largest segment (connected set of indices) in a mesh.
In case a surface patch is fragmented, we select the largest fragment,
remove extraneous triangular faces, and reindex indices.
Parameters
----------
points : list of lists of 3 floats
x,y,z coordinates for each vertex of the structure
faces : list of lists of 3 integers
3 indices to vertices that form a triangle on the mesh
exclude_labels : list of integers
background values to exclude
areas : numpy array or list of floats (or None)
surface area scalar values for all vertices
reindex : Boolean
reindex indices in faces?
Returns
-------
points : list of lists of 3 floats
x,y,z coordinates for each vertex of the structure
faces : list of lists of 3 integers
3 indices to vertices that form a triangle on the mesh
Examples
--------
>>> # Spectrum for one label (artificial composite), two fragments:
>>> import os
>>> import numpy as np
>>> from mindboggle.utils.io_vtk import read_scalars, read_vtk, write_vtk
>>> from mindboggle.utils.mesh import remove_faces
>>> from mindboggle.utils.segment import select_largest
>>> path = os.environ['MINDBOGGLE_DATA']
>>> label_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT31.manual.vtk')
>>> area_file = os.path.join(path, 'arno', 'shapes', 'lh.pial.area.vtk')
>>> exclude_labels = [-1]
>>> faces, lines, indices, points, u1, labels, u2,u3 = read_vtk(label_file,
>>> return_first=True, return_array=True)
>>> I19 = [i for i,x in enumerate(labels) if x==19] # pars orbitalis
>>> I22 = [i for i,x in enumerate(labels) if x==22] # postcentral
>>> I19.extend(I22)
>>> faces = remove_faces(faces, I19)
>>> areas, u1 = read_scalars(area_file, True, True)
>>> reindex = True
>>> #
>>> points, faces = select_largest(points, faces, exclude_labels, areas,
>>> reindex)
>>> # View:
>>> from mindboggle.utils.plots import plot_vtk
>>> scalars = np.zeros(np.shape(labels))
>>> scalars[I19] = 1
>>> vtk_file = 'test_two_labels.vtk'
>>> write_vtk(vtk_file, points, indices, lines, faces,
>>> scalars, scalar_names='scalars')
>>> plot_vtk(vtk_file)
"""
import numpy as np
from mindboggle.utils.mesh import find_neighbors, remove_faces, \
reindex_faces_points
from mindboggle.utils.segment import segment
# Areas:
use_area = False
if isinstance(areas, np.ndarray) and np.shape(areas):
use_area = True
elif isinstance(areas, list) and len(areas):
areas = np.array(areas)
use_area = True
# Check to see if there are enough points:
min_npoints = 4
npoints = len(points)
if npoints < min_npoints or len(faces) < min_npoints:
print("The input size {0} ({1} faces) should be much larger "
"than {2}". format(npoints, len(faces), min_npoints))
return None
else:
#---------------------------------------------------------------------
# Segment the indices into connected sets of indices:
#---------------------------------------------------------------------
# Construct neighbor lists:
neighbor_lists = find_neighbors(faces, npoints)
# Determine the indices:
indices = [x for sublst in faces for x in sublst]
# Segment:
segments = segment(indices, neighbor_lists, min_region_size=1,
seed_lists=[], keep_seeding=False, spread_within_labels=False,
labels=[], label_lists=[], values=[], max_steps='', verbose=False)
#---------------------------------------------------------------------
# Select the largest segment (connected set of indices):
#---------------------------------------------------------------------
unique_segments = [x for x in np.unique(segments)
if x not in exclude_labels]
if len(unique_segments) > 1:
select_indices = []
max_segment_area = 0
for segment_number in unique_segments:
segment_indices = [i for i,x in enumerate(segments)
if x == segment_number]
if use_area:
segment_area = np.sum(areas[segment_indices])
else:
segment_area = len(segment_indices)
if segment_area > max_segment_area:
select_indices = segment_indices
max_segment_area = len(select_indices)
print('Maximum size of {0} segments: {1} vertices'.
format(len(unique_segments), len(select_indices)))
#-----------------------------------------------------------------
# Extract points and renumber faces for the selected indices:
#-----------------------------------------------------------------
faces = remove_faces(faces, select_indices)
else:
select_indices = indices
# Alert if the number of indices is small:
if len(select_indices) < min_npoints:
print("The input size {0} is too small.".format(len(select_indices)))
return None
elif faces:
#-----------------------------------------------------------------
# Reindex indices in faces:
#-----------------------------------------------------------------
if reindex:
faces, points = reindex_faces_points(faces, points)
return points, faces
else:
points = np.array(points)
points = points[select_indices].tolist()
return points, faces
else:
return None
def rewrite_scalars(input_vtk, output_vtk, new_scalars,
new_scalar_names=['scalars'], filter_scalars=[],
background_value=-1):
"""
Load VTK format file and save a subset of scalars into a new file.
Parameters
----------
input_vtk : string
input VTK file name
output_vtk : string
output VTK file name
new_scalars : list of lists of floats (or single list or array of floats)
each list (lookup table) contains new values to assign to the vertices
new_scalar_names : string or list of strings
each element is the new name for a lookup table
filter_scalars : list or numpy array (optional)
scalar values used to filter faces (foreground values retained)
background_value : integer
background value
Returns
-------
output_vtk : string
output VTK file name
Examples
--------
>>> # Write vtk file with curvature values on sulci
>>> import os
>>> from mindboggle.utils.io_vtk import read_scalars, rewrite_scalars
>>> path = os.environ['MINDBOGGLE_DATA']
>>> input_vtk = os.path.join(path, 'arno', 'shapes', 'lh.pial.mean_curvature.vtk')
>>> sulci_file = os.path.join(path, 'arno', 'features', 'sulci.vtk')
>>> output_vtk = 'rewrite_scalars.vtk'
>>> curvs, name = read_scalars(input_vtk, True,True)
>>> sulci, name = read_scalars(sulci_file)
>>> new_scalars = [curvs, sulci]
>>> new_scalar_names = ['curvs', 'sulci']
>>> filter_scalars = sulci
>>> background_value = -1
>>> #
>>> rewrite_scalars(input_vtk, output_vtk, new_scalars, new_scalar_names, filter_scalars, background_value)
>>> #
>>> # View:
>>> from mindboggle.utils.plots import plot_surfaces
>>> plot_surfaces('rewrite_scalars.vtk')
"""
import os
import numpy as np
from mindboggle.utils.mesh import remove_faces
from mindboggle.utils.io_vtk import write_header, write_points, \
write_vertices, write_faces, write_scalars, read_vtk, scalars_checker
# Convert numpy arrays to lists
if isinstance(new_scalars, np.ndarray):
new_scalars = new_scalars.tolist()
if isinstance(filter_scalars, np.ndarray):
filter_scalars = filter_scalars.tolist()
# Output VTK file to current working directory
output_vtk = os.path.join(os.getcwd(), output_vtk)
# Load VTK file
faces, lines, indices, points, npoints, scalars, name, \
input_vtk = read_vtk(input_vtk)
# Find indices to foreground values
if filter_scalars:
indices_keep = [i for i,x in enumerate(filter_scalars)
if x != background_value]
indices_remove = [i for i,x in enumerate(filter_scalars)
if x == background_value]
# Remove surface faces whose three vertices are not all in indices
faces = remove_faces(faces, indices_keep)
# Write VTK file
Fp = open(output_vtk,'w')
write_header(Fp)
write_points(Fp, points)
if indices:
write_vertices(Fp, indices)
if faces:
write_faces(Fp, faces)
if new_scalars:
new_scalars, new_scalar_names = scalars_checker(new_scalars,
new_scalar_names)
# scalars_checker() returns a list of lists for scalars:
for i, new_scalar_list in enumerate(new_scalars):
if filter_scalars:
for iremove in indices_remove:
new_scalar_list[iremove] = background_value
if np.ndim(new_scalar_list) == 1:
scalar_type = type(new_scalar_list[0]).__name__
elif np.ndim(new_scalar_list) == 2:
scalar_type = type(new_scalar_list[0][0]).__name__
else:
print("Undefined scalar type!")
if i == 0:
new_scalar_name = new_scalar_names[0]
write_scalars(Fp, new_scalar_list, new_scalar_name,
begin_scalars=True,
scalar_type=scalar_type)
else:
if len(new_scalar_names) < i + 1:
new_scalar_name = new_scalar_names[0]
else:
new_scalar_name = new_scalar_names[i]
write_scalars(Fp, new_scalar_list, new_scalar_name,
begin_scalars=False,
scalar_type=scalar_type)
else:
print('Error: new_scalars is empty')
exit()
Fp.close()
if not os.path.exists(output_vtk):
raise(IOError(output_vtk + " not found"))
return output_vtk
def plot_mask_surface(vtk_file, mask_file='', nonmask_value=-1,
masked_output='', remove_nonmask=False,
program='vtkviewer',
use_colormap=False, colormap_file=''):
"""
Use vtkviewer or mayavi2 to visualize VTK surface mesh data.
If a mask_file is provided, a temporary masked file is saved,
and it is this file that is viewed.
If using vtkviewer, can optionally provide colormap file
or set $COLORMAP environment variable.
Parameters
----------
vtk_file : string
name of VTK surface mesh file
mask_file : string
name of VTK surface mesh file to mask vtk_file vertices
nonmask_value : integer
nonmask (usually background) value
masked_output : string
temporary masked output file name
remove_nonmask : Boolean
remove vertices that are not in mask? (otherwise assign nonmask_value)
program : string {'vtkviewer', 'mayavi2'}
program to visualize VTK file
use_colormap : Boolean
use Paraview-style XML colormap file set by $COLORMAP env variable?
colormap_file : string
use colormap in given file if use_colormap==True? if empty and
use_colormap==True, use file set by $COLORMAP environment variable
Examples
--------
>>> import os
>>> from mindboggle.utils.plots import plot_mask_surface
>>> path = os.environ['MINDBOGGLE_DATA']
>>> vtk_file = os.path.join(path, 'arno', 'labels', 'lh.labels.DKT31.manual.vtk')
>>> mask_file = os.path.join(path, 'test_one_label.vtk')
>>> nonmask_value = 0 #-1
>>> masked_output = ''
>>> remove_nonmask = True
>>> program = 'vtkviewer'
>>> use_colormap = True
>>> colormap_file = '' #'/software/mindboggle_tools/colormap.xml'
>>> plot_mask_surface(vtk_file, mask_file, nonmask_value, masked_output, remove_nonmask, program, use_colormap, colormap_file)
"""
import os
import numpy as np
from mindboggle.utils.mesh import remove_faces, reindex_faces_points
from mindboggle.utils.utils import execute
from mindboggle.utils.plots import plot_surfaces
from mindboggle.utils.io_vtk import read_scalars, rewrite_scalars, \
read_vtk, write_vtk
#-------------------------------------------------------------------------
# Filter mesh with non-background values from a second (same-size) mesh:
#-------------------------------------------------------------------------
if mask_file:
mask, name = read_scalars(mask_file, True, True)
if not masked_output:
masked_output = os.path.join(os.getcwd(), 'temp.vtk')
file_to_plot = masked_output
#---------------------------------------------------------------------
# Remove nonmask-valued vertices:
#---------------------------------------------------------------------
if remove_nonmask:
#-----------------------------------------------------------------
# Load VTK files:
#-----------------------------------------------------------------
faces, lines, indices, points, npoints, scalars, scalar_names, \
o1 = read_vtk(vtk_file, True, True)
#-----------------------------------------------------------------
# Find mask indices, remove nonmask faces, and reindex:
#-----------------------------------------------------------------
Imask = [i for i,x in enumerate(mask) if x != nonmask_value]
mask_faces = remove_faces(faces, Imask)
mask_faces, points, \
original_indices = reindex_faces_points(mask_faces, points)
#-----------------------------------------------------------------
# Write VTK file with scalar values:
#-----------------------------------------------------------------
if np.ndim(scalars) == 1:
scalar_type = type(scalars[0]).__name__
elif np.ndim(scalars) == 2:
scalar_type = type(scalars[0][0]).__name__
else:
print("Undefined scalar type!")
write_vtk(file_to_plot, points, [], [], mask_faces,
scalars[original_indices].tolist(), scalar_names,
scalar_type=scalar_type)
else:
scalars, name = read_scalars(vtk_file, True, True)
scalars[mask == nonmask_value] = nonmask_value
rewrite_scalars(vtk_file, file_to_plot, scalars)
else:
file_to_plot = vtk_file
#-------------------------------------------------------------------------
# Display with vtkviewer.py:
#-------------------------------------------------------------------------
if program == 'vtkviewer':
plot_surfaces(file_to_plot, use_colormap=use_colormap,
colormap_file=colormap_file)
#-------------------------------------------------------------------------
# Display with mayavi2:
#-------------------------------------------------------------------------
elif program == 'mayavi2':
cmd = ["mayavi2", "-d", file_to_plot, "-m", "Surface", "&"]
execute(cmd, 'os')
def explode_scalars(input_indices_vtk, input_values_vtk='', output_stem='',
exclude_values=[-1], background_value=-1,
output_scalar_name='scalars',
remove_background_faces=True, reindex=True):
"""
Write out a separate VTK file for each integer (not in exclude_values)
in (the first) scalar list of an input VTK file.
Optionally write the values drawn from a second VTK file,
remove background values, and reindex indices.
Parameters
----------
input_indices_vtk : string
path of the input VTK file that contains indices as scalars
(assumes that the scalars are a list of floats or integers)
input_values_vtk : string
path of the input VTK file that contains values as scalars
output_stem : string
path and stem of the output VTK file
exclude_values : list or array
values to exclude
background_value : integer or float
background value in output VTK files
remove_background_faces : Boolean
remove all faces whose three vertices are not all a given index?
reindex : Boolean
reindex all indices in faces?
Examples
--------
>>> # Example 1: explode sulci with thickness values
>>> import os
>>> from mindboggle.utils.io_vtk import explode_scalars
>>> from mindboggle.utils.plots import plot_surfaces
>>> path = os.environ['MINDBOGGLE_DATA']
>>> input_indices_vtk = os.path.join(path, 'arno', 'features', 'sulci.vtk')
>>> input_values_vtk = os.path.join(path, 'arno', 'shapes', 'lh.pial.travel_depth.vtk')
>>> output_stem = 'sulci_depth'
>>> #
>>> explode_scalars(input_indices_vtk, input_values_vtk, output_stem)
>>> #
>>> # View:
>>> example_vtk = os.path.join(os.getcwd(), output_stem + '0.vtk')
>>> plot_surfaces(example_vtk)
>>> #
>>> # Example 2: explode labels
>>> import os
>>> from mindboggle.utils.io_vtk import explode_scalars
>>> from mindboggle.utils.plots import plot_surfaces
>>> path = os.environ['MINDBOGGLE_DATA']
>>> input_values_vtk = os.path.join(path, 'arno', 'labels',
>>> 'lh.labels.DKT25.manual.vtk')
>>> input_indices_vtk = input_values_vtk
>>> output_stem = 'label'
>>> exclude_values = [-1]
>>> background_value = -1,
>>> output_scalar_name = 'scalars'
>>> remove_background_faces = True
>>> reindex = True
>>> #
>>> explode_scalars(input_indices_vtk, input_values_vtk, output_stem,
>>> exclude_values, background_value,
>>> output_scalar_name, remove_background_faces, reindex)
>>> # View:
>>> example_vtk = os.path.join(os.getcwd(), output_stem + '2.vtk')
>>> plot_surfaces(example_vtk)
"""
import os
import numpy as np
from mindboggle.utils.io_vtk import read_scalars, read_vtk, write_vtk
from mindboggle.utils.mesh import reindex_faces_points, remove_faces
# Load VTK file:
faces, lines, indices, points, npoints, scalars, scalar_names, \
foo1 = read_vtk(input_indices_vtk, True, True)
print("Explode the scalar list in {0}".
format(os.path.basename(input_indices_vtk)))
if input_values_vtk != input_indices_vtk:
values, name = read_scalars(input_values_vtk, True, True)
print("Explode the scalar list of values in {0} "
"with the scalar list of indices in {1}".
format(os.path.basename(input_values_vtk),
os.path.basename(input_indices_vtk)))
else:
values = np.copy(scalars)
# Loop through unique (non-excluded) scalar values:
unique_scalars = np.unique(scalars)
if all(unique_scalars==np.round(unique_scalars)):
unique_scalars = [int(x) for x in unique_scalars
if x not in exclude_values]
else:
unique_scalars = [x for x in unique_scalars
if x not in exclude_values]
for scalar in unique_scalars:
# Remove background (keep only faces with the scalar):
if remove_background_faces:
scalar_indices = [i for i,x in enumerate(scalars) if x == scalar]
scalar_faces = remove_faces(faces, scalar_indices)
else:
scalar_faces = faces
# Reindex:
if reindex:
scalar_faces, select_points, \
o1 = reindex_faces_points(scalar_faces, points)
else:
select_points = points
# Create array and indices for scalar value:
if reindex:
len_indices = len(select_points)
select_values = scalar * np.ones(len_indices)
else:
select_values = np.copy(values)
select_values[scalars != scalar] = background_value
len_indices = len([i for i,x in enumerate(select_values)
if x != background_value])
print(" Scalar {0}: {1} vertices".format(scalar, len_indices))
# Write VTK file with scalar values (list of values):
if np.ndim(select_values) == 1:
scalar_type = type(select_values[0]).__name__
elif np.ndim(select_values) == 2:
scalar_type = type(select_values[0][0]).__name__
else:
print("Undefined scalar type!")
output_vtk = os.path.join(os.getcwd(),
output_stem + str(scalar) + '.vtk')
write_vtk(output_vtk, select_points, indices, lines, scalar_faces,
select_values.tolist(), output_scalar_name,
scalar_type=scalar_type)
def zernike_moments_per_label(vtk_file,
order=10,
exclude_labels=[-1],
scale_input=True,
decimate_fraction=0,
decimate_smooth=25):
"""
Compute the Zernike moments per labeled region in a file.
Optionally decimate the input mesh.
Parameters
----------
vtk_file : string
name of VTK surface mesh file containing index scalars (labels)
order : integer
number of moments to compute
exclude_labels : list of integers
labels to be excluded
scale_input : Boolean
translate and scale each object so it is bounded by a unit sphere?
(this is the expected input to zernike_moments())
decimate_fraction : float
fraction of mesh faces to remove for decimation (1 for no decimation)
decimate_smooth : integer
number of smoothing steps for decimation
Returns
-------
descriptors_lists : list of lists of floats
Zernike descriptors per label
label_list : list of integers
list of unique labels for which moments are computed
Examples
--------
>>> # Uncomment "if label==22:" below to run example:
>>> # Twins-2-1 left postcentral (22) pial surface:
>>> import os
>>> from mindboggle.shapes.zernike.zernike import zernike_moments_per_label
>>> path = os.path.join(os.environ['HOME'], 'mindboggled', 'OASIS-TRT-20-1')
>>> vtk_file = os.path.join(path, 'labels', 'left_surface', 'relabeled_classifier.vtk')
>>> order = 3
>>> exclude_labels = [-1, 0]
>>> scale_input = True
>>> zernike_moments_per_label(vtk_file, order, exclude_labels, scale_input)
([[0.00528486237819844,
0.009571754617699853,
0.0033489494903015944,
0.00875603468268444,
0.0015879536633349918,
0.0008080165707033097]],
[22])
([[0.0018758013185778298,
0.001757973693050823,
0.002352403177686726,
0.0032281044369938286,
0.002215900343702539,
0.0019646380916703856]],
[14.0])
Arthur Mikhno's result:
1.0e+07 *
0.0000
0.0179
0.0008
4.2547
0.0534
4.4043
"""
import numpy as np
from mindboggle.utils.io_vtk import read_vtk
from mindboggle.utils.mesh import remove_faces
from mindboggle.shapes.zernike.zernike import zernike_moments
min_points_faces = 4
#-------------------------------------------------------------------------
# Read VTK surface mesh file:
#-------------------------------------------------------------------------
faces, u1, u2, points, u3, labels, u4, u5 = read_vtk(vtk_file)
#-------------------------------------------------------------------------
# Loop through labeled regions:
#-------------------------------------------------------------------------
ulabels = [x for x in np.unique(labels) if x not in exclude_labels]
label_list = []
descriptors_lists = []
for label in ulabels:
#if label == 1022: # 22:
# print("DEBUG: COMPUTE FOR ONLY ONE LABEL")
#---------------------------------------------------------------------
# Determine the indices per label:
#---------------------------------------------------------------------
Ilabel = [i for i, x in enumerate(labels) if x == label]
print(' {0} vertices for label {1}'.format(len(Ilabel), label))
if len(Ilabel) > min_points_faces:
#-----------------------------------------------------------------
# Remove background faces:
#-----------------------------------------------------------------
pick_faces = remove_faces(faces, Ilabel)
if len(pick_faces) > min_points_faces:
#-------------------------------------------------------------
# Compute Zernike moments for the label:
#-------------------------------------------------------------
descriptors = zernike_moments(points, pick_faces, order,
scale_input, decimate_fraction,
decimate_smooth)
#-------------------------------------------------------------
# Append to a list of lists of spectra:
#-------------------------------------------------------------
descriptors_lists.append(descriptors)
label_list.append(label)
return descriptors_lists, label_list
def evaluate_deep_features(features_file,
labels_file,
sulci_file='',
hemi='',
excludeIDs=[-1],
output_vtk_name='',
verbose=True):
"""
Evaluate deep surface features by computing the minimum distance from each
label border vertex to all of the feature vertices in the same sulcus,
and from each feature vertex to all of the label border vertices in the
same sulcus. The label borders run along the deepest parts of sulci
and correspond to fundi in the DKT cortical labeling protocol.
Parameters
----------
features_file : string
VTK surface file with feature numbers for vertex scalars
labels_file : string
VTK surface file with label numbers for vertex scalars
sulci_file : string
VTK surface file with sulcus numbers for vertex scalars
excludeIDs : list of integers
feature/sulcus/label IDs to exclude (background set to -1)
output_vtk_name : Boolean
if not empty, output a VTK file beginning with output_vtk_name that
contains a surface with mean distances as scalars
verbose : Boolean
print mean distances to standard output?
Returns
-------
feature_to_border_mean_distances : numpy array [number of features x 1]
mean distance from each feature to sulcus label border
feature_to_border_sd_distances : numpy array [number of features x 1]
standard deviations of feature-to-border distances
feature_to_border_distances_vtk : string
VTK surface file containing feature-to-border distances
border_to_feature_mean_distances : numpy array [number of features x 1]
mean distances from each sulcus label border to feature
border_to_feature_sd_distances : numpy array [number of features x 1]
standard deviations of border-to-feature distances
border_to_feature_distances_vtk : string
VTK surface file containing border-to-feature distances
"""
import os
import sys
import numpy as np
from mindboggle.utils.io_vtk import read_vtk, read_scalars, write_vtk
from mindboggle.utils.mesh import find_neighbors, remove_faces
from mindboggle.utils.segment import extract_borders
from mindboggle.utils.compute import source_to_target_distances
from mindboggle.LABELS import DKTprotocol
dkt = DKTprotocol()
#-------------------------------------------------------------------------
# Load labels, features, and sulci:
#-------------------------------------------------------------------------
faces, lines, indices, points, npoints, labels, scalar_names, \
input_vtk = read_vtk(labels_file, True, True)
features, name = read_scalars(features_file, True, True)
if sulci_file:
sulci, name = read_scalars(sulci_file, True, True)
# List of indices to sulcus vertices:
sulcus_indices = [i for i, x in enumerate(sulci) if x != -1]
segmentIDs = sulci
sulcus_faces = remove_faces(faces, sulcus_indices)
else:
sulcus_indices = range(len(labels))
segmentIDs = []
sulcus_faces = faces
#-------------------------------------------------------------------------
# Prepare neighbors, label pairs, border IDs, and outputs:
#-------------------------------------------------------------------------
# Calculate neighbor lists for all points:
print('Find neighbors for all vertices...')
neighbor_lists = find_neighbors(faces, npoints)
# Find label border points in any of the sulci:
print('Find label border points in any of the sulci...')
border_indices, border_label_tuples, unique_border_label_tuples = \
extract_borders(sulcus_indices, labels, neighbor_lists,
ignore_values=[], return_label_pairs=True)
if not len(border_indices):
sys.exit('There are no label border points!')
# Initialize an array of label border IDs
# (label border vertices that define sulci in the labeling protocol):
print('Build an array of label border IDs...')
label_borders = -1 * np.ones(npoints)
if hemi == 'lh':
nsulcus_lists = len(dkt.left_sulcus_label_pair_lists)
else:
nsulcus_lists = len(dkt.right_sulcus_label_pair_lists)
feature_to_border_mean_distances = -1 * np.ones(nsulcus_lists)
feature_to_border_sd_distances = -1 * np.ones(nsulcus_lists)
border_to_feature_mean_distances = -1 * np.ones(nsulcus_lists)
border_to_feature_sd_distances = -1 * np.ones(nsulcus_lists)
feature_to_border_distances_vtk = ''
border_to_feature_distances_vtk = ''
#-------------------------------------------------------------------------
# Loop through sulci:
#-------------------------------------------------------------------------
# For each list of sorted label pairs (corresponding to a sulcus):
for isulcus, label_pairs in enumerate(dkt.sulcus_label_pair_lists):
# Keep the border points with label pair labels:
label_pair_border_indices = [
x for i, x in enumerate(border_indices)
if np.unique(border_label_tuples[i]).tolist() in label_pairs
]
# Store the points as sulcus IDs in the border IDs array:
if label_pair_border_indices:
label_borders[label_pair_border_indices] = isulcus
if len(np.unique(label_borders)) > 1:
#---------------------------------------------------------------------
# Construct a feature-to-border distance matrix and VTK file:
#---------------------------------------------------------------------
# Construct a distance matrix:
print('Construct a feature-to-border distance matrix...')
sourceIDs = features
targetIDs = label_borders
distances, distance_matrix = source_to_target_distances(
sourceIDs, targetIDs, points, segmentIDs, excludeIDs)
# Compute mean distances for each feature:
nfeatures = min(np.shape(distance_matrix)[1], nsulcus_lists)
for ifeature in range(nfeatures):
feature_distances = [
x for x in distance_matrix[:, ifeature] if x != -1
]
feature_to_border_mean_distances[ifeature] = \
np.mean(feature_distances)
feature_to_border_sd_distances[ifeature] = \
np.std(feature_distances)
if verbose:
print('Feature-to-border mean distances:')
print(feature_to_border_mean_distances)
print('Feature-to-border standard deviations of distances:')
print(feature_to_border_sd_distances)
# Write resulting feature-label border distances to VTK file:
if output_vtk_name:
feature_to_border_distances_vtk = os.path.join(
os.getcwd(),
output_vtk_name + '_feature_to_border_mean_distances.vtk')
print('Write feature-to-border distances to {0}...'.format(
feature_to_border_distances_vtk))
write_vtk(feature_to_border_distances_vtk, points, [], [],
sulcus_faces, [distances],
['feature-to-border_distances'], 'float')
#---------------------------------------------------------------------
# Construct a border-to-feature distance matrix and VTK file:
#---------------------------------------------------------------------
# Construct a distance matrix:
print('Construct a border-to-feature distance matrix...')
sourceIDs = label_borders
targetIDs = features
distances, distance_matrix = source_to_target_distances(
sourceIDs, targetIDs, points, segmentIDs, excludeIDs)
# Compute mean distances for each feature:
nfeatures = min(np.shape(distance_matrix)[1], nsulcus_lists)
for ifeature in range(nfeatures):
border_distances = [
x for x in distance_matrix[:, ifeature] if x != -1
]
border_to_feature_mean_distances[ifeature] = \
np.mean(border_distances)
border_to_feature_sd_distances[ifeature] = \
np.std(border_distances)
if verbose:
print('border-to-feature mean distances:')
print(border_to_feature_mean_distances)
print('border-to-feature standard deviations of distances:')
print(border_to_feature_sd_distances)
# Write resulting feature-label border distances to VTK file:
if output_vtk_name:
border_to_feature_distances_vtk = os.path.join(
os.getcwd(),
output_vtk_name + '_border_to_feature_mean_distances.vtk')
print('Write border-to-feature distances to {0}...'.format(
border_to_feature_distances_vtk))
write_vtk(border_to_feature_distances_vtk, points, [], [],
sulcus_faces, [distances],
['border-to-feature_distances'], 'float')
#-------------------------------------------------------------------------
# Return outputs:
#-------------------------------------------------------------------------
return feature_to_border_mean_distances, feature_to_border_sd_distances,\
feature_to_border_distances_vtk,\
border_to_feature_mean_distances, border_to_feature_sd_distances,\
border_to_feature_distances_vtk