def spectrum_per_label(vtk_file,
spectrum_size=10,
exclude_labels=[-1],
normalization='areaindex',
area_file='',
largest_segment=True,
verbose=False):
"""
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
if None, no normalization is used
if "area", use area of the 2D structure as in Reuter et al. 2006
if "index", divide eigenvalue by index to account for linear trend
if "areaindex", do both (default)
area_file : string (optional)
name of VTK file with surface area scalar values
largest_segment : bool
compute spectrum only for largest segment with a given label?
verbose : bool
print statements?
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 numpy as np
>>> from mindboggle.shapes.laplace_beltrami import spectrum_per_label
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> vtk_file = fetch_data(urls['left_freesurfer_labels'], '', '.vtk')
>>> area_file = fetch_data(urls['left_area'], '', '.vtk')
>>> spectrum_size = 6
>>> exclude_labels = [0] #[-1]
>>> largest_segment = True
>>> verbose = False
>>> spectrum_lists, label_list = spectrum_per_label(vtk_file,
... spectrum_size, exclude_labels, None, area_file, largest_segment,
... verbose)
>>> [np.float("{0:.{1}f}".format(x, 5)) for x in spectrum_lists[0]]
[0.0, 0.00054, 0.00244, 0.00291, 0.00456, 0.00575]
>>> label_list[0:10]
[1029, 1005, 1011, 1021, 1008, 1025, 999, 1013, 1007, 1022]
"""
from mindboggle.mio.vtks import read_vtk, read_scalars
from mindboggle.guts.mesh import keep_faces, reindex_faces_points
from mindboggle.shapes.laplace_beltrami import fem_laplacian,\
spectrum_of_largest
# Read VTK surface mesh file:
points, indices, lines, faces, labels, scalar_names, npoints, \
input_vtk = 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]
if verbose:
print('{0} vertices for label {1}'.format(len(Ilabel), label))
# Remove background faces:
pick_faces = keep_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, verbose)
else:
spectrum = fem_laplacian(pick_points, pick_faces, spectrum_size,
normalization, verbose)
# Append to a list of lists of spectra:
spectrum_lists.append(spectrum)
label_list.append(label)
return spectrum_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 (optional)
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.mio.vtks import read_vtk, read_scalars
from mindboggle.guts.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_per_label(vtk_file, spectrum_size=10, exclude_labels=[-1],
normalization='area', area_file='',
largest_segment=True, verbose=False):
"""
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 (optional)
name of VTK file with surface area scalar values
largest_segment : bool
compute spectrum only for largest segment with a given label?
verbose : bool
print statements?
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 numpy as np
>>> from mindboggle.shapes.laplace_beltrami import spectrum_per_label
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> vtk_file = fetch_data(urls['left_freesurfer_labels'], '', '.vtk')
>>> area_file = fetch_data(urls['left_area'], '', '.vtk')
>>> spectrum_size = 6
>>> exclude_labels = [0] #[-1]
>>> largest_segment = True
>>> verbose = False
>>> spectrum_lists, label_list = spectrum_per_label(vtk_file,
... spectrum_size, exclude_labels, None, area_file, largest_segment,
... verbose)
>>> print(np.array_str(np.array(spectrum_lists[0][1::]),
... precision=5, suppress_small=True))
[ 0.00054 0.00244 0.00291 0.00456 0.00575]
>>> label_list[0:10]
[1029, 1005, 1011, 1021, 1008, 1025, 999, 1013, 1007, 1022]
"""
from mindboggle.mio.vtks import read_vtk, read_scalars
from mindboggle.guts.mesh import keep_faces, reindex_faces_points
from mindboggle.shapes.laplace_beltrami import fem_laplacian,\
spectrum_of_largest
# Read VTK surface mesh file:
points, indices, lines, faces, labels, scalar_names, npoints, \
input_vtk = 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]
if verbose:
print('{0} vertices for label {1}'.format(len(Ilabel), label))
# Remove background faces:
pick_faces = keep_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, verbose)
else:
spectrum = fem_laplacian(pick_points, pick_faces, spectrum_size,
normalization, verbose)
# Append to a list of lists of spectra:
spectrum_lists.append(spectrum)
label_list.append(label)
return spectrum_lists, label_list
def plot_mask_surface(vtk_file,
mask_file='',
nonmask_value=-1,
masked_output='',
remove_nonmask=False,
program='vtkviewer',
use_colormap=False,
colormap_file='',
background_value=-1):
"""
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, 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 : bool
remove vertices that are not in mask? (otherwise assign nonmask_value)
program : string {'vtkviewer', 'mayavi2'}
program to visualize VTK file
use_colormap : bool
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
background_value : integer or float
background value
Examples
--------
>>> import os
>>> from mindboggle.mio.plots import plot_mask_surface
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> vtk_file = fetch_data(urls['freesurfer_labels'], '', '.vtk')
>>> os.rename(vtk_file, vtk_file + '.nii.gz')
>>> vtk_file = vtk_file + '.nii.gz'
>>> mask_file = ''
>>> nonmask_value = 0 #-1
>>> masked_output = ''
>>> remove_nonmask = True
>>> program = 'vtkviewer'
>>> use_colormap = True
>>> colormap_file = ''
>>> background_value = -1
>>> plot_mask_surface(vtk_file, mask_file, nonmask_value, masked_output,
... remove_nonmask, program, use_colormap, colormap_file,
... background_value) # doctest: +SKIP
"""
import os
import numpy as np
from mindboggle.guts.mesh import keep_faces, reindex_faces_points
from mindboggle.guts.utilities import execute
from mindboggle.mio.plots import plot_surfaces
from mindboggle.mio.vtks 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:
# ----------------------------------------------------------------
points, indices, lines, faces, scalars, scalar_names, npoints, \
input_vtk = 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 = keep_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, ['scalars'], [],
background_value)
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 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.mio.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/surface_cpp_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.guts.mesh import remove_faces, reindex_faces_points
from mindboggle.guts.utilities import execute
from mindboggle.mio.plots import plot_surfaces
from mindboggle.mio.vtks 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:
#-----------------------------------------------------------------
points, indices, lines, faces, scalars, scalar_names, npoints, \
input_vtk = 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 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 (optional)
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.mio.vtks import read_vtk, read_scalars
from mindboggle.guts.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
