def area(command, surface_file, verbose=False):
"""
Measure area of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : string
Voronoi-based surface area C++ executable command
surface_file : string
vtk file with surface mesh
verbose : bool
print statements?
Returns
-------
area_file: string
vtk file with surface area per vertex of mesh
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import area
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'area', 'PointAreaMain')
>>> area_file = area(command, surface_file, verbose)
>>>
>>> scalars, name = read_scalars(area_file)
>>> np.allclose(scalars[0:8],
... [0.48270401731, 0.39661528543, 0.57813454792, 0.70574099571,
... 0.84318527207, 0.57642554119, 0.66942016035, 0.70629953593])
True
"""
import os
from nipype.interfaces.base import CommandLine
basename = os.path.splitext(os.path.basename(surface_file))[0]
area_file = os.path.join(os.getcwd(), basename + '.area.vtk')
args = ' '.join([surface_file, area_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = args
cli.terminal_output = 'file'
cli.run()
if not os.path.exists(area_file):
raise IOError(area_file + " not found")
return area_file
def area(command, surface_file, verbose=False):
"""
Measure area of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : string
Voronoi-based surface area C++ executable command
surface_file : string
vtk file with surface mesh
verbose : bool
print statements?
Returns
-------
area_file: string
vtk file with surface area per vertex of mesh
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import area
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'area', 'PointAreaMain')
>>> area_file = area(command, surface_file, verbose)
>>> scalars, name = read_scalars(area_file)
>>> np.allclose(scalars[0:8],
... [0.48270401731, 0.39661528543, 0.57813454792, 0.70574099571,
... 0.84318527207, 0.57642554119, 0.66942016035, 0.70629953593])
True
"""
import os
from nipype.interfaces.base import CommandLine
basename = os.path.splitext(os.path.basename(surface_file))[0]
area_file = os.path.join(os.getcwd(), basename + '.area.vtk')
args = ' '.join([surface_file, area_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = args
cli.terminal_output = 'file'
cli.run()
if not os.path.exists(area_file):
raise IOError(area_file + " not found")
return area_file
def travel_depth(command, surface_file, verbose=False):
"""
Measure "travel depth" of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : string
travel depth C++ executable command
surface_file : string
vtk file
verbose : bool
print statements?
Returns
-------
depth_file: string
vtk file with travel depth per vertex of mesh
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import travel_depth
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'travel_depth', 'TravelDepthMain')
>>> depth_file = travel_depth(command, surface_file, verbose)
>>> scalars, name = read_scalars(depth_file)
>>> np.allclose(scalars[0:8], [0.020259869839, 0.06009166489, 0.12858575442, 0.045639221313, 0.007742772964, 0.052839111255, 0.053538904296, 0.013158746337])
True
"""
import os
from nipype.interfaces.base import CommandLine
basename = os.path.splitext(os.path.basename(surface_file))[0]
depth_file = os.path.join(os.getcwd(), basename + '.travel_depth.vtk')
args = ' '.join([surface_file, depth_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = args
cli.terminal_output = 'file'
cli.run()
if not os.path.exists(depth_file):
raise IOError(depth_file + " not found")
return depth_file
def travel_depth(command, surface_file, verbose=False):
"""
Measure "travel depth" of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : string
travel depth C++ executable command
surface_file : string
vtk file
verbose : bool
print statements?
Returns
-------
depth_file: string
vtk file with travel depth per vertex of mesh
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import travel_depth
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'travel_depth', 'TravelDepthMain')
>>> depth_file = travel_depth(command, surface_file, verbose)
>>> scalars, name = read_scalars(depth_file)
>>> np.allclose(scalars[0:8], [0.020259869839, 0.06009166489, 0.12858575442, 0.045639221313, 0.007742772964, 0.052839111255, 0.053538904296, 0.013158746337])
True
"""
import os
from nipype.interfaces.base import CommandLine
basename = os.path.splitext(os.path.basename(surface_file))[0]
depth_file = os.path.join(os.getcwd(), basename + '.travel_depth.vtk')
args = ' '.join([surface_file, depth_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = args
cli.terminal_output = 'file'
cli.run()
if not os.path.exists(depth_file):
raise IOError(depth_file + " not found")
return depth_file
def curvature(command, method, arguments, surface_file, verbose=False):
"""
Measure curvature values of each vertex in a surface mesh (-m 0).
(Calls Joachim Giard's C++ code)
Command line usage:
CurvatureMain [Options] InputVTKMesh MeanCurvatureOutput
Command line options:
-m Method: set the method used to compute curvature(s) (default 0):
0: Use ComputePrincipalCurvatures() function to compute both
mean and Gaussian curvatures based on the relative direction
of the normal vectors in a small neighborhood
1: Use ComputeBothCurvatures() function to compute both mean
and Gaussian curvatures based on the local ratios between
a filtered surface and the original surface area
2: Use ComputeCurvature() function to compute the mean curvature
based on the direction of the displacement vectors during
a Laplacian filtering
-n Neighborhood: neighborhood size (default 0.7)
-g GaussianCurvVTK: save Gaussian curvature (for -m 0 or 1)
-x MaxCurvVTK: save maximum curvature (for -m 0)
-i MinCurvVTK: save minimum curvature (for -m 0)
-d DirectionVTK: save minimal curvature's direction (for -m 0)
Command line example:
CurvatureMain -m 2 -n 0.7 lh.pial.vtk lh.pial.mean_curvature.vtk
Command line example:
CurvatureMain -m 0 -n 2
-i lh.min_curv.vtk -x lh.max_curv.vtk -g lh.gaussian_curv.vtk
-d lh.min_dir.vtk lh.pial.vtk lh.mean_curv.vtk
Notes:
-m 0 is best if you have low resolution or want local peaks,
but can be too sensitive to the local linear geometry of the mesh,
unless the neighborhood parameter is set high enough (like 2).
-m 1 is not well tested and the filtering is done using Euclidean
distances, so it's only good for incorrect but fast visualization.
-m 2 is a good approximation based on the Laplacian, but very large
curvatures (negative or positive) are underestimated (saturation).
Parameters
----------
command : string
C++ executable command for computing curvature
method : integer {0,1,2}
method number
arguments : string
additional arguments, such as neighborhood parameter
surface_file : string
name of VTK surface mesh file
verbose : bool
print statements?
Returns
-------
mean_curvature_file : string
mean curvature file
gauss_curvature_file : string
gauss curvature file
max_curvature_file : string
max curvature file
min_curvature_file : string
min curvature file
min_curvature_vector_file : string
min curvature vector file
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import curvature
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> method = 2
>>> arguments = '-n 0.7'
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'curvature', 'CurvatureMain')
>>> mean_curvature_file, f1,f2,f3,f4 = curvature(command, method,
... arguments, surface_file, verbose)
>>> scalars, name = read_scalars(mean_curvature_file)
>>> np.allclose(scalars[0:8], [-5.8136068088, -5.9312990469, -6.2805500474, -5.6210018286, -5.6963067208, -5.8039874097, -5.8726460688, -5.7106966401])
True
"""
import os
from nipype.interfaces.base import CommandLine
args = ['-m', str(method)]
gauss_curvature_file = None
max_curvature_file = None
min_curvature_file = None
min_curvature_vector_file = None
basename = os.path.splitext(os.path.basename(surface_file))[0]
stem = os.path.join(os.getcwd(), basename)
mean_curvature_file = stem + '.mean_curvature.vtk'
if method in [0, 1]:
gauss_curvature_file = stem + '.gauss_curvature.vtk'
args.extend(['-g', gauss_curvature_file])
if method == 0:
max_curvature_file = stem + '.max_curvature.vtk'
min_curvature_file = stem + '.min_curvature.vtk'
min_curvature_vector_file = stem + '.min_curvature.txt'
args.extend([
'-x', max_curvature_file, '-i', min_curvature_file, '-d',
min_curvature_vector_file
])
if arguments:
args.extend([arguments])
args.extend([surface_file, mean_curvature_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = ' '.join(args)
cli.terminal_output = 'file'
cli.run()
return mean_curvature_file, gauss_curvature_file, \
max_curvature_file, min_curvature_file, min_curvature_vector_file
def curvature(command, method, arguments, surface_file, verbose=False):
"""
Measure curvature values of each vertex in a surface mesh (-m 0).
(Calls Joachim Giard's C++ code)
Command line usage:
CurvatureMain [Options] InputVTKMesh MeanCurvatureOutput
Command line options:
-m Method: set the method used to compute curvature(s) (default 0):
0: Use ComputePrincipalCurvatures() function to compute both
mean and Gaussian curvatures based on the relative direction
of the normal vectors in a small neighborhood
1: Use ComputeBothCurvatures() function to compute both mean
and Gaussian curvatures based on the local ratios between
a filtered surface and the original surface area
2: Use ComputeCurvature() function to compute the mean curvature
based on the direction of the displacement vectors during
a Laplacian filtering
-n Neighborhood: neighborhood size (default 0.7)
-g GaussianCurvVTK: save Gaussian curvature (for -m 0 or 1)
-x MaxCurvVTK: save maximum curvature (for -m 0)
-i MinCurvVTK: save minimum curvature (for -m 0)
-d DirectionVTK: save minimal curvature's direction (for -m 0)
Command line example:
CurvatureMain -m 2 -n 0.7 lh.pial.vtk lh.pial.mean_curvature.vtk
Command line example:
CurvatureMain -m 0 -n 2
-i lh.min_curv.vtk -x lh.max_curv.vtk -g lh.gaussian_curv.vtk
-d lh.min_dir.vtk lh.pial.vtk lh.mean_curv.vtk
Notes:
-m 0 is best if you have low resolution or want local peaks,
but can be too sensitive to the local linear geometry of the mesh,
unless the neighborhood parameter is set high enough (like 2).
-m 1 is not well tested and the filtering is done using Euclidean
distances, so it's only good for incorrect but fast visualization.
-m 2 is a good approximation based on the Laplacian, but very large
curvatures (negative or positive) are underestimated (saturation).
Parameters
----------
command : string
C++ executable command for computing curvature
method : integer {0,1,2}
method number
arguments : string
additional arguments, such as neighborhood parameter
surface_file : string
name of VTK surface mesh file
verbose : bool
print statements?
Returns
-------
mean_curvature_file : string
mean curvature file
gauss_curvature_file : string
gauss curvature file
max_curvature_file : string
max curvature file
min_curvature_file : string
min curvature file
min_curvature_vector_file : string
min curvature vector file
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import curvature
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> method = 2
>>> arguments = '-n 0.7'
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'curvature', 'CurvatureMain')
>>> mean_curvature_file, f1,f2,f3,f4 = curvature(command, method,
... arguments, surface_file, verbose)
>>> scalars, name = read_scalars(mean_curvature_file)
>>> np.allclose(scalars[0:8], [-5.8136068088, -5.9312990469, -6.2805500474, -5.6210018286, -5.6963067208, -5.8039874097, -5.8726460688, -5.7106966401])
True
"""
import os
from nipype.interfaces.base import CommandLine
args = ['-m', str(method)]
gauss_curvature_file = None
max_curvature_file = None
min_curvature_file = None
min_curvature_vector_file = None
basename = os.path.splitext(os.path.basename(surface_file))[0]
mean_curvature_file = os.path.join(os.getcwd(), basename) + \
'.mean_curvature.vtk'
if method in [0, 1]:
gauss_curvature_file = stem + '.gauss_curvature.vtk'
args.extend(['-g', gauss_curvature_file])
if method == 0:
max_curvature_file = stem + '.max_curvature.vtk'
min_curvature_file = stem + '.min_curvature.vtk'
min_curvature_vector_file = stem + '.min_curvature.txt'
args.extend(['-x', max_curvature_file,
'-i', min_curvature_file,
'-d', min_curvature_vector_file])
if arguments:
args.extend([arguments])
args.extend([surface_file, mean_curvature_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = ' '.join(args)
cli.terminal_output = 'file'
cli.run()
return mean_curvature_file, gauss_curvature_file, \
max_curvature_file, min_curvature_file, min_curvature_vector_file
