algorithms.mesh¶
ComputeMeshWarp¶
Calculates a the vertex-wise warping to get surface2 from surface1. It also reports the average distance of vertices, using the norm specified as input.
Example:
import nipype.algorithms.mesh as m
dist = m.ComputeMeshWarp()
dist.inputs.surface1 = 'surf1.vtk'
dist.inputs.surface2 = 'surf2.vtk'
res = dist.run()
Inputs:
[Mandatory]
surface1: (a pathlike object or string representing an existing file)
Reference surface (vtk format) to which compute distance.
surface2: (a pathlike object or string representing an existing file)
Test surface (vtk format) from which compute distance.
[Optional]
metric: ('euclidean' or 'sqeuclidean', nipype default value:
euclidean)
norm used to report distance
weighting: ('none' or 'area', nipype default value: none)
"none": no weighting is performed, surface": edge distance is
weighted by the corresponding surface area
out_warp: (a pathlike object or string representing a file, nipype
default value: surfwarp.vtk)
vtk file based on surface1 and warpings mapping it to surface2
out_file: (a pathlike object or string representing a file, nipype
default value: distance.npy)
numpy file keeping computed distances and weights
Outputs:
distance: (a float)
computed distance
out_warp: (a pathlike object or string representing an existing file)
vtk file with the vertex-wise mapping of surface1 to surface2
out_file: (a pathlike object or string representing an existing file)
numpy file keeping computed distances and weights
MeshWarpMaths¶
Performs the most basic mathematical operations on the warping field defined at each vertex of the input surface. A surface with scalar or vector data can be used as operator for non-uniform operations.
Example:
import nipype.algorithms.mesh as m
mmath = m.MeshWarpMaths()
mmath.inputs.in_surf = 'surf1.vtk'
mmath.inputs.operator = 'surf2.vtk'
mmath.inputs.operation = 'mul'
res = mmath.run()
Inputs:
[Mandatory]
in_surf: (a pathlike object or string representing an existing file)
Input surface in vtk format, with associated warp field as point
data (ie. from ComputeMeshWarp
operator: (a float or a tuple of the form: (a float, a float, a
float) or a pathlike object or string representing an existing
file, nipype default value: 1.0)
image, float or tuple of floats to act as operator
[Optional]
float_trait: (a float or a tuple of the form: (a float, a float, a
float))
operation: ('sum' or 'sub' or 'mul' or 'div', nipype default value:
sum)
operation to be performed
out_warp: (a pathlike object or string representing a file, nipype
default value: warp_maths.vtk)
vtk file based on in_surf and warpings mapping it to out_file
out_file: (a pathlike object or string representing a file, nipype
default value: warped_surf.vtk)
vtk with surface warped
Outputs:
out_warp: (a pathlike object or string representing an existing file)
vtk file with the vertex-wise mapping of surface1 to surface2
out_file: (a pathlike object or string representing an existing file)
vtk with surface warped
P2PDistance¶
Calculates a point-to-point (p2p) distance between two corresponding VTK-readable meshes or contours.
A point-to-point correspondence between nodes is required
Deprecated since version 1.0-dev: Use ComputeMeshWarp
instead.
Inputs:
[Mandatory]
surface1: (a pathlike object or string representing an existing file)
Reference surface (vtk format) to which compute distance.
surface2: (a pathlike object or string representing an existing file)
Test surface (vtk format) from which compute distance.
[Optional]
metric: ('euclidean' or 'sqeuclidean', nipype default value:
euclidean)
norm used to report distance
weighting: ('none' or 'area', nipype default value: none)
"none": no weighting is performed, surface": edge distance is
weighted by the corresponding surface area
out_warp: (a pathlike object or string representing a file, nipype
default value: surfwarp.vtk)
vtk file based on surface1 and warpings mapping it to surface2
out_file: (a pathlike object or string representing a file, nipype
default value: distance.npy)
numpy file keeping computed distances and weights
Outputs:
distance: (a float)
computed distance
out_warp: (a pathlike object or string representing an existing file)
vtk file with the vertex-wise mapping of surface1 to surface2
out_file: (a pathlike object or string representing an existing file)
numpy file keeping computed distances and weights
WarpPoints¶
Applies a displacement field to a point set given in vtk format.
Any discrete deformation field, given in physical coordinates and
which volume covers the extent of the vtk point set, is a valid
warp
file. FSL interfaces are compatible, for instance any
field computed with nipype.interfaces.fsl.utils.ConvertWarp
.
Example:
from nipype.algorithms.mesh import WarpPoints
wp = WarpPoints()
wp.inputs.points = 'surf1.vtk'
wp.inputs.warp = 'warpfield.nii'
res = wp.run()
Inputs:
[Mandatory]
points: (a pathlike object or string representing an existing file)
file containing the point set
warp: (a pathlike object or string representing an existing file)
dense deformation field to be applied
interp: ('cubic' or 'nearest' or 'linear', nipype default value:
cubic)
interpolation
[Optional]
out_points: (a pathlike object or string representing a file)
the warped point set
Outputs:
out_points: (a pathlike object or string representing a file)
the warped point set