nipype.algorithms.mesh module

Miscellaneous algorithms for 2D contours and 3D triangularized meshes handling

ComputeMeshWarp

Link to code

Bases: TVTKBaseInterface

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()
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.
metric : ‘euclidean’ or ‘sqeuclidean’
Norm used to report distance. (Nipype default value: euclidean)
out_file : a pathlike object or string representing a file
Numpy file keeping computed distances and weights. (Nipype default value: distance.npy)
out_warp : a pathlike object or string representing a file
Vtk file based on surface1 and warpings mapping it to surface2. (Nipype default value: surfwarp.vtk)
weighting : ‘none’ or ‘area’
“none”: no weighting is performed, surface”: edge distance is weighted by the corresponding surface area. (Nipype default value: none)
distance : a float
Computed distance.
out_file : a pathlike object or string representing an existing file
Numpy file keeping computed distances and weights.
out_warp : a pathlike object or string representing an existing file
Vtk file with the vertex-wise mapping of surface1 to surface2.

MeshWarpMaths

Link to code

Bases: TVTKBaseInterface

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()
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
Image, float or tuple of floats to act as operator. (Nipype default value: 1.0)

float_trait : a float or a tuple of the form: (a float, a float, a float) operation : ‘sum’ or ‘sub’ or ‘mul’ or ‘div’

Operation to be performed. (Nipype default value: sum)
out_file : a pathlike object or string representing a file
Vtk with surface warped. (Nipype default value: warped_surf.vtk)
out_warp : a pathlike object or string representing a file
Vtk file based on in_surf and warpings mapping it to out_file. (Nipype default value: warp_maths.vtk)
out_file : a pathlike object or string representing an existing file
Vtk with surface warped.
out_warp : a pathlike object or string representing an existing file
Vtk file with the vertex-wise mapping of surface1 to surface2.

P2PDistance

Link to code

Bases: ComputeMeshWarp

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.

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.
metric : ‘euclidean’ or ‘sqeuclidean’
Norm used to report distance. (Nipype default value: euclidean)
out_file : a pathlike object or string representing a file
Numpy file keeping computed distances and weights. (Nipype default value: distance.npy)
out_warp : a pathlike object or string representing a file
Vtk file based on surface1 and warpings mapping it to surface2. (Nipype default value: surfwarp.vtk)
weighting : ‘none’ or ‘area’
“none”: no weighting is performed, surface”: edge distance is weighted by the corresponding surface area. (Nipype default value: none)
distance : a float
Computed distance.
out_file : a pathlike object or string representing an existing file
Numpy file keeping computed distances and weights.
out_warp : a pathlike object or string representing an existing file
Vtk file with the vertex-wise mapping of surface1 to surface2.

TVTKBaseInterface

Link to code

Bases: BaseInterface

A base class for interfaces using VTK

WarpPoints

Link to code

Bases: TVTKBaseInterface

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()
interp : ‘cubic’ or ‘nearest’ or ‘linear’
Interpolation. (Nipype default value: cubic)
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.
out_points : a pathlike object or string representing a file
The warped point set.
out_points : a pathlike object or string representing a file
The warped point set.