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()
surface1a pathlike object or string representing an existing file

Reference surface (vtk format) to which compute distance.

surface2a 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_filea pathlike object or string representing a file

Numpy file keeping computed distances and weights. (Nipype default value: distance.npy)

out_warpa 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)

distancea float

Computed distance.

out_filea pathlike object or string representing an existing file

Numpy file keeping computed distances and weights.

out_warpa 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_surfa pathlike object or string representing an existing file

Input surface in vtk format, with associated warp field as point data (ie. from ComputeMeshWarp.

operatora 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_filea pathlike object or string representing a file

Vtk with surface warped. (Nipype default value: warped_surf.vtk)

out_warpa 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_filea pathlike object or string representing an existing file

Vtk with surface warped.

out_warpa 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.

surface1a pathlike object or string representing an existing file

Reference surface (vtk format) to which compute distance.

surface2a 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_filea pathlike object or string representing a file

Numpy file keeping computed distances and weights. (Nipype default value: distance.npy)

out_warpa 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)

distancea float

Computed distance.

out_filea pathlike object or string representing an existing file

Numpy file keeping computed distances and weights.

out_warpa 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)

pointsa pathlike object or string representing an existing file

File containing the point set.

warpa pathlike object or string representing an existing file

Dense deformation field to be applied.

out_pointsa pathlike object or string representing a file

The warped point set.

out_pointsa pathlike object or string representing a file

The warped point set.