interfaces.meshfix¶
MeshFix¶
Wraps the executable command meshfix
.
MeshFix v1.2-alpha - by Marco Attene, Mirko Windhoff, Axel Thielscher.
See also
- http://jmeshlib.sourceforge.net
- Sourceforge page
- http://simnibs.de/installation/meshfixandgetfem
- Ubuntu installation instructions
If MeshFix is used for research purposes, please cite the following paper: M. Attene - A lightweight approach to repairing digitized polygon meshes. The Visual Computer, 2010. (c) Springer.
Accepted input formats are OFF, PLY and STL. Other formats (like .msh for gmsh) are supported only partially.
Example¶
>>> import nipype.interfaces.meshfix as mf
>>> fix = mf.MeshFix()
>>> fix.inputs.in_file1 = 'lh-pial.stl'
>>> fix.inputs.in_file2 = 'rh-pial.stl'
>>> fix.run() # doctest: +SKIP
>>> fix.cmdline
'meshfix lh-pial.stl rh-pial.stl -o lh-pial_fixed.off'
Inputs:
[Mandatory]
in_file1: (a pathlike object or string representing an existing file)
argument: ``%s``, position: 1
[Optional]
number_of_biggest_shells: (an integer (int or long))
Only the N biggest shells are kept
argument: ``--shells %d``
epsilon_angle: (0.0 <= a floating point number <= 2.0)
Epsilon angle in degrees (must be between 0 and 2)
argument: ``-a %f``
join_overlapping_largest_components: (a boolean)
Join 2 biggest components if they overlap, remove the rest.
argument: ``-j``
mutually_exclusive: join_closest_components
join_closest_components: (a boolean)
Join the closest pair of components.
argument: ``-jc``
mutually_exclusive: join_closest_components
quiet_mode: (a boolean)
Quiet mode, don't write much to stdout.
argument: ``-q``
dont_clean: (a boolean)
Don't Clean
argument: ``--no-clean``
save_as_stl: (a boolean)
Result is saved in stereolithographic format (.stl)
argument: ``--stl``
mutually_exclusive: save_as_vrml, save_as_freesurfer_mesh
save_as_vrml: (a boolean)
Result is saved in VRML1.0 format (.wrl)
argument: ``--wrl``
mutually_exclusive: save_as_stl, save_as_freesurfer_mesh
save_as_freesurfer_mesh: (a boolean)
Result is saved in freesurfer mesh format
argument: ``--fsmesh``
mutually_exclusive: save_as_vrml, save_as_stl
remove_handles: (a boolean)
Remove handles
argument: ``--remove-handles``
uniform_remeshing_steps: (an integer (int or long))
Number of steps for uniform remeshing of the whole mesh
argument: ``-u %d``
requires: uniform_remeshing_vertices
uniform_remeshing_vertices: (an integer (int or long))
Constrains the number of vertices.Must be used with
uniform_remeshing_steps
argument: ``--vertices %d``
requires: uniform_remeshing_steps
laplacian_smoothing_steps: (an integer (int or long))
The number of laplacian smoothing steps to apply
argument: ``--smooth %d``
x_shift: (an integer (int or long))
Shifts the coordinates of the vertices when saving. Output must be
in FreeSurfer format
argument: ``--smooth %d``
cut_outer: (an integer (int or long))
Remove triangles of 1st that are outside of the 2nd shell.
argument: ``--cut-outer %d``
cut_inner: (an integer (int or long))
Remove triangles of 1st that are inside of the 2nd shell. Dilate 2nd
by N; Fill holes and keep only 1st afterwards.
argument: ``--cut-inner %d``
decouple_inin: (an integer (int or long))
Treat 1st file as inner, 2nd file as outer component.Resolve
overlaps by moving inners triangles inwards. Constrain the min
distance between the components > d.
argument: ``--decouple-inin %d``
decouple_outin: (an integer (int or long))
Treat 1st file as outer, 2nd file as inner component.Resolve
overlaps by moving outers triangles inwards. Constrain the min
distance between the components > d.
argument: ``--decouple-outin %d``
decouple_outout: (an integer (int or long))
Treat 1st file as outer, 2nd file as inner component.Resolve
overlaps by moving outers triangles outwards. Constrain the min
distance between the components > d.
argument: ``--decouple-outout %d``
finetuning_inwards: (a boolean)
Used to fine-tune the minimal distance between surfaces.
argument: ``--fineTuneIn ``, position: -3
requires: finetuning_distance, finetuning_substeps
finetuning_outwards: (a boolean)
Similar to finetuning_inwards, but ensures minimal distance in the
other direction
argument: ``--fineTuneOut ``, position: -3
mutually_exclusive: finetuning_inwards
requires: finetuning_distance, finetuning_substeps
finetuning_distance: (a float)
Used to fine-tune the minimal distance between surfaces.A minimal
distance d is ensured, and reached in n substeps. When using the
surfaces for subsequent volume meshing by gmsh, this step prevent
too flat tetrahedra2)
argument: ``%f``, position: -2
requires: finetuning_substeps
finetuning_substeps: (an integer (int or long))
Used to fine-tune the minimal distance between surfaces.A minimal
distance d is ensured, and reached in n substeps. When using the
surfaces for subsequent volume meshing by gmsh, this step prevent
too flat tetrahedra2)
argument: ``%d``, position: -1
requires: finetuning_distance
dilation: (an integer (int or long))
Dilate the surface by d. d < 0 means shrinking.
argument: ``--dilate %d``
set_intersections_to_one: (a boolean)
If the mesh contains intersections, return value = 1.If saved in
gmsh format, intersections will be highlighted.
argument: ``--intersect``
in_file2: (a pathlike object or string representing an existing file)
argument: ``%s``, position: 2
output_type: ('stl' or 'msh' or 'wrl' or 'vrml' or 'fs' or 'off',
nipype default value: off)
The output type to save the file as.
out_filename: (a pathlike object or string representing a file)
The output filename for the fixed mesh file
argument: ``-o %s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a
value of class 'str', nipype default value: {})
Environment variables
Outputs:
mesh_file: (a pathlike object or string representing an existing
file)
The output mesh file