interfaces.meshfix

MeshFix

Link to code

Wraps 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()                                    
>>> fix.cmdline
'meshfix lh-pial.stl rh-pial.stl -o lh-pial_fixed.off'

Inputs:

[Mandatory]
in_file1: (an existing file name)
        flag: %s, position: 1

[Optional]
args: (a string)
        Additional parameters to the command
        flag: %s
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.
        flag: --cut-inner %d
cut_outer: (an integer (int or long))
        Remove triangles of 1st that are outside of the 2nd shell.
        flag: --cut-outer %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.
        flag: --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.
        flag: --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.
        flag: --decouple-outout %d
dilation: (an integer (int or long))
        Dilate the surface by d. d < 0 means shrinking.
        flag: --dilate %d
dont_clean: (a boolean)
        Don't Clean
        flag: --no-clean
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
epsilon_angle: (0.0 <= a floating point number <= 2.0)
        Epsilon angle in degrees (must be between 0 and 2)
        flag: -a %f
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)
        flag: %f
        requires: finetuning_substeps
finetuning_inwards: (a boolean)
        flag: --fineTuneIn
        requires: finetuning_distance, finetuning_substeps
finetuning_outwards: (a boolean)
        Similar to finetuning_inwards, but ensures minimal distance in the
        other direction
        flag: --fineTuneIn
        mutually_exclusive: finetuning_inwards
        requires: finetuning_distance, 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)
        flag: %d
        requires: finetuning_distance
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_file2: (an existing file name)
        flag: %s, position: 2
join_closest_components: (a boolean)
        Join the closest pair of components.
        flag: -jc
        mutually_exclusive: join_closest_components
join_overlapping_largest_components: (a boolean)
        Join 2 biggest components if they overlap, remove the rest.
        flag: -j
        mutually_exclusive: join_closest_components
laplacian_smoothing_steps: (an integer (int or long))
        The number of laplacian smoothing steps to apply
        flag: --smooth %d
number_of_biggest_shells: (an integer (int or long))
        Only the N biggest shells are kept
        flag: --shells %d
out_filename: (a file name)
        The output filename for the fixed mesh file
        flag: -o %s
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.
quiet_mode: (a boolean)
        Quiet mode, don't write much to stdout.
        flag: -q
remove_handles: (a boolean)
        Remove handles
        flag: --remove-handles
save_as_freesurfer_mesh: (a boolean)
        Result is saved in freesurfer mesh format
        flag: --fsmesh
        mutually_exclusive: save_as_vrml, save_as_stl
save_as_stl: (a boolean)
        Result is saved in stereolithographic format (.stl)
        flag: --stl
        mutually_exclusive: save_as_vmrl, save_as_freesurfer_mesh
save_as_vmrl: (a boolean)
        Result is saved in VRML1.0 format (.wrl)
        flag: --wrl
        mutually_exclusive: save_as_stl, save_as_freesurfer_mesh
set_intersections_to_one: (a boolean)
        If the mesh contains intersections, return value = 1.If saved in
        gmsh format, intersections will be highlighted.
        flag: --intersect
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
uniform_remeshing_steps: (an integer (int or long))
        Number of steps for uniform remeshing of the whole mesh
        flag: -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
        flag: --vertices %d
        requires: uniform_remeshing_steps
x_shift: (an integer (int or long))
        Shifts the coordinates of the vertices when saving. Output must be
        in FreeSurfer format
        flag: --smooth %d

Outputs:

mesh_file: (an existing file name)
        The output mesh file