Home · Quickstart · User Guide and Examples · Interfaces Index · Developers · About · Nipy

# nipype.interfaces.meshfix module

MeshFix corrects topological errors in polygonal meshes.

## MeshFix

Link to code

> Bases: CommandLine

> Wrapped executable: `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'

> in_file1a pathlike object or string representing an existing file

>   Maps to a command-line argument: `%s` (position: 1).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> cut_inneran integer

>   Remove triangles of 1st that are inside of the 2nd shell. Dilate 2nd by N; Fill holes and keep only 1st afterwards. Maps to a command-line argument: `--cut-inner %d`.

> cut_outeran integer

>   Remove triangles of 1st that are outside of the 2nd shell. Maps to a command-line argument: `--cut-outer %d`.

> decouple_ininan integer

>   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. Maps to a command-line argument: `--decouple-inin %d`.

> decouple_outinan integer

>   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. Maps to a command-line argument: `--decouple-outin %d`.

> decouple_outoutan integer

>   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. Maps to a command-line argument: `--decouple-outout %d`.

> dilationan integer

>   Dilate the surface by d. d < 0 means shrinking. Maps to a command-line argument: `--dilate %d`.

> dont_cleana boolean

>   Don’t Clean. Maps to a command-line argument: `--no-clean`.

> environa 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’

>   Environment variables. (Nipype default value: `{}`)

> epsilon_angle0.0 <= a floating point number <= 2.0

>   Epsilon angle in degrees (must be between 0 and 2). Maps to a command-line argument: `-a %f`.

> finetuning_distancea 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). Maps to a command-line argument: `%f` (position: -2). Requires inputs: `finetuning_substeps`.

> finetuning_inwardsa boolean

>   Used to fine-tune the minimal distance between surfaces. Maps to a command-line argument: `--fineTuneIn` (position: -3). Requires inputs: `finetuning_distance`, `finetuning_substeps`.

> finetuning_outwardsa boolean

>   Similar to finetuning_inwards, but ensures minimal distance in the other direction. Maps to a command-line argument: `--fineTuneOut` (position: -3). Mutually exclusive with inputs: `finetuning_inwards`. Requires inputs: `finetuning_distance`, `finetuning_substeps`.

> finetuning_substepsan integer

>   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). Maps to a command-line argument: `%d` (position: -1). Requires inputs: `finetuning_distance`.

> in_file2a pathlike object or string representing an existing file

>   Maps to a command-line argument: `%s` (position: 2).

> join_closest_componentsa boolean

>   Join the closest pair of components. Maps to a command-line argument: `-jc`. Mutually exclusive with inputs: `join_closest_components`.

> join_overlapping_largest_componentsa boolean

>   Join 2 biggest components if they overlap, remove the rest. Maps to a command-line argument: `-j`. Mutually exclusive with inputs: `join_closest_components`.

> laplacian_smoothing_stepsan integer

>   The number of laplacian smoothing steps to apply. Maps to a command-line argument: `--smooth %d`.

> number_of_biggest_shellsan integer

>   Only the N biggest shells are kept. Maps to a command-line argument: `--shells %d`.

> out_filenamea pathlike object or string representing a file

>   The output filename for the fixed mesh file. Maps to a command-line argument: `-o %s`.

> output_type‘stl’ or ‘msh’ or ‘wrl’ or ‘vrml’ or ‘fs’ or ‘off’

>   The output type to save the file as. (Nipype default value: `off`)

> quiet_modea boolean

>   Quiet mode, don’t write much to stdout. Maps to a command-line argument: `-q`.

> remove_handlesa boolean

>   Remove handles. Maps to a command-line argument: `--remove-handles`.

> save_as_freesurfer_mesha boolean

>   Result is saved in freesurfer mesh format. Maps to a command-line argument: `--fsmesh`. Mutually exclusive with inputs: `save_as_vrml`, `save_as_stl`.

> save_as_stla boolean

>   Result is saved in stereolithographic format (.stl). Maps to a command-line argument: `--stl`. Mutually exclusive with inputs: `save_as_vrml`, `save_as_freesurfer_mesh`.

> save_as_vrmla boolean

>   Result is saved in VRML1.0 format (.wrl). Maps to a command-line argument: `--wrl`. Mutually exclusive with inputs: `save_as_stl`, `save_as_freesurfer_mesh`.

> set_intersections_to_onea boolean

>   If the mesh contains intersections, return value = 1.If saved in gmsh format, intersections will be highlighted. Maps to a command-line argument: `--intersect`.

> uniform_remeshing_stepsan integer

>   Number of steps for uniform remeshing of the whole mesh. Maps to a command-line argument: `-u %d`. Requires inputs: `uniform_remeshing_vertices`.

> uniform_remeshing_verticesan integer

>   Constrains the number of vertices.Must be used with uniform_remeshing_steps. Maps to a command-line argument: `--vertices %d`. Requires inputs: `uniform_remeshing_steps`.

> x_shiftan integer

>   Shifts the coordinates of the vertices when saving. Output must be in FreeSurfer format. Maps to a command-line argument: `--smooth %d`.

> mesh_filea pathlike object or string representing an existing file

>   The output mesh file.