nipype.interfaces.meshfix module¶
MeshFix corrects topological errors in polygonal meshes.
MeshFix¶
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() # doctest: +SKIP >>> fix.cmdline 'meshfix lh-pial.stl rh-pial.stl -o lh-pial_fixed.off'
- in_file1 : a pathlike object or string representing an existing file
- Maps to a command-line argument:
%s(position: 1).
- args : a unicode string
- Additional parameters to the command. Maps to a command-line argument:
%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. Maps to a command-line argument:
--cut-inner %d.- cut_outer : an integer (int or long)
- Remove triangles of 1st that are outside of the 2nd shell. Maps to a command-line argument:
--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. Maps to a command-line 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. Maps to a command-line 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. Maps to a command-line argument:
--decouple-outout %d.- dilation : an integer (int or long)
- Dilate the surface by d. d < 0 means shrinking. Maps to a command-line argument:
--dilate %d.- dont_clean : a boolean
- Don’t Clean. Maps to a command-line argument:
--no-clean.- 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’
- Environment variables. (Nipype default value:
{})- epsilon_angle : 0.0 <= 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_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). Maps to a command-line argument:
%f(position: -2). Requires inputs:finetuning_substeps.- finetuning_inwards : a 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_outwards : a 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_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). Maps to a command-line argument:
%d(position: -1). Requires inputs:finetuning_distance.- in_file2 : a pathlike object or string representing an existing file
- Maps to a command-line argument:
%s(position: 2).- join_closest_components : a boolean
- Join the closest pair of components. Maps to a command-line argument:
-jc. Mutually exclusive with inputs:join_closest_components.- join_overlapping_largest_components : a 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_steps : an integer (int or long)
- The number of laplacian smoothing steps to apply. Maps to a command-line argument:
--smooth %d.- number_of_biggest_shells : an integer (int or long)
- Only the N biggest shells are kept. Maps to a command-line argument:
--shells %d.- out_filename : a 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_mode : a boolean
- Quiet mode, don’t write much to stdout. Maps to a command-line argument:
-q.- remove_handles : a boolean
- Remove handles. Maps to a command-line argument:
--remove-handles.- save_as_freesurfer_mesh : a 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_stl : a 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_vrml : a 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_one : a 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_steps : an integer (int or long)
- 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_vertices : an integer (int or long)
- 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_shift : an integer (int or long)
- Shifts the coordinates of the vertices when saving. Output must be in FreeSurfer format. Maps to a command-line argument:
--smooth %d.
- mesh_file : a pathlike object or string representing an existing file
- The output mesh file.