3 dw!@sndZddljZddlmZddlmZmZm Z m Z m Z m Z GdddeZ Gd d d e ZGd d d eZdS) z8MeshFix corrects topological errors in polygonal meshes.N)split_filename) CommandLineCommandLineInputSpectraits TraitedSpec isdefinedFilec@seZdZejdddZejdddddZejd d gd d Z ejd d gdd Z ejdddZ ejdddZ ejddgdddZ ejdddgdd Zejdddgdd ZejdddZejdd gd!d"Zejd#d$gd%d"Zejd&d'dZejd&d(dZejd)d*dZejd+d,dZejd-d.dZejd/d0dZejd1d2dZejd3d4d5gdVd7d8Zejd9d4d5gdWd:gd;d<Zejd=d5gdXd?d8Zejd@d4gdYd?d8ZejdBdCdZejdDdEdZ e!dFdGdAdFdHZ"e!dFdGd>dIZ#ej$dJdKdLdMdNdOdJgdFdPdQZ%e!dFdRdSdTZ&dUS)ZMeshFixInputSpecz --shells %dz"Only the N biggest shells are kept)argstrdescz-a %fgg@z2Epsilon angle in degrees (must be between 0 and 2))r lowhighr z-jjoin_closest_componentsz;Join 2 biggest components if they overlap, remove the rest.)r xorr z-jcz$Join the closest pair of components.z-qz'Quiet mode, don't write much to stdout.z --no-cleanz Don't Clean save_as_vrmlsave_as_freesurfer_meshz--stlz3Result is saved in stereolithographic format (.stl))rr r z--wrl save_as_stlz(Result is saved in VRML1.0 format (.wrl)z--fsmeshz)Result is saved in freesurfer mesh formatz--remove-handleszRemove handlesz-u %duniform_remeshing_verticesz7Number of steps for uniform remeshing of the whole mesh)r requiresr z --vertices %duniform_remeshing_stepszKConstrains the number of vertices.Must be used with uniform_remeshing_stepsz --smooth %dz0The number of laplacian smoothing steps to applyzWShifts the coordinates of the vertices when saving. Output must be in FreeSurfer formatz--cut-outer %dz:Remove triangles of 1st that are outside of the 2nd shell.z--cut-inner %dzsRemove triangles of 1st that are inside of the 2nd shell. Dilate 2nd by N; Fill holes and keep only 1st afterwards.z--decouple-inin %dzTreat 1st file as inner, 2nd file as outer component.Resolve overlaps by moving inners triangles inwards. Constrain the min distance between the components > d.z--decouple-outin %dzTreat 1st file as outer, 2nd file as inner component.Resolve overlaps by moving outers triangles inwards. Constrain the min distance between the components > d.z--decouple-outout %dzTreat 1st file as outer, 2nd file as inner component.Resolve overlaps by moving outers triangles outwards. Constrain the min distance between the components > d.z --fineTuneIn finetuning_distancefinetuning_substepsz8Used to fine-tune the minimal distance between surfaces.)r rpositionr z--fineTuneOut finetuning_inwardszRSimilar to finetuning_inwards, but ensures minimal distance in the other direction)r rrrr z%frzUsed 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)z%drz --dilate %dz/Dilate the surface by d. d < 0 means shrinking.z --intersectzpIf the mesh contains intersections, return value = 1.If saved in gmsh format, intersections will be highlighted.Tz%s)existsr r mandatory)rr roffstlmshwrlvrmlfsz$The output type to save the file as.)Z usedefaultr z-o %sz+The output filename for the fixed mesh file)Zgenfiler r Nr%)'__name__ __module__ __qualname__rZIntZnumber_of_biggest_shellsZRangeZ epsilon_angleZBoolZ#join_overlapping_largest_componentsrZ quiet_modeZ dont_cleanrrrZremove_handlesrrZlaplacian_smoothing_stepsZx_shiftZ cut_outerZ cut_innerZ decouple_ininZdecouple_outinZdecouple_outoutrZfinetuning_outwardsZFloatrrZdilationZset_intersections_to_oner in_file1Zin_file2Enum output_type out_filenamer/r/;/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/meshfix.pyr s    r c@seZdZedddZdS)MeshFixOutputSpecTzThe output mesh file)rr N)r(r)r*r mesh_filer/r/r/r0r1sr1c@s4eZdZdZdZeZeZddZ ddZ ddZ d S) MeshFixa MeshFix v1.2-alpha - by Marco Attene, Mirko Windhoff, Axel Thielscher. .. seealso:: 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' Zmeshfixcs|jj}t|jjrt|jj\}}jddddddddg}tfd d |Drptj |jj|d <qtj |d|jj |d <ntj |j |d <|S) N.r r!r"r#r$rc3s|]}|jkVqdS)N)lower).0Zout_type)extr/r0 sz(MeshFix._list_outputs..r2) output_specgetr inputsr.rreplaceanyopabspathr-_gen_outfilename)selfoutputspathnameZ out_typesr/)r8r0 _list_outputss   zMeshFix._list_outputscCs|dkr|jSdSdS)Nr.)rA)rBrEr/r/r0 _gen_filenameszMeshFix._gen_filenamecCst|jj\}}}|jjs&|jjdkr6d|j_d|j_|jjsJ|jjdkrZd|j_d|j_|jjsn|jjdkr~d|j_d|j_|d|jjS)Nr$Tr r#z_fixed.)rr<r+rr-rr)rB_rEr/r/r0rAszMeshFix._gen_outfilenameN) r(r)r*__doc__Z_cmdr Z input_specr1r:rFrGrAr/r/r/r0r3sr3)rIos.pathrDr?Zutils.filemaniprbaserrrrr r r r1r3r/r/r/r0s