文件列表:

iso2mesh (0, 2009-05-05)
iso2mesh\bin (0, 2009-05-05)
iso2mesh\doc (0, 2009-05-05)
iso2mesh\sample (0, 2009-05-05)
iso2mesh\AUTHOR (401, 2009-02-12)
iso2mesh\bbxflatsegment.m (2524, 2009-04-12)
iso2mesh\binsurface.m (2562, 2009-04-12)
iso2mesh\bwislands.m (784, 2009-04-12)
iso2mesh\ChangeLog (5003, 2009-05-05)
iso2mesh\COPYING (18007, 2008-10-26)
iso2mesh\deislands2d.m (1285, 2009-04-12)
iso2mesh\deislands3d.m (933, 2009-04-12)
iso2mesh\delendelem.m (495, 2009-04-12)
iso2mesh\deletemeshfile.m (969, 2009-04-12)
iso2mesh\extractloops.m (1314, 2009-04-12)
iso2mesh\fillholes3d.m (576, 2009-04-14)
iso2mesh\finddisconnsurf.m (784, 2009-04-12)
iso2mesh\flatsegment.m (1190, 2009-04-12)
iso2mesh\getexeext.m (612, 2009-04-12)
iso2mesh\getintersecttri.m (840, 2009-04-12)
iso2mesh\getplanefrom3pt.m (698, 2009-04-12)
iso2mesh\getvarfrom.m (578, 2009-04-12)
iso2mesh\imedge3d.m (1097, 2009-04-12)
iso2mesh\internalpoint.m (1265, 2009-04-12)
iso2mesh\isoctavemesh.m (334, 2009-04-12)
iso2mesh\maxsurf.m (625, 2009-04-12)
iso2mesh\mcpath.m (1014, 2009-04-12)
iso2mesh\meshcentroid.m (588, 2009-04-12)
iso2mesh\meshcheckrepair.m (1546, 2009-05-05)
iso2mesh\meshconn.m (933, 2009-04-12)
iso2mesh\meshresample.m (1113, 2009-04-12)
iso2mesh\mwpath.m (1043, 2009-04-12)
iso2mesh\neighborelem.m (878, 2009-04-12)
iso2mesh\orderloopedge.m (964, 2009-04-12)
iso2mesh\qmeshcut.m (3781, 2009-04-12)
iso2mesh\readasc.m (885, 2009-04-12)
iso2mesh\readinr.m (1795, 2009-05-04)
iso2mesh\readoff.m (771, 2009-04-12)
iso2mesh\readsmf.m (823, 2009-04-12)
... ...

---------------------------------------------------------------------- = iso2mesh: an image-based 3D surface and volumetric mesh generator = ---------------------------------------------------------------------- '''Author''': Qianqian Fang : Martinos Center for Biomedical Imaging : Massachusetts General Hospital (Harvard Medical School) : Bldg. 149, 13th St., Charlestown, MA 02148 '''Version''': 0.8.0 (Hotpot) '''License''': GPL v2 or later (see COPYING) : (this license does not cover the binaries in the bin/ : directory, see section III for more details) '''URL''': http://iso2mesh.sf.net == Table of Content == == # Introduction == "iso2mesh" is a Matlab/Octave-based mesh generation toolbox. It contains a number of optimized mesh processing scripts and interfaces with a number of free meshing tools, such as surface mesh simplifier and extraction utilities (based on CGAL), tetgen, and mesh validation&repairing utility (based on JMeshLib). Iso2mesh toolbox provides a simple yet powerful way to create quality tetrahedral volumetric mesh directly from 3D binary, segmented or gray-scale images such as those from MRI or CT scans. To be able to create volumetric finite-element mesh from 3D volumetric images is of great interest for researchers in the field of image-based modeling and analysis. Unfortunately, very limited software packages for this purpose can be found in publications and market; they are either limited in functionalities or very expensive (such as Amira from Mercury Computer Systems). This toolbox was developed as a free alternative to the expensive commertial tools and provides researchers a complete workflow from 3D binary image preprocessing (hole-filling and island-removing), to surface mesh modeling (extraction, remeshing, validation, repairing, and smoothing) and volumetric mesh creation. Users can either choose the streamlined wrapper scripts to create 3D mesh with a fully automated process, or to call invidual subroutines to perform specific meshing tasks, such as closed surface extraction or boundary extraction. == # List of functions == === # Streamlined Mesh Generation (wrapper) === ==== vol2mesh.m ==== function [node,elem,bound]=vol2mesh(img,ix,iy,iz,opt,maxvol,dofix,method,isovalues) or function [node,elem,face]=v2m(img,isovalues,opt,maxvol,method) convert a binary (or multi-valued) volume to tetrahedral mesh author: Qianqian Fang (fangq nmr.mgh.harvard.edu) inputs: img: a volumetric binary image ix,iy,iz: subvolume selection indices in x,y,z directions opt: see vol2surf maxvol: target maximum tetrahedral elem volume dofix: 1: perform mesh validation&repair, 0: skip repairing method: see vol2surf isovalues: extract level-sets at the specified isovalues and fill the volume in-between; if not specified, will use all distinct labels in the image. outputs: node: output, node coordinates of the tetrahedral mesh elem: output, element list of the tetrahedral mesh bound: output, mesh surface element list of the tetrahedral mesh the last column denotes the boundary ID ==== vol2surf.m ==== function [no,el,regions,holes]=vol2surf(img,ix,iy,iz,opt,dofix,method,isovalues) or function [no,el,regions,holes]=v2s(img,isovalues,opt,method) converting a 3D volumetric image to surfaces author: Qianqian Fang (fangq nmr.mgh.harvard.edu) inputs: img: a volumetric binary image; if img is empty, vol2surf will return user defined surfaces via opt.surf if it exists ix,iy,iz: subvolume selection indices in x,y,z directions opt: function parameters if method is 'cgalsurf': opt=a float number>1: max radius of the Delaunay sphere(element size) opt.radbound: same as above, max radius of the Delaunay sphere opt(1,2,...).radbound: same as above, for each levelset if method is 'simplify': opt=a float number<1: compression rate for surf. simplification opt.keeyratio=a float less than 1: same as above, same for all surf. opt(1,2,..).keeyratio: setting compression rate for each levelset opt(1,2,..).maxsurf: 1 - only use the largest disjointed surface 0 - use all surfaces for that levelset opt(1,2,..).holes: user specified holes interior pt list opt(1,2,..).regions: user specified regions interior pt list opt(1,2,..).surf.{node,elem}: add additional surfaces opt(1,2,..).{A,B}: linear transformation for each surface dofix: 1: perform mesh validation&repair, 0: skip repairing method: - if method is 'simplify', iso2mesh will first call binsurface to generate a voxel-based surface mesh and then use meshresample/meshcheckrepair to create a coarser mesh; - if method is 'cgalsurf', iso2mesh will call the surface extraction program from CGAL to make surface mesh - if method is not specified, 'cgalsurf' is assumed by default isovalues: extract level-sets at the specified isovalues and fill the volume in-between; if not specified, will use all distinct labels in the image. outputs: no: list of nodes on the resulting suface mesh, 3 columns for x,y,z el: list of trianglular elements on the surface, [n1,n2,n3,region_id] regions: list of interior points for all sub-region, [x,y,z] holes: list of interior points for all holes, [x,y,z] ==== surf2mesh.m ==== function [node,elem,bound]=surf2mesh(v,f,p0,p1,keepratio,maxvol) or function [node,elem,face]=s2m(v,f,keepratio,maxvol) surf2mesh - create quality volumetric mesh from isosurface patches author: fangq (fangq nmr.mgh.harvard.edu) parameters: v: input, isosurface node list, dimension (nn,3) f: input, isosurface face element list, dimension (be,3) p0: input, coordinates of one corner of the bounding box, p0=[x0 y0 z0] p1: input, coordinates of the other corner of the bounding box, p1=[x1 y1 z1] keepratio: input, percentage of elements being kept after the simplification maxvol: input, maximum tetrahedra element volume node: output, node coordinates of the tetrahedral mesh elem: output, element list of the tetrahedral mesh bound: output, mesh surface element list of the tetrahedral mesh the last column denotes the boundary ID === # Mesh simplification === ==== meshresample.m ==== function [node,elem]=meshresample(v,f,elemnum) meshresample: resample mesh using CGAL mesh simplification utility author: Qianqian Fang (fangq nmr.mgh.harvard.edu) ==== bbxflatsegment.m ==== function seg=bbxflatsegment(node,loop) bbxflatsegment: decompose edge loops into flat segments alone x/y/z planes of the bounding box author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: node: x,y,z coordinates of each node of the mesh loop: input, a single vector separated by NaN, each segment is a close-polygon consisted by node IDs seg: output, a single vector separated by NaN, each segment is a close-polygon on x/y/z plane === # Mesh repair === ==== meshcheckrepair.m ==== function [node,elem]=meshcheckrepair(node,elem,opt) check and repair a surface mesh author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: node: input/output, surface node list, dimension (nn,3) elem: input/output, surface face element list, dimension (be,3) opt: options, including 'duplicated': remove duplicated elements 'isolated': remove isolated nodes 'deep': call external jmeshlib to remove non-manifold vertices ==== removedupelem.m ==== function elem=removedupelem(elem) remove doubly duplicated elements ==== removeisolatednode.m ==== function [no,el]=removeisolatednode(node,elem) remove isolated nodes: nodes that are not included in any element ==== delendelem.m ==== function elem=delendelem(elem,mask) delendelem - delete elements whose nodes are all edge nodes author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: elem: input/output, surface/volumetric element list mask: node label, =0 for internal nodes, =1 for edge nodes ==== surfaceclean.m ==== function f=surfaceclean(f,v) surfaceclean: remove surface patches that are located inside the bounding box faces author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: v: input, surface node list, dimension (nn,3) f: input, surface face element list, dimension (be,3) f: output, faces free of those on the bounding box ==== smoothsurf.m ==== function nodenew=smoothsurf(node,mask,conn,iter,method) smoothsurf: smooth a surface mesh by 3 smoothing algorithms author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: node: node coordinates of a surface mesh mask: of length of node number, =0 for internal nodes, =1 for edge nodes conn: input, a cell structure of length size(node), conn{n} contains a list of all neighboring node ID for node n iter: smoothing iteration number method: 'laplacian','laplacianhc' and 'lowpass' nodenew: output, the smoothed node coordinates === # Mesh decomposition and query === ==== finddisconnsurf.m ==== function facecell=finddisconnsurf(f) subroutine to extract disconnected surfaces from a cluster of surfaces author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: facelist: input, node indices for all surface triangles facecell: separated disconnected surface node indices ==== maxsurf.m ==== function f=maxsurf(facecell) return a surface with contains the most elements in a collection of surfaces (stored in a cell array) ==== extractloops.m ==== function loops=extractloops(edges) extractloops: extract individual loops from an edge table of a loop collection author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: edges: two column matrix recording the starting/ending points of all edge segments loops: output, a single vector separated by NaN, each segment is a close-polygon consisted by node IDs ==== flatsegment.m ==== function mask=flatsegment(node,edge) flatsegment: decompose edge loops into flat segments alone arbitrary planes of the bounding box author: Qianqian Fang (fangq nmr.mgh.harvard.edu) this code is fragile: it can not handle curves with many co-linear nodes near the corner point parameters: node: x,y,z coordinates of each node of the mesh edge: input, a single vector separated by NaN, each segment is a close-polygon consisted by node IDs mask: output, a cell, each element is a close-polygon on x/y/z plane ==== internalpoint.m ==== function p=internalpoint(v,aloop) internalpoint: imperical function to find an internal point of a planar polygon author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: v: x,y,z coordinates of each node of the mesh aloop: input, a single vector separated by NaN, each segment is a close-polygon consisted by node IDs p: output, [x y z] of an internal point of aloop ==== meshconn.m ==== function [conn,connnum,count]=meshconn(elem,nn); meshconn: create node neighbor list from a mesh author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: elem: element table of a mesh nn : total node number of the mesh conn: output, a cell structure of length nn, conn{n} contains a list of all neighboring node ID for node n connnum: vector of length nn, denotes the neighbor number of each node count: total neighbor numbers ==== orderloopedge.m ==== function newedge=orderloopedge(edge) order the node list of a simple loop based on connection sequence author: Qianqian Fang (fangq nmr.mgh.harvard.edu) inputs: edge: a loop consisted by a sequence of edges, each row is an edge with two integers: start/end node index newedge: reordered edge node list (this subroutine can not process bifercation) ==== surfedge.m ==== function tri=surfedge(f) surfedge: find the edge of an open surface author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: v: input, surface node list, dimension (nn,3) f: input, surface face element list, dimension (be,3) === # Binary image pre-processing (hole-filling and island removing) === ==== bwislands.m ==== function islands=bwislands(img) decompose a 2D binary image into isolated regions and return the indices of the region pixels as a cell array author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: img: a binary (0-1) 2D image islands:a cell array of length of region numbers, each element stores all indices in img for that region ==== deislands2d.m ==== function cleanimg=deislands2d(img,sizelim) remove all small islands smaller than specified size from a binary image author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: img: a binary (0-1) 2D image sizelim: maximum pixel counts of the islands to be removed cleanimg: a binary image after removing the small islands ==== deislands3d.m ==== function cleanimg=deislands3d(img,sizelim) remove all small islands smaller than specified size from a 3D binary image (it applies deislands2d for each image slice) author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: img: a binary (0-1) 3D image sizelim: maximum pixel counts of the islands to be removed cleanimg: a binary image after removing the small islands === # File IO === ==== readoff.m ==== function [node,elem]=readoff(fname) readoff: read Geomview Object File Format by FangQ, 2008/03/28 ==== readsmf.m ==== function [node,elem]=readsmf(fname) readsmf: read simple model format by FangQ, 2007/11/21 ==== readtetgen.m ==== function [node,elem,bound]=readtetgen(fstub) readtetgen: read tetgen output files author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: fstub: file name stub ==== saveoff.m ==== function saveoff(v,f,fname) saveoff: save a surface mesh to Geomview Object File Format author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: v: input, surface node list, dimension (nn,3) f: input, surface face element list, dimension (be,3) fname: output file name ==== savesmf.m ==== function savesmf(v,f,fname) savesmf: save a surface mesh to smf format author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: v: input, surface node list, dimension (nn,3) f: input, surface face element list, dimension (be,3) fname: output file name ==== savesurfpoly.m ==== function savesurfpoly(v,f,p0,p1,fname) meshconn: create node neighbor list from a mesh author: Qianqian Fang (fangq nmr.mgh.harvard.edu) parameters: v: input, surface node list, dimension (nn,3) f: input, surface face element list, dimension (be,3) p0: input, coordinates of one corner of the bounding box, p0=[x0 y0 z0] p1: input, coordinates of the other corner of the bounding box, p1=[x1 y1 z1] fname: output file name ==== mwpath.m ==== function fullname=mwpath(fname) get full temp-file name by prepend working-directory and current session name. author: Qianqian Fang (fangq nmr.mgh.harvard.edu) if global variable ISO2MESH_TEMP is set in 'base', it will use it as the working directory; otherwise, will use matlab function tempdir to return a working directory. if global variable ISO2MESH_SESSION is set in 'base', it will be prepended for each file name, otherwise, use supplied file name. ==== mcpath.m ==== function fullname=mcpath(cmdname) get full executable path by prepending a command directory path if global variable ISO2MESH_BIN is set in 'base', it will use [ISO2MESH_BIN filesep cmdname] as the command full path, otherwise, let matlab pass the cmdname to the shell, which will search command in the directories listed in system $PATH variable. == # Acknowledgement == This toolbox interacts with a number external meshing tools to perform the essential functionalities. These tools are listed below: === bin/tetgen === *Summary:tetgen is a compact and fast 3D mesh generator, it performs *License: ('''IMPORTANT''') tetgen is free for academic research \ and non-commertial uses only. *URL: http://tetgen.berlios.de/ *Author: Hang Si ::Research Group: Numerical Mathematics and Scientific Computing ::Weierstrass Institute for Applied Analysis and Stochastics ::Mohrenstr. 39, 10117 Berlin, Germany === bin/cgalsurf === *Summary: cgalsurf is a utility to extract a surface mesh from \ gray-scale or binary 3D images *Source: it is a slightly modified version from Surface_mesher \ example from CGAL 3.4 *License: CGAL v3 library is licensed under LGPL v2.1 (Lesser \ General Public License) *URL: http://www.cgal.org/Manual/3.3/doc_html/cgal_manual/Surface_mesher/Chapter_main.html === bin/cgalsimp2 === *Summary: cgalsimp2 performs surface mesh simplification in iso2mesh. *Source: it is adapted from Surface_mesh_simplification example of CGAL library *License: CGAL v3 library is licensed under LGPL v2.1 (Lesser \ General Public License) *URL: http://www.cgal.org/ === bin/meshfix === *Summary: meshfix is adapted from the sample code of JMeshLib *License: GPL (GNU General Public License) v2 or later *URL:http://jmeshlib.sourceforge.net/ *Author:Marco Attene ::Istituto di Matematica Applicata e Tecnologie Informatiche ::Consiglio Nazionale delle Ricerche ::Via De Marini, 6 (Torre di Francia) ::16149 Genoa - ITALY === bin/tetview === *Summary:tetview is a 3D mesh viewer *License: see bin/tetgen *URL: http://tetgen.berlios.de/tetview.html *Author: see bin/tetgen Note: iso2mesh and the above meshing utilities are considered as an "aggregate" rather than "derived work", based on the definitions in GPL FAQ (http://www.gnu.org/licenses/gpl-faq.html#MereAggregation) Therefore, the license of iso2mesh and these utilities are independent. The iso2mesh license only applies to the scripts and documents/data in this package and exclude those programs stored in the bin/ directory. The source codes of the modified meshing utilities are available separatly at iso2mesh's website and retain their upstream licenses. Your acknowledgement of iso2mesh in your publications or presentations would be greatly appreciated by the author of this toolbox. Reference: *Qianqian Fang and David Boas, "Tetrahedral mesh generation from volumetric binary and \ gray-scale images," IEEE International Symposium on Biomedical Imaging 2009, Boston, USA

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