[node,elem,face]=v2m(img,isovalues,opt,maxvol,method) volumetric mesh generation from binary or gray-scale volumetric images shortcut for vol2mesh inputs and outputs are similar to those defined in vol2mesh
[no,el,regions,holes]=v2s(img,isovalues,opt,method) surface mesh generation from binary or gray-scale volumetric images shortcut for vol2surf inputs and outputs are similar to those defined in vol2surf
[node,elem,face]=s2m(v,f,keepratio,maxvol) volumetric mesh generation from a closed surface, shortcut for surf2mesh inputs and outputs are similar to those defined in surf2mesh
img=s2v(node,face,div) shortcut for surf2vol, coverting a surface to a volumetric image input: node: node list of the triangular surface, 3 columns for x/y/z face: triangle node indices, each row is a triangle div: division number along the shortest edge of the mesh (resolution) if not given, div=50 output: img: a volumetric binary image at position of ndgrid(xi,yi,zi)
newnode=sms(node,face,iter,useralpha,method) simplified version of surface mesh smoothing input: node: node coordinates of a surface mesh face: face element list of the surface mesh iter: smoothing iteration number alpha: scaler, smoothing parameter, v(k+1)=alpha*v(k)+(1-alpha)*mean(neighbors) method: same as in smoothsurf, default is 'laplacianhc' output: newnode: output, the smoothed node coordinates
[node,elem,face,regions]=vol2mesh(img,ix,iy,iz,opt,maxvol,dofix,method,isovalues) convert a binary (or multi-valued) volume to tetrahedral mesh input: img: a volumetric binary image ix,iy,iz: subvolume selection indices in x,y,z directions opt: as defined in vol2surf.m maxvol: target maximum tetrahedral elem volume dofix: 1: perform mesh validation&repair, 0: skip repairing method: 'cgalsurf' or omit: use CGAL surface mesher 'simplify': use binsurface and then simplify 'cgalmesh': use CGAL 3.5 3D mesher for direct mesh generation [new] generally speaking, 'cgalmesh' is the most robust path if you want to product meshes from binary or multi-region volumes, however, its limitations include 1) only accept uint8 volume, and 2) can not extract meshes from gray-scale volumes. If ones goal is to process a gray-scale volume, he/she should use the 'cgalsurf' option. 'simplify' approach is not recommended unless other options failed. isovalues: a list of isovalues where the levelset is defined output: node: output, node coordinates of the tetrahedral mesh elem: output, element list of the tetrahedral mesh, the last column is the region ID face: output, mesh surface element list of the tetrahedral mesh the last column denotes the boundary ID region: optional output. if opt.autoregion is set to 1, region saves the interior points for each closed surface component
[no,el,regions,holes]=vol2surf(img,ix,iy,iz,opt,dofix,method,isovalues) converting a 3D volumetric image to surfaces input: 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' or 'cgalpoly': 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.distbound: maximum deviation from the specified isosurfaces 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,..).side: - 'upper': threshold at upper interface 'lower': threshold at lower interface opt(1,2,..).maxnode: - the maximum number of surface node per 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 opt.autoregion: if set to 1, vol2surf will try to determine the interior points for each closed surface automatically 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: a list of isovalues where the levelset is defined output: 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]
[node,elem,face]=surf2mesh(v,f,p0,p1,keepratio,maxvol,regions,holes,forcebox) create quality volumetric mesh from isosurface patches input parameters: v: input, isosurface node list, dimension (nn,3) if v has 4 columns, the last column specifies mesh density near each node 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 regions: list of regions, specifying by an internal point for each region holes: list of holes, similar to regions forcebox: 1: add bounding box, 0: automatic outputs: node: output, node coordinates of the tetrahedral mesh elem: output, element list of the tetrahedral mesh face: output, mesh surface element list of the tetrahedral mesh the last column denotes the boundary ID
img=surf2vol(node,face,xi,yi,zi) convert a triangular surface to a shell of voxels in a 3D image input: node: node list of the triangular surface, 3 columns for x/y/z face: triangle node indices, each row is a triangle xi,yi,zi: x/y/z grid for the resulting volume output: img: a volumetric binary image at position of ndgrid(xi,yi,zi)
[node,elem]=binsurface(img,nface) fast isosurface extraction from 3D binary images input: img: a 3D binary image nface: nface=3 or ignored - for triangular faces, nface=4 - square faces nface=0 - return a boundary mask image via node output elem: integer array with dimensions of NE x nface, each row represents a surface mesh face element node: node coordinates, 3 columns for x, y and z respectively the outputs of this subroutine can be easily plotted using patch('Vertices',node,'faces',elem,'FaceVertexCData',node(:,3), 'FaceColor','interp'); if the surface mesh has triangular faces, one can plot it with trisurf(elem,node(:,1),node(:,2),node(:,3))
[node,elem,face]=cgalv2m(vol,opt,maxvol) wrapper for CGAL 3D mesher (CGAL 3.5 or up) convert a binary (or multi-valued) volume to tetrahedral mesh http://www.cgal.org/Manual/3.5/doc_html/cgal_manual/Mesh_3/Chapter_main.html input: vol: a volumetric binary image ix,iy,iz: subvolume selection indices in x,y,z directions opt: parameters for CGAL mesher, if opt is a structure, then opt.radbound: defines the maximum surface element size opt.angbound: defines the miminum angle of a surface triangle opt.distbound: defines the maximum distance between the center of the surface bounding circle and center of the element bounding sphere opt.reratio: maximum radius-edge ratio if opt is a scalar, it only specifies radbound. maxvol: target maximum tetrahedral elem volume output: node: output, node coordinates of the tetrahedral mesh elem: output, element list of the tetrahedral mesh, the last column is the region id face: output, mesh surface element list of the tetrahedral mesh the last column denotes the boundary ID note: each triangle will appear twice in the face list with each one attaches to each side of the interface. one can remove the redundant triangles by unique(face(:,1:3),'rows')
[node,elem,face]=cgals2m(v,f,opt,maxvol) wrapper for CGAL 3D mesher (CGAL 3.5 and newer) convert a binary (or multi-valued) volume to tetrahedral mesh http://www.cgal.org/Manual/3.5/doc_html/cgal_manual/Mesh_3/Chapter_main.html input: v: the node coordinate list of a surface mesh (nn x 3) f: the face element list of a surface mesh (be x 3) opt: parameters for CGAL mesher, if opt is a structure, then opt.radbound: defines the maximum surface element size opt.angbound: defines the miminum angle of a surface triangle opt.distbound: defines the maximum distance between the center of the surface bounding circle and center of the element bounding sphere opt.reratio: maximum radius-edge ratio if opt is a scalar, it only specifies radbound. maxvol: target maximum tetrahedral elem volume output: node: output, node coordinates of the tetrahedral mesh elem: output, element list of the tetrahedral mesh, the last column is the region id face: output, mesh surface element list of the tetrahedral mesh the last column denotes the boundary ID
[node,elem]=vol2restrictedtri(vol,thres,cent,brad,ang,radbound,distbound,maxnode) surface mesh extraction using CGAL mesher input: vol: a 3D volumetric image thres: a scalar as the threshold of of the extraction cent: a 3d position (x,y,z) which locates inside the resulting mesh, this is automatically computed from vol2surf brad: maximum bounding sphere squared of the resulting mesh ang: minimum angular constrains of the resulting tranglar elements (in degrees) radbound: maximum triangle delaunay circle radius distbound: maximum delaunay sphere distances maxnode: maximum number of surface nodes (even radbound is not reached) output: node: the list of 3d nodes in the resulting surface (x,y,z) elem: the element list of the resulting mesh (3 columns of integers)
img=surf2volz(node,face,xi,yi,zi) convert a triangular surface to a shell of voxels in a 3D image along the z-axis input: node: node list of the triangular surface, 3 columns for x/y/z face: triangle node indices, each row is a triangle xi,yi,zi: x/y/z grid for the resulting volume output: img: a volumetric binary image at position of ndgrid(xi,yi,zi)
[node,elem,face]=meshabox(p0,p1,opt,maxvol) create the surface and tetrahedral mesh of a box geometry input: p0: coordinates (x,y,z) for one end of the box diagnoal p1: coordinates (x,y,z) for the other end of the box diagnoal opt: maximum volume of the tetrahedral elements nodesize: 1 or a 8x1 array, size of the element near each vertex output: node: node coordinates, 3 columns for x, y and z respectively face: integer array with dimensions of NB x 3, each row represents a surface mesh face element elem: integer array with dimensions of NE x 4, each row represents a tetrahedron example: [node,elem,face]=meshabox([2 3 2],[6 12 15],0.1,1); plotmesh(node,elem,'x>4');
[node,face,elem]=meshasphere(c0,r,tsize,maxvol) create the surface and tetrahedral mesh of a sphere input: c0: center coordinates (x0,y0,z0) of the sphere r: radius of the sphere tsize: maximum surface triangle size on the sphere maxvol: maximu volume of the tetrahedral elements output node: node coordinates, 3 columns for x, y and z respectively face: integer array with dimensions of NB x 3, each row represents a surface mesh face element elem: integer array with dimensions of NE x 4, each row represents a tetrahedron
[node,face,elem]=meshanellip(c0,rr,opt) create the surface and tetrahedral mesh of an ellipsoid input: c0: center coordinates (x0,y0,z0) of the ellipsoid rr: radii of an ellipsoid, if rr is a scalar, this is a sphere with radius rr if rr is a 1x3 or 3x1 vector, it specifies the ellipsoid radii [a,b,c] if rr is a 1x5 or 5x1 vector, it specifies [a,b,c,theta,phi] where theta and phi are the rotation angles along z and x axes, respectively. Rotation is applied before translation. tsize: maximum surface triangle size on the sphere maxvol: maximu volume of the tetrahedral elements output: node: node coordinates, 3 columns for x, y and z respectively face: integer array with dimensions of NB x 3, each row represents a surface mesh face element elem: integer array with dimensions of NE x 4, each row represents a tetrahedron; if ignored, only produces the surface example: [node,face,elem]=meshanellip([10,10,-10],[30,20,10,pi/4,pi/4],0.5,0.4); plotmesh(node,elem,'x>10');axis equal;
[node,face,elem]=meshunitsphere(tsize,maxvol) create the surface and/or volumetric mesh of a unit sphere centered at [0 0 0] and radius 1 input: tsize: maximum size of the surface triangles (from 0 to 1) maxvol: maximum volume of the tetrahedron; if one wants to return elem without specifying maxvol, maxvol=tsize^3 output: node: node coordinates, 3 columns for x, y and z respectively face: integer array with dimensions of NB x 3, each row represents a surface mesh face element elem: integer array with dimensions of NE x 4, each row represents a tetrahedron. If ignored, this function only produces the surface example: [node,face]=meshunitsphere(0.05); [node,face,elem]=meshunitsphere(0.05,0.01); plotmesh(node,elem,'x>0'); axis equal;
facecell=finddisconnsurf(f) subroutine to extract disconnected surfaces from a cluster of surfaces Date: 2008/03/06 input: f: faces defined by node indices for all surface triangles output: facecell: separated disconnected surface node indices
openedge=surfedge(f) find the edge of an open surface or surface of a volume input: f: input, surface face element list, dimension (be,3) output: openedge: list of edges of the specified surface
openface=volface(t) find the surface patches of a volume input: t: input, volumetric element list, dimension (ne,4) output: openface: list of faces of the specified volume
loops=extractloops(edges) extract individual loops from an edge table of a loop collection input: edges: two column matrix recording the starting/ending points of all edge segments output: loops: output, a single vector separated by NaN, each segment is a close-polygon consisted by node IDs
[conn,connnum,count]=meshconn(elem,nn) create node neighbor list from a mesh input: elem: element table of a mesh nn : total node number of the mesh output: 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
centroid=meshcentroid(v,f) compute the centroids of a mesh defined by nodes and elements (surface or tetrahedra) in R^n space input: v: surface node list, dimension (nn,3) f: surface face element list, dimension (be,3) output: centroid: centroid positions, one row for each element
nodevol=nodevolume(node,elem) calculate the Voronoi volume of each node in a simplex mesh input: node: node coordinates elem: element table of a mesh output: nodevol: volume values for all nodes
vol=elemvolume(node,elem,option) calculate the volume for a list of simplexes input: node: node coordinates elem: element table of a mesh option: if option='signed', the volume is the raw determinant, else, the results will be the absolute values output vol: volume values for all elements
[conn,connnum,count]=neighborelem(elem,nn) create node neighbor list from a mesh input: elem: element table of a mesh nn : total node number of the mesh output: conn: output, a cell structure of length nn, conn{n} contains a list of all neighboring elem ID for node n connnum: vector of length nn, denotes the neighbor number of each node count: total neighbor numbers
facenb=faceneighbors(t,opt) to find 4 face-neighboring elements of a tetrahedron input: t: tetrahedron element list, 4 columns of integers opt: if opt='surface', return boundary triangle list (should be the same as the face output from v2m) otherwise, return the element list for each element: each row contains 4 numbers, representing the element indices sharing triangular faces [1 2 3],[1 2 4],[1 3 4] and [2 3 4] in order, where 1~4 is the node local index. if the index is 0, indicating the face has no neighbor (i.e. a boundary face) output: facenb: see opt
edgenb=edgeneighbors(t,opt) to find neighboring triangular elements in a triangule surface input: t: a triangular surface element list, 3 columns of integers opt: if opt='general', return the edge neighbors for a general triangular surface: each edge can be shared by more than 2 triangles; if ignored, we assume all triangles are shared by no more than 2 triangles. output: edgenb: if opt is not supplied, edgenb is a size(t,1) by 3 array with each element being the triangle ID of the edge neighbor of that triangle. For each row, the order of the neighbors is listed as those sharing edges [1 2], [2 3] and [3 1] between the triangle nodes. when opt='general', edgenb is a cell array with a length of size(t). each member of the cell array is a list of edge neighbors (the order is not defined).
f=maxsurf(facecell) return the surface with the maximum element number (not necessarily in area) from a cell arry of surfaces input: facecell: a cell array, each element is a face array output: f: the surface data (node indices) for the surface with most elements
mask=flatsegment(node,edge) decompose edge loops into flat segments alone arbitrary planes of the bounding box this code is fragile: it can not handle curves with many co-linear nodes near the corner point input: 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 output: mask: output, a cell, each element is a close-polygon on x/y/z plane
[newedge]=orderloopedge(edge) order the node list of a simple loop based on connection sequence input: edge: a loop consisted by a sequence of edges, each row is an edge with two integers: start/end node index output: newedge: reordered edge node list
[X,V,E,F]=mesheuler(face) Euler's charastistics of a mesh input: face: a closed surface mesh output: X: Euler's charastistics V: number of vertices E: number of edges F: number of faces
seg=bbxflatsegment(node,loop) decompose edge loops into flat segments alone x/y/z planes of the bounding box input: 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 output: seg: output, a single vector separated by NaN, each segment is a close-polygon on x/y/z plane
plane=surfplane(node,face) plane equation coefficients for each face in a surface input: node: a list of node coordinates (nn x 3) face: a surface mesh triangle list (ne x 3) output: plane: a (ne x 4) array, in each row, it has [a b c d] to denote the plane equation as "a*x+b*y+c*z+d=0"
[pt,p0,v0,t,idx]=surfinterior(node,face) identify a point that is enclosed by the (closed) surface input: node: a list of node coordinates (nn x 3) face: a surface mesh triangle list (ne x 3) output: pt: the interior point coordinates [x y z] p0: ray origin used to determine the interior point v0: the vector used to determine the interior point t : ray-tracing intersection distances (with signs) from p0. the intersection coordinates can be expressed as p0+t(i)*v0 idx: index to the face elements that intersect with the ray, order match that of t
seeds=surfseeds(node,face) calculate a set of interior points with each enclosed by a closed component of a surface input: node: a list of node coordinates (nn x 3) face: a surface mesh triangle list (ne x 3) output: seeds: the interior points coordinates for each closed-surface component
quality=meshquality(node,elem) compute Joe-Liu mesh quality measure of a tetrahedral mesh input: node: node coordinates of the mesh (nn x 3) elem: element table of a tetrahedral mesh (ne x 4) output edge: edge list; each row is an edge, specified by the starting and ending node indices, the total edge number is size(elem,1) x nchoosek(size(elem,2),2). All edges are ordered by looping through each element first.
edges=meshedge(elem) return all edges in a surface or volumetric mesh input: elem: element table of a mesh (support N-d space element) output edge: edge list; each row is an edge, specified by the starting and ending node indices, the total edge number is size(elem,1) x nchoosek(size(elem,2),2). All edges are ordered by looping through each element first.
[node,elem]=meshcheckrepair(node,elem,opt) check and repair a surface mesh input/output: 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
newelem=meshreorient(node,elem) reorder nodes in a surface or tetrahedral mesh to ensure all elements are oriented consistently input: node: list of nodes elem: list of elements (each row are indices of nodes of each element) output: newelem: the element list with consistent ordering
elem=removedupelem(elem) remove doubly duplicated elements input: elem: list of elements (node indices) output: elem: element list after removing the duplicated elements
[newnode,newelem]=removedupnodes(node,elem) removing the duplicated nodes from a mesh input: elem: integer array with dimensions of NE x 4, each row contains the indices of all the nodes for each tetrahedron node: node coordinates, 3 columns for x, y and z respectively output: newnode: nodes without duplicates newelem: elements with only the unique nodes
[no,el]=removeisolatednode(node,elem) remove isolated nodes: nodes that are not included in any element input: node: list of node coordinates elem: list of elements of the mesh output: no: node coordinates after removing the isolated nodes el: element list of the resulting mesh
fnew=removeisolatedsurf(v,f,maxdiameter) remove disjointed surface fragment by using mesh diameter input: v: list of nodes of the input surface f: list of triangles of the input surface maxdiameter: maximum bounding box size for surface removal ouput: fnew: new face list after removing the components smaller than maxdiameter
f=surfaceclean(f,v) remove surface patches that are located inside the bounding box faces input: v: surface node list, dimension (nn,3) f: surface face element list, dimension (be,3) output: f: faces free of those on the bounding box
eid=getintersecttri(tmppath) get the IDs of self-intersecting elements from tetgen call this when tetgen complains about self-intersection input: tmppath: working dir, use mwpath('') in most cases output: eid: an array of all intersecting surface elements, one can read the corresponding node/elem by [no,el]=readoff(mwpath('post_vmesh.off'));
elem=delendelem(elem,mask) delete elements whose nodes are all edge nodes input/output: elem: input/output, surface/volumetric element list mask: of length of node number, =0 for internal nodes, =1 for edge nodes
[node,elem]=meshresample(v,f,keepratio) resample mesh using CGAL mesh simplification utility input: v: list of nodes f: list of surface elements (each row for each triangle) keepratio: decimation rate, a number less than 1, as the percentage of the elements after the sampling output: node: the node coordinates of the sampled surface mesh elem: the element list of the sampled surface mesh
[newno,newfc]=remeshsurf(node,face,opt) remesh a triangular surface and the output is guaranteed to be free of self-intersecting element. This function is similar to meshresample, but it can both downsample or upsample a mesh input: node: list of nodes on the input suface mesh, 3 columns for x,y,z face: list of trianglular elements on the surface, [n1,n2,n3,region_id] opt: function parameters opt.gridsize: resolution for the voxelization of the mesh opt.closesize: if there are openings, set the closing diameter opt.elemsize: the size of the element of the output surface if opt is a scalar, it defines the elemsize and gridsize=opt/4 output: newno: list of nodes on the resulting suface mesh, 3 columns for x,y,z newfc: list of trianglular elements on the surface, [n1,n2,n3,region_id]
p=smoothsurf(node,mask,conn,iter,useralpha,usermethod,userbeta) smoothing a surface mesh input: node: node coordinates of a surface mesh mask: flag whether a node is movable: 0 movable, 1 non-movable if mask=[], it assumes all nodes are movable conn: input, a cell structure of length size(node), conn{n} contains a list of all neighboring node ID for node n, this can be computed from meshconn function iter: smoothing iteration number useralpha: scaler, smoothing parameter, v(k+1)=alpha*v(k)+(1-alpha)*mean(neighbors) usermethod: smoothing method, including 'laplacian','laplacianhc' and 'lowpass' userbeta: scaler, smoothing parameter, for 'laplacianhc' output: p: output, the smoothed node coordinates recommendations Based on [Bade2006], 'Lowpass' method outperforms 'Laplacian-HC' in volume preserving and both are significantly better than the standard Laplacian method [Bade2006] R. Bade, H. Haase, B. Preim, "Comparison of Fundamental Mesh Smoothing Algorithms for Medical Surface Models," Simulation and Visualization, pp. 289-304, 2006.
[no,el,fc]=sortmesh(origin,node,elem,face) sort nodes and elements in a mesh so that the indexed nodes and elements are closer to each order (this may reduce cache-miss in a calculation) input: origin: sorting all nodes and elements with the distance and angles wrt this location, if origin=[], it will be node(1,:) node: list of nodes elem: list of elements (each row are indices of nodes of each element) ecol: list of columns in elem to participate sorting face: list of surface triangles (this can be omitted) fcol: list of columns in face to participate sorting output: no: node coordinates in the sorted order el: the element list in the sorted order fc: the surface triangle list in the sorted order (can be ignored) nodemap: the new node mapping order, no=node(nodemap,:)
[newnode,newelem]=mergemesh(node,elem,varargin) merge two or more tetrahedral meshes or triangular surfaces input: node: node coordinates, dimension (nn,3) elem: tetrahedral element or triangle surface (nn,3) to (nn,5) output: newnode: the node coordinates after merging, dimension (nn,3) newelem: tetrahedral element or surfaces after merging (nn,4) or (nhn,5) note: you can call meshcheckrepair for the output newnode and newelem to remove the duplicated nodes or elements example: [node1,elem1,face1]=meshabox([0 0 0],[10 10 10],1,1); [node2,face2,elem2]=meshasphere([5 5 13.1],3,0.3,3); [newnode,newelem]=mergemesh(node1,elem1,node2,elem2); plotmesh(newnode,newelem); figure; [newnode,newface]=mergemesh(node1,face1,node2,face2); plotmesh(newnode,newface,'x>5');
saveasc(v,f,fname) save a surface mesh to FreeSurfer ASC mesh format input: v: input, surface node list, dimension (nn,3) f: input, surface face element list, dimension (be,3) fname: output file name
savedxf(node,face,elem,fname) save a surface mesh to DXF format input: node: input, surface node list, dimension (nn,3) face: input, surface face element list, dimension (be,3) elem: input, tetrahedral element list, dimension (ne,4) fname: output file name
saveinr(vol,fname) save a surface mesh to INR Format input: vol: input, a binary volume fname: output file name
saveoff(v,f,fname) save a surface mesh to Geomview Object File Format (OFF) input: v: input, surface node list, dimension (nn,3) f: input, surface face element list, dimension (be,3) fname: output file name
savesmf(v,f,fname) save a surface mesh to smf format input: v: input, surface node list, dimension (nn,3) f: input, surface face element list, dimension (be,3) fname: output file name
savesurfpoly(v,f,holelist,regionlist,p0,p1,fname) save a set of surfaces into poly format (for tetgen) input: v: input, surface node list, dimension (nn,3) if v has 4 columns, the last column specifies mesh density near each node f: input, surface face element list, dimension (be,3) holelist: list of holes, each hole is represented by an internal point regionlist: list of regions, similar to holelist p0: coordinate of one of the end of the bounding box p1: coordinate for the other end of the bounding box fname: output file name forcebox: non-empty: add bounding box, []: automatic if forcebox is a 8x1 vector, it will be used to specify max-edge size near the bounding box corners
savevrml(node,face,elem,fname) save a surface mesh to VRML 1.0 format input: node: input, surface node list, dimension (nn,3) face: input, surface face element list, dimension (be,3) elem: input, tetrahedral element list, dimension (ne,4) fname: output file name
[node,elem]=readasc(fname) read FreeSurfer ASC mesh format input: fname: name of the asc file output: node: node positions of the mesh elem: element list of the mesh
vol=readinr(fname) load a volume from an INR file input: fname: input file name output: dat: output, data read from the inr file
[node,elem,face]=readmedit(filename) read Medit mesh format input: fname: name of the medit data file output: node: node coordinates of the mesh elem: list of elements of the mesh face: list of surface triangles of the mesh
[node,elem]=readoff(fname) read Geomview Object File Format (OFF) input: fname: name of the OFF data file output: node: node coordinates of the mesh elem: list of elements of the mesh
[node,elem]=readsmf(fname) read simple model format (SMF) input: fname: name of the SMF data file output: node: node coordinates of the mesh elem: list of elements of the mesh
[node,elem,face]=readtetgen(fstub) read tetgen output files input: fstub: file name stub output: node: node coordinates of the tetgen mesh elem: tetrahedra element list of the tetgen mesh face: surface triangles of the tetgen mesh
flag=deletemeshfile(fname) delete a given work mesh file under the working directory input: fname: specified file name (without path) output: flag: not used
binname=mcpath(fname) get full executable path by prepending a command directory path parameters: input: fname: input, a file name string output: binname: output, full file name located in the bin directory 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.
tempname=meshtemppath(fname) get full temp-file name by prepend working-directory and current session name input: fname: input, a file name string output: tempname: output, full file name located in the working directory 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.
savedmedit(node,face,elem,fname) save a surface or tetrahedral mesh to Medit format input: node: input, surface node list, dimension (nn,3 or 4) face: input, surface face element list, dimension (be,3 or 4) elem: input, tetrahedral element list, dimension (ne,4 or 5) fname: output file name
islands=bwislands(img) return the indices of non-zero elements in a 2D or 3D image grouped by connected regions in a cell array input: img: a 2D or 3D array output: islands: a cell array, each cell records the indices of the non-zero elements in img for a connected region (or an island)
resimg=fillholes3d(img,ballsize) close a 3D image with the speicified gap size and then fill the holes input: img: a 3D binary image ballsize: maximum gap size for image closing output: resimg: the image free of holes this function requires the image processing toolbox for matlab/octave
cleanimg=deislands2d(img,sizelim) remove isolated islands on a 2D image below speicified size limit input: img: a 2D binary image sizelim: a integer as the maximum pixel size of a isolated region output: cleanimg: a binary image after removing islands below sizelim
cleanimg=deislands3d(img,sizelim) remove isolated islands for 3D image (for each slice) input: img: a 3D volumetric image sizelim: maximum island size (in pixels) for each x/y/z slice output: cleanimg: 3D image after removing the islands
imgdiff=imedge3d(binimg,isdiff) Extract the boundary voxels from a binary image author: Aslak Grinsted <ag at glaciology.net> input: binimg: a 3D binary image isdiff: if isdiff=1, output will be all voxels which is different from its neighbors; if isdiff=0 or ignored, output will be the edge voxels of the non-zero regions in binimg output: imgdiff: a 3D logical array with the same size as binimg with 1 for voxels on the boundary and 0 otherwise
p=internalpoint(v,aloop) imperical function to find an internal point of a planar polygon input: 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 output: p: output, [x y z] of an internal point of aloop
vol=smoothbinvol(vol,layer) perform a memory-limited 3D image smoothing input: vol: a 3D volumetric image to be smoothed layer: number of iterations for the smoothing output: vol: the volumetric image after smoothing
vol=thickenbinvol(vol,layer) thickening a binary volume by a given pixel width this is similar to bwmorph(vol,'thicken',3) except this does it in 3d and only does thickening for non-zero elements (and hopefully faster) input: vol: a volumetric binary image layer: number of iterations for the thickenining output: vol: the volume image after the thickening
vol=thinbinvol(vol,layer) thinning a binary volume by a given pixel width this is similar to bwmorph(vol,'thin',n) except this does it in 3d and only does thinning for non-zero elements (and hopefully faster) input: vol: a volumetric binary image layer: number of iterations for the thickenining output: vol: the volume image after the thickening
hm=plotmesh(node,face,elem,opt) plot surface and volumetric meshes input: node: a node coordinate list, 3 columns for x/y/z; if node has a 4th column, it will be used to set the color at each node. face: a triangular surface face list; if face has a 4th column, it will be used to separate the surface into sub-surfaces and display them in different colors. elem: a tetrahedral element list; if elem has a 5th column, it will be used to separate the mesh into sub-domains and display them in different colors. opt: additional options for the plotting for simple point plotting, opt can be markers or color options, such as 'r.', or opt can be a logic statement to select a subset of the mesh, such as 'x>0 & y+z<1'; opt can have more than one items to combine these options, for example: plotmesh(...,'x>0','r.'); the range selector must appear before the color/marker specifier in the event where all of the above inputs have extra settings related to the color of the plot, the priorities are given in the following order: opt > node(:,4) > elem(:,5) > face(:,4) output: hm: handle or handles (vector) to the plotted surfaces example: h=plotmesh(node,'r.'); h=plotmesh(node,'x<20','r.'); h=plotmesh(node,face); h=plotmesh(node,face,'y>10'); h=plotmesh(node,face,'facecolor','r'); h=plotmesh(node,elem,'x<20'); h=plotmesh(node,elem,'x<20 & y>0'); h=plotmesh(node,face,elem); h=plotmesh(node,face,elem,'linestyle','--');
hm=plotsurf(node,face,opt) plot 3D surface meshes input: node: node coordinates, dimension (nn,3); if node has a 4th column, it will be used to set the color at each node. face: triangular surface face list; if face has a 4th column, it will be used to separate the surface into sub-surfaces and display them in different colors. opt: additional options for the plotting, see plotmesh output: hm: handle or handles (vector) to the plotted surfaces example: h=plotsurf(node,face); h=plotsurf(node,face,'facecolor','r');
hm=plottetra(node,elem,opt) plot 3D surface meshes input: node: a node coordinate list, 3 columns for x/y/z; if node has a 4th column, it will be used to set the color at each node. elem: a tetrahedral element list; if elem has a 5th column, it will be used to separate the mesh into sub-domains and display them in different colors. opt: additional options for a patch object, see plotmesh output: hm: handle or handles (vector) to the plotted surfaces example: h=plottetra(node,elem); h=plottetra(node,elem,'facealpha',0.5);
[cutpos,cutvalue,facedata]=qmeshcut(elem,node,value,plane) fast tetrahedral mesh cross-section plot input: elem: integer array with dimensions of NE x 4, each row contains the indices of all the nodes for each tetrahedron node: node coordinates, 3 columns for x, y and z respectively value: a scalar array with the length of node numbers, can have multiple columns plane: defines a plane by 3 points: plane=[x1 y1 z1;x2 y2 z2;x3 y3 z3] output: cutpos: all the intersections of mesh edges by the plane cutpos is similar to node, containing 3 columns for x/y/z cutvalue: interpolated values at the intersections, with row number being the num. of the intersections, column number being the same as "value". facedata: define the intersection polygons in the form of patch "Faces" the outputs of this subroutine can be easily plotted using patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',cutvalue,... 'FaceColor','interp');
plottetview(session,method) wrapper for tetview to plot the generated mesh input: session: a string to identify the output files for plotting, '' for the default session method: method can be 'cgalsurf' (default), 'simplify', 'cgalpoly' 'cgalmesh' and 'remesh'
valnew=surfdiffuse(node,tri,val,ddt,iter,type1,opt) apply a smoothing/diffusion process on a surface input: node: list of nodes of the surface mesh tri: triangular element list of the surface val: vector, scalar value for each node ddt: diffusion coefficient multiplied by delta t iter: iterations for applying the smoothing type1: indices of the nodes which will not be updated opt: method, 'grad' for gradient based, and 'simple' for simple average output: valnew: nodal value vector after the smoothing
[node,elem,face]=volmap2mesh(img,ix,iy,iz,thickness,elemnum,maxvol,A,B) convert a binary volume to tetrahedral mesh followed by an Affine transform input: img, ix,iy,iz, elemnum and maxvol: see vol2mesh.m thickness: scale z-dimension of the mesh to specified thickness, if thickness==0, scaling is bypassed Amat: a 3x3 transformation matrix Bvec: a 3x1 vector Amat and Bvec maps the image index space to real world coordnate system by [x,y,z]_new=Amat*[x,y,z]_old+Bvec
isoctave=isoctavemesh determine whether the code is running in octave output: isoctave: 1 if in octave, otherwise 0
p=getvarfrom(ws,name) get variable value by name from specified work-space input: ws: name of the work-space, for example, 'base' name: name string of the variable output: p: the value of the specified variable, if the variable does not exist, return empty array
[t,u,v]=raytrace(p,v,node,face) perform a Havel-styled ray tracing for a triangular surface input: p: starting point coordinate of the ray v: directional vector of the ray node: a list of node coordinates (nn x 3) face: a surface mesh triangle list (ne x 3) output: t: signed distance from p to the intersection point u: bary-centric coordinate 1 of the intersection point v: bary-centric coordinate 2 of the intersection point the final bary-centric triplet is [u,v,1-u-v] users can find the IDs of the elements intersecting with the ray by idx=find(u>=0 & v>=0 & u+v<=1.0); Reference: [1] J. Havel and A. Herout, "Yet faster ray-triangle intersection (using SSE4)," IEEE Trans. on Visualization and Computer Graphics, 16(3):434-438 (2010) [2] Q. Fang, "Comment on 'A study on tetrahedron-based inhomogeneous Monte-Carlo optical simulation'," Biomed. Opt. Express, (in press)
[a,b,c,d]=getplanefrom3pt(plane) define a plane equation ax+by+cz+d=0 from three 3D points input: plane: a 3x3 matrix with each row specifying a 3D point (x,y,z) output: a,b,c,d: the coefficient for plane equation ax+by+cz+d=0
exesuff=getexeext() get meshing external tool extension names for the current platform output: exesuff: file extension for iso2mesh tool binaries
exesuff=fallbackexeext(exesuffix, exename) get the fallback external tool extension names for the current platform input: exesuffix: the output executable suffix from getexeext exename: the executable name output: exesuff: file extension for iso2mesh tool binaries
[major,minor,patchnum,extra]=iso2meshver or v=iso2meshver get the version number of iso2mesh toolbox output: if you ask for a single output: v: a string denotes the current version number; the string is typically in the following format: "major.minor.patch-extra" where major/minor/patch are typically integers, and extra can be an arbitrary string and is optional if you ask for 4 outputs: [major,minor,patchnum,extra] are each field of the version string