Iso2Mesh - a powerful yet easy-to-use mesh generator

Iso2Mesh ChangeLog (key features are marked by *):

2024/10/20 (1.9.8, codename: Pot Stickers)

 2024-10-19 [a3d12dc] [ci] add macos-14, break into smaller steps
 2024-10-18 [2682c76] [tools] using maci64 binary for tetgen 1.4.3
 2024-10-18 [66be46d] [ci] workaround due to octave 9.x windows fscanf bug reported at https://savannah.gnu.org/bugs/?66161
 2024-10-17 [902b0a9] [ci] remove demo_vol2mesh_ex3; build tools
 2024-10-17 [0917a2b] [meshfix] not sure when, but the origin was changed, revert
 2024-10-17 [820e1b8] [ci] fix submodule checkout error
 2024-10-17 [5316f69] [ci] fix fragile test
 2024-10-17*[c442361] [ci] test demo scripts to github action
 2024-10-17*[7438820] [doc] update jsonlab repo
 2024-10-17 [f40bfe4] [doc] update documentation for v1.9.8
 2024-10-17 [8fd183e] [io] update embedded IO toolboxes: jsonlab, jnifty, jsnirfy, easyh5
 2024-10-17 [0d31813] [format] complete reformat of code using miss_hit
 2024-08-19 [0dd6ce2] [deploy] add the missing cgalsimp2 for arm64 mac, fix #80
 2024-08-18*[90e4c94] Merge pull request #79 from sloriot/CGAL-6.0
 2024-08-13 [1dd27fa] compatibility with CGAL 5.0
 2024-07-25 [3dc1ce3] [format] add recommended output variable test, #77
 2024-07-25 [1d98ade] Merge pull request #77 from harmening/removeisolatednode
 2024-07-22 [d767904] backward compatibility
 2024-07-22 [4eef5ff] compatibility with CGAL 6.0
 2024-06-14 [aa78f3a] [feat] add native arm64 apple silicon binaries
 2024-04-01 [252f382] [jsonlab] update bundled jsonlab to v2.9.8 release
 2024-03-05 [4e0746d] [feat] update readobjmesh with more robust parsing
 2024-03-05 [25d5e20] [feat] add readobjmesh function
 2024-02-22 [381d5fd] include faces
 2024-01-15 [8a0f460] Merge branch 'master' of github.com:fangq/iso2mesh
 2024-01-15 [3df2ceb] [bug] fix loading nii.gz with extension
 2023-10-28 [29bedc6] resync meshfix and PoissonRecon submodules, fix #73
 2023-10-28 [cd94624] update jsonlab to the latest version
 2023-06-11 [607c5e4] sync jsonlab and jnifty to the latest versions
 2023-04-08 [ab2878a] sync with brain2mesh, polylinelen output oriented curve
 2023-04-08 [ee3f867] fix self intersection testing in surfboolean
 2023-02-25 [556f4c3] merge loadjd and savejd conflicts
 2023-02-25 [0ccb658] sync jnifty and jsonlab to the latest github version
 2022-11-10 [e3ff264] Merge pull request #69 from ithron/fix68_saveinr_single
 2022-11-09 [8b4725a] Fix #68 - saveinr() not working for single volumes.
 2022-10-07 [d87d60c] update jsonlab to git version
 2022-05-03 [70baeb6] Merge branch 'master' of github.com:fangq/iso2mesh
 2022-05-03 [1907f32] fix file name typo, close fangq/brain2mesh#13
 2022-04-12 [7d94249] fix loadjmesh function name
 2022-04-03 [e3664e6] update jsonlab to the latest to include loadjd and savejd
 2022-03-31 [f2af7cd] automatically reorient all surfaces and elements after each key function call
 2022-03-31 [9b55562] Merge branch 'master' of github.com:fangq/iso2mesh
 2022-03-30 [a3ac212] update bundled jsonlab
 2022-03-29 [3324c0b] update jmesh parser URLs in _DataInfo_
 2022-03-13 [80d2138] update savejson after fixing fangq/jsonlab#78
 2022-03-12 [978de05] sync jsonlab and jnifti with git version, add metadata to savejmesh
 2022-02-10 [f498ca2] upgrade jsonlab to 2.9.8-git20220210
 2021-09-22 [a7673f5] Merge pull request #60 from lrineau/modify_README
 2021-09-21 [29a1828] Update README.md for CGAL
 2021-09-20 [5c69f61] Merge pull request #59 from lrineau/improve_cgalmesh__images_with_1D_features
 2021-09-20 [081d41f] Respect 1D features in volume
 2021-09-12 [238c987] remove loop in savemphtxt, patch by @brainwatcher,close #50
 2021-09-12 [180618d] make region id positive in savemsh, close #58
 2021-09-08 [2162547] fix octave warning when loading tiff file
 2021-08-18 [7776f86] fix meshfix invalid commit hash, close #55
 2021-07-30 [8c35d0d] can handle both 2D and 3D image in bwislands
 2021-07-12 [28a09c8] remove readnifti, use loadnifti
 2021-04-21 [e8fb05c] print tetgen message when it fails
 2021-02-21 [3de31f9] add windows PoissonRecon binary
 2021-02-21 [71b1ab7] add PoissonRecon binary for Mac OS, add author and license info in README
 2021-02-21 [d611d7a] add PoissonRecon, prepare for the point cloud processing feature
 2021-02-21*[e6638c0] add PoissonRecon v8 as submodule
 2021-02-21 [f8f3fc2] make meshremap compatible with old matlab and octave
 2021-01-25 [0ead04f] export negative volume elem indices in meshreorient
 2021-01-15 [c7eec85] set initial value for meshinterp
 2020-12-31 [58de92c] qmeshcut returns node id

2020/09/05 (1.9.6, codename: Lion's Head)

 2020-09-05 [12e7e8e] update octave toolbox info
 2020-09-05 [f110ef3] bump version number to 1.9.6
 2020-09-05 [dbe4d82] sync with jsonlab fangq/jsonlab@d0fb684
 2020-09-05 [e22964e] fix Fedora bug#1865133 due to CGAL header file changes
 2020-07-28 [3869f6a] update cork and surfboolean to add remesh support
 2020-07-07 [e8c45a2] add the missing polylineinterp function from brain2mesh

2020/07/01 (1.9.5, codename: Lion's Head - beta)

 2020-07-01 [c89164a] fallback all executables to system PATH
 2020-06-30 [786b2c0] add cgalsurf manual
 2020-06-30 [e682958] add man page
 2020-06-17 [f36c220] fix octave DESCRIPTION file
 2020-06-17 [db9bd71] Update README.md
 2020-06-17 [4a85c4c] update reference, update build requires packages
 2020-06-17 [a791382] add git filters for version printing
 2020-06-16 [be35b28] revert the regression
 2020-06-16 [94ffa22] cgal windows binary permission set
 2020-06-17 [a231e14] enable windows 64bit binaries
 2020-06-16 [3bfbf62] add new 64bit cgal windows bianries
 2020-06-16 [dce0f62] remove unwanted dll
 2020-06-16 [477625f] add 64bit windows binaries
 2020-06-16 [51b6d06] update cork for 64bit windows
 2020-06-15 [cb5c449] update gendocs script, create octave package files
 2020-06-15 [9d488f9] test mesh2vol on both matlab 2010 and 2020
 2020-06-15 [b9dc1e0] make metch demo 2 work with octave
 2020-06-15 [c1dea88] make metchgui_one compatible with octave
 2020-06-15 [45a2ec2] make metchgui work again with matlab 2020a
 2020-06-15 [d2896be] merge metch toolbox with iso2mesh
 2020-06-15 [b9fbbf7] update jsonlab to v2.0
 2020-05-28 [4c76cd7] fix permission on windows
 2020-05-27 [168a578] add polyline functions from brain2mesh toolbox
 2020-03-23 [555ffce] remove degenerated surfaces to avoid matlab edge flipping in convhulln
 2020-03-18 [afebb6b] fix type conversion errors, thanks to John Richards
 2020-03-18 [9c503e5] use the correct row dimension for edges
 2020-03-05 [3d10fc0] add ndimfilter
 2020-03-01 [246d178] avoid degenerated edges in extractloops, needed by brain1020
 2020-02-21 [3630f03] remove gtsset, cork is stable
 2020-02-21 [ddc9a16] make mcpath to support 64bit windows exe, add cork_x86-64.exe, fix #43
 2020-02-19 [8454bf6] allow deletemeshfile to use wildcards
 2020-02-19 [db6eb75] fix mergesurf help info typos

2020/02/13 (1.9.2 for integration with Brainstrom)

 2020-02-11 [f69eae2] Merge pull request #42 from ftadel/master
 2020-02-03 [000138f] Calling mwpath with no inputs
 2019-11-12 [c394673] sync jsonlab after fixing ubjson bug
 2019-11-08 [2de6ac5] README.md for better readability in Github
 2019-10-25 [59869c6] sync jsonlab to v1.9.8
 2019-10-18 [1245a7c] allow meshfix to be built on both Ubuntu and Fedora, fix #39

2019/10/01 (1.9.1 for packaging iso2mesh)

 2019-10-01 [24736f5] update submodule to compile on fedora
 2019-10-01 [60b1b4c] fall back to system search path in mcpath
 2019-10-01 [6b687fc] make cgalmesh compilable with newer cgal where AABB_intersections.h was removed
 2019-09-16 [7b7385c] update jsonlab to support lz4, update jnifti toolbox to v0.5
 2019-08-20 [903791b] fix table transpose issue in jdatadecode
 2019-08-13 [5c15873] use iso2mesh original function isoctavemesh in place of isoctave
 2019-08-13 [4c276f8] Merge branch 'master' of https://github.com/fangq/iso2mesh
 2019-08-13 [33262fb] update function list
 2019-08-10 [4b969f3] add the missing isoctave for savejmesh
 2019-08-03 [999104b] plot window receive keyboard events
 2019-07-19 [80bffdf] update jsonlab to use the zmat v0.8 folder structure
 2019-07-08 [2d59124] reorient element before exporting to mphtxt
 2019-06-27 [7977137] refine meshes with square faces can cause inconsistency
 2019-06-25 [981ea63] update jsonlab to the latest
 2019-06-21 [9dbe3e7] add JNIfTI toolbox
 2019-06-20 [231654d] update savejmesh help info
 2019-06-20 [fe21139] update jsonlab
 2019-06-20 [5dbae5c] update savejmesh to support the current draft of jmesh format: https://github.com/fangq/jmesh
 2019-06-20 [af02073] update jsonlab to 2.0 beta
 2019-06-03 [4c93361] massive update of jsonlab to 1.9.8 - msgpack support and speed improvement
 2019-05-07 [14d64c7] update jsonlab to v1.9 to support data compression
 2019-01-21 [dae0242] support tetgen command option in surf2mesh and s2m, override ISO2MESH_TETGENOPT

2018/07/19 (1.9.0, codename: Century Egg - final)

  2018-07-19*[67ae478] update jsonlab to v1.8
  2018-07-19 [0af072c] compiling jmeshlib and tetgen1.5 from source
  2018-07-19 [c75ce08] use meshfix 1.2 from an old copy
  2018-07-18 [f49286b] use system binaries first, then use locally built suffix-less binaries, then prebuilt ones
  2018-07-18 [8d015f4] add makefile to compile all external tools and copy exe to bin
  2018-07-18*[17bf732] add source codes for embedded tool for deployment
  2018-06-27 [2baaf0d] fix bugs in meshinterp and meshremap when elemid contains nan
  2018-06-26 [3413cf6] add meshremap and meshinterp to map values between a pair of meshes
  2018-05-30 [f111940] add examples for readnirfast and savenirfast
  2018-05-30*[6ec9dbc] support importing and exporting NIRFAST mesh files
  2018-05-25 [312d1ff] nodevolume can be calculated using elemvolume
  2018-05-02 [39bc663] fix missing command in the meshconn output
  2018-04-11 [65a0f2a] Update tetgen1.5 executable for Windows to TetGen v1.5.1-beta1
  2017-11-08*[98d9fb4] add extrudesurf function to expand an open surface into a solid
  2017-10-02 [9f5e9f1] support cone trunk in meshacylinder
  2017-09-13 [914d9e9] Fix bug in surf2mesh
  2017-08-30*[a6070a9] add top and bottom faces for extrudecurve
  2017-08-06 [6cd2747] merge phong's surfboolean, make s2m/surf2mesh support tetgen1.5
  2017-07-19 [f6d8d7f] remove isoloated nodes for cell represented surfaces
  2017-06-29 [4ff9ed9] support removing duplicated nodes in cell face input
  2017-06-20 [dab6afe] close open surfaces by the bounding box
  2017-06-20 [059f98a] support initial angle in orthdisk
  2017-06-12 [5d22c41] apply a patch from Riccardo to correct surface orientation
  2017-05-29 [48f30d5] update meshfix binary for windows, add 64bit meshfix from https://github.com/MarcoAttene/MeshFix-V2.1/
  2017-05-11 [d11dbc4] add new function to create extruded surfaces from orthogonal 2D spline curves
  2017-03-05 [41da47d] create 10-node tet from 4-node tet

2017/01/16 (1.8.0, codename: Deviled Egg - final)

        1.**robust surface boolean operator based on Cork
        2. update tetgen 1.5 to 1.5.1
        3. new function: insurface for point-in-surface test
        4.*new function: fillsurf for tesselating a closed surface
        5. new function: surfvolume for calculating the volume of an enclosed surface
        6.*new function: innersurf/outersurf: interior and exterior parts of a surface
        7. meshcylinders supports a series of segments, also returns PLC
        8. surfedge/volface return tet element id for the face triangles
        9. plotmesh supports element-based colormap
       10. s2v outputs mesh-to-voxel transformation matrix
       11.*JSONlab updates to 1.5 Nominus alpha
       12. display binary utility download URL when missing
       13. faceneighbor returns row- or column-major facelist
       14. fix half-voxel offset bug in cgalmesher
       15. surf2vol and s2v now rasterize labeled surfaces and tetrahedral mesh
       16. disable binary compression for Mac OS to avoid crashes
       17. fix uniqedges edgemap output bug

2015/09/19 (1.7.9, codename: Deviled Egg - beta)

        1. make v2m(method=cgalmesh) output repeatable
        2.**JSONlab update to 1.1
        3. qmeshcut allows to exact plane that are exactly parallel to the faces
        4.*surf2mesh supports region-based volume control
        5. fix getvarfrom workspace bug
        6.*meshrefine can insert external nodes to the mesh
        7. allow binsurface to mesh a 2d image
        8.**significantly improved meshrefine - sizing field, new nodes etc
        9. support OSX Yosemite
        10. fix s2m face label bug
        11.*plotmesh supports plotting 3d polyline and loop objects
        12. extract junction lines from a surface group
        13. extractloops now supports open contours
        14. latticegrid - 3D lattice function
        15.**GPU accelerated mesh rasterization - mesh2mask/mesh2vol/m2v (experimental)
        16. add regular grid generation by meshgrid5 and meshgrid6
        17. fix plotmesh bugs
        18. export to GMSH format (by Riccardo Scorretti)

2013/07/16 (1.5.0, codename: Laba Porridge)

        1.*label-wise mesh density control in CGAL 3D mesher (Peter Varga)
        2. plotting mesh slices with the "{x,y,z}=value" syntax in plotmesh

2013/01/20 (1.4.9, codename: Laba Porridge - beta)

        1.*loadjson and savejson for unified 3D mesh data exchange
        2. support COMSOL mphtxt file format (Donghyeon Kim)
        3. raytrace outputs intersection element ID list
        4.*qmeshcut supports more flexible mesh slicing options
        5. plotmesh accepts cell array face list for general polyhedra handling
        6. s2m supports 'cgalpoly' option
        7. fix remeshsurf coordinate offset bug
        8. return region seeds from v2s
        9. new function meshrefine for mesh refinement
       10. saving surface mesh to STL (ASCII or binary) format
       11. new function meshacylinder to mesh a 3D cylinder
       12.**surface mesh boolean operations (surfboolean) via GTS library
       13. qmeshcut supports element-based value list
       14. fast mesh intersection testing utilities surfboolean('self')
       15.**self-intersecting surface repairing and decoupling using meshfix utility
       16. export mesh to ABAQUS format
       17.*add binaries for 32/64bit Intel Mac OS and Raspberry Pi (armhf)
       18.*define a JSON-based mesh format (JMesh) for general-purpose data exchange
       19. add surfreorient,readgts,savegts,uniqedges,raysurf,savejmesh and many more

2011/06/03 (1.0.1, codename: Mapo Tofu - Update 1)

        1. added 64bit CGAL binaries for Linux (Windows/MacOS are not yet supported)
        2.*plotmesh can use the 4th column of node input as colormap/value
        3.*accept "cgalpoly" method option in v2m and vol2mesh
        4. savemedit output supports the label column
        5.*orient all triangles counter-clockwise for surface plotting
        6. added edgeneighbors to report neighboring triangles in a surface

2011/02/27 (1.0.0, codename: Mapo Tofu)

        1. fixed mwpath/mcpath octave warning
	2. used consistent opt.distbound flag for cgalv2m and cgalv2s
	3. fixed a bug in plotmesh to allow using plotting styles
	4. added a method parameter in sms
	5. fixed a bug in mergemesh with more than 2 inputs
	6. added mesh quality metric function (Joe-Liu metric)
	7.*added ray-tracing functions (using the Havel's method)
	8.*robust and fast surface interior point determination
	9.*label multi-part surfaces inside vol2surf
       10. new functions surfplane/surfseeds/surfinterior/meshedge
       11. use SVN revison number as the default extra version tag

2011/01/31 (0.9.9, codename: Mapo Tofu-RC1)

        1.*specifying seeds for cgalsurf and cgalmesh modules
        2.*perturbing isovalues to avoid non-manifold geometries
        3. added plottetview to call tetview for mesh display on octave
        4. added a new demo - a "hello world" example
        5. speed optimization for octave
        6. optimized memory use for surf2vol
        7. made nodevolume support surfaces
        8. added savemedit to export tetrahedral mesh in Medit format
        9. compress most binaries with upx to save space
       10. set up binary file extension fallback to help Mac users
       11.*added functions to mesh simple geometries such as a sphere etc
       12. added meshmerge to merge multiple meshes and surfaces
       13. added s2v shortcut for surf2vol
       14. updated cgalsurf to specify initial point cloud size
       15. added iso2meshver to track version numbers
       16. automatic handling of label column in face and elem plots

2010/07/14 (0.9.8, codename: Mapo Tofu-beta)

        1.*added surf2vol, converting a closed surface to a binary volume
        2. fixed deletemeshfile bug for Windows
        3. automatic repairing when meshresample fails
        4. fast faceneighbors unit
        5.*added CGAL 3D mesher for robust meshing of segmented volumes
        6. added CGAL 3D polyhedral mesher as an alternative to tetgen
        7. corrected bugs in Laplacian+HC and Lowpass smoothing algorithms
        8. added sms.m as the shortcut for surfsmooth
        9. added exporters for DXF and VRML mesh formats
       10. added user name to the temporary files to avoid permission conflict
       11. added force-bounding-box option for surf2mesh
       12. added nodevolume, elemvolume from FEMcore and meshreorient
       13. added sortmesh to optimize node and element ordering
       14.*mesh refinement using the 4-th column of surface node
       15. thining a volumetric binary image
       16.*added remeshsurf to repair self-intersecting surfaces
       17. added demo scripts for remeshsurf and mesh smoothing
       18. unify help text format, add bash script to generate function list
       19. use opt.side to specify upper/lower interface of a labeled region
       20.*added a mesh plotting function - plotmesh

2009/05/04 (0.8.0, codename: Hotpot)

        1. added stopping criteria for cgalsurf surface extractor to 
           avoid hanging for certain datasets
        2.*added support for mesh generation from 3D gray-scale images
        3. more robust and fast imedge3d (thanks to Aslak Grinsted)
        4. fixed the origins for 'simplify' and 'cgalsurf', the origin is now
           set to the exterior vertex for voxel (1,1,1) (as a cube)
        5. updated documents
        6. renamed "bound" to "face" to avoid confusions
        7.*added v2m, v2s and s2m as the shortcuts for vol2mesh, vol2surf 
           and surf2mesh, respectively; added demo script for shortcuts
        8. mcpath searches <iso2mesh>/bin first, no PATH setting is required
           (thanks to Aslak Grinsted)
        9. many other minor fixes and cleaning

2009/02/11 (0.7.9-1, codename: Hotpot-beta)

        1. compiled all the binaries on Mac OS (PowerPC) and
           tested on an Intel Mac
        2.*recompiled all linux and windows binaries with optimized speed
           and reduced system dependencies
        3. speeded up bounary field calculation with dedicated imedge3d
        4. added TODO

2009/02/07 (0.7.9, codename: Hotpot-alpha)

        1.*incorporated CGAL Surface mesher as the default vol2surf
           mesh extraction scheme (thank to Pierre Alliez's suggestion
           and Laurent Rineau and Mariette Yvinec for developing this utility)
        2. added sub-region labeling for multi-valued images
        3. added cgalsurf binaries for Windows
        4. tested the toolbox with Octave for Windows on a vista machine,
           applied a few fixes to make it compatible
        5. recompiled tetgen.exe to get the max-element-volume constraint
           finally work

2008/12/27 (0.7.8, codename: Hotpot-alpha)

        1. try to handle the self-intersecting element problems, 
           added getintersecttri.m to extract intesecting element IDs
        2. implemented Laplacian+HC and Low-pass filter mesh smoothing
           algorithms; unfortunately, they are not effective to remove the 
           self-intersecting elements
        3. sent email to CGAL list to ask advices to handle self-intersecting
           element.

2008/12/05 (0.6.0, codename: Quesadilla)

        1. iso2mesh is now compatible with GNU Octave.
        2. replaced matlab's isosurface by a home-made binsurface to produce
           well-behaved triangular or cubic surfaces from binary images
        3. added qmeshcut, a fast tetrahedral mesh cross-section plot
        4. updated tetgen binary for 64bit Linux (mexa64), which caused some crashes
        5. provided instructions when user encounters a "permission denied" error

2008/11/08 (0.5.1, codename: Footlong)

        1. added meshing tool binaries for Windows (95-vista)
        2. added meshing tool binaries for Mac OS
        3. tagged all bin/ files and binaries files in sample/
           with -kb option in the cvs

2008/10/30 (0.5, alpha release, codename: Footlong)

        1. created a sourceforge project, pointing to 
           the project main page at orbit.
        2. wrote documents and polish file structures
        3. included more sample codes and data
        4. defined a global variable "ISO2MESH_TEMP" to control the 
           temporary file directory; "ISO2MESH_BIN" for bin folder
           location and "ISO2MESH_SESSION" for temporary file prefix
           and enable parallel meshing sessions and restricted user 
           environments
        5. renamed all temporary files as pre_smesh/post_smesh/
           pre_remesh/post_remeshpre_vmesh/post_vmesh to identify
           the processing stage
        6. split vol2mesh into vol2surf and surf2mesh
        7. uploading wiki pages with documentation drafts and 
           examples outputs

2008/10/10 (0.4)

        1. added subroutines for mesh validation and repairing
        2. included JMeshLib for non-manifold node removal

2008/01/10 (0.3)

        1. added vol2mesh and the related scripts
        2. iso2mesh is able to mesh breast geometry from 3D 
           tomosynthesis scan and a mouse head model from CT images.

2008/04/08 (0.2)

        1. qslim produces self-intersecting meshes after 
           simplification, which is not good. It is now replaced
           by CGAL mesh simplification module
        2. modified CGAL mesh simplification code to preserve all
           edges nodes (keep them co-planar)

2007/12/27 (0.1.1)

        1. used mexext to distinguish binaries for different platforms

2007/11/25 (0.1)

        1. initial upload to cvs, as a module of redbird2
        2. used qslim to perform mesh simplification and tetgen 
         for mesh generation
        3. supported both win32 and Linux
        4. added sample data and scripts