#[1]iso2mesh: a Matlab/Octave-based mesh generator

Advanced Features in iso2mesh

Global variables

   ISO2MESH_TEMP
          controls the temporary file output directory

   The default output directory is under the system's temporary directory,
   i.e. the output of mwpath(''). However, if one does not have permission
   to write to this folder, or if this contains outputs from other users
   who shares the same output folder (for example, /tmp/iso2mesh-username
   on Linux), one can avoid the permission error by setting his own output
   folder. To do this, he need to define
   ISO2MESH_TEMP='/folder/path/you/can/write';

   in Matlab/Octave's "base workspace". The iso2mesh commands afterward
   will output the intermediate files under the specified temp directory.

   ISO2MESH_SESSION
          controls the output file name prefix

   If two users share a common output directory (for example /tmp for GNU
   Linux) on a single machine, some of the users may not able to write
   intermediate output files and encountered errors. If this happens, one
   can set "ISO2MESH_TEMP" to define a new output folder, alternatively,
   one can set ISO2MESH_SESSION to label all his output by a unique
   prefix. For example, if one define
   ISO2MESH_SESSION='foo_';

   this will prepend 'foo_' to all output file names, if this string is
   unique, users can produce all their output files without conflict with
   other users.

   ISO2MESH_BIN
          specifies the folder where to look for the external binaries

   There are several external tools are essential for iso2mesh. These
   pre-compiled binaries are saved under iso2mesh/bin folder. In our
   [2]Installation instructions, we ask the users to add this path to
   their PATH environment variable. If user for some reason not be able to
   do this, iso2mesh will do two things to look for these binaries:
    1. it will first check a global variable ISO2MESH_BIN and see if it is
       defined in the 'base' workspace, if it is defined and the folder
       exist, it will execute the binaries from that folder
    2. if no ISO2MESH_BIN defined, or it has a value which does not exist,
       iso2mesh will use the relative path "iso2mesh/bin" to load those
       binaries
    3. otherwise, it will give an error message, complaining the binary
       can not be found.

   ISO2MESH_RANDSEED
          sets the seed for the random number generators in the CGAL
          modules

   Iso2mesh versions later than 1.0.0 can make reproducible meshes across
   multiple runs. This was done by setting proper seeds for the random
   number generators called inside the CGAL executables. By default,
   iso2mesh will use 0x623F9A9E as the seed. If you prefer to set your own
   seed, please define a global variable named ISO2MESH_RANDSEED in the
   "base" workspace. The value of ISO2MESH_RANDSEED must be a positive
   integer. If iso2mesh detects the definition of ISO2MESH_RANDSEED, it
   will use it to seed the RNGs.

Intermediate outputs

   For each step of the mesh generation along the [3]work-flow, iso2mesh
   will save some intermediate outputs as logs. These outputs are saved
   under the output of mwpath('') (see the explanations for ISO2MESH_TEMP
   above).

   pre_extract.inr
          if one use the default 'cgalsurf' method in vol2surf to extract
          an isosurface from a binary image, this file will save the raw
          binary image for each level set (only the last levelset stays)

   post_extract.off
          the output surface mesh from 'cgalsurf' method (vol2surf)

   pre_remesh.off
          if one use the 'simplify' option of vol2surf, this file saves
          the voxel-resolution surface mesh extracted using binsurface
          subroutine

   post_remesh.off
          this file records the triangular surface after mesh
          simplifications (meshresample)

   pre_sclean.off
          for 'simplify' approach, this file is the surface mesh before
          the mesh validation (meshcheckrepair)

   post_sclean.off
          this is the output from 'mechcheckrepair' subroutine.

   post_vmesh.poly
          when generating the 3D tetrahedral mesh, tetgen needs an input
          file with PLC (piece-wise linear complexes) which is saved in
          this poly file.

   post_vmesh.off
          if no bounding box needed, this file saves the same info as the
          poly file, except it is in off format.

   post_vmesh.1.ele
          tetgen output: tetrahedral element file

   post_vmesh.1.face
          tetgen output: boundary surface element file

   post_vmesh.1.node
          tetgen output: node file

References

   1. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?action=rss
   2. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Installation
   3. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Workflow