The NIH/NIGMS
Center for Integrative Biomedical Computing

Acknowledgement: Cleaver is an Open Source software project that is principally funded through the SCI Institute's NIH/NIGMS CIBC Center. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of NIH/NIGMS CIBC software or data sets.

"This project was supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant numbers P41 GM103545 and R24 GM136986.”

 • Cleaver Citation: [bibtex citation] [Endnote citation]

MIT License

Copyright (C) 2012, Jonathan Bronson,
Scientific Computing & Imaging Institute, University of Utah

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files ( the "Software" ), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

cmake [src]
make

Alternatively, if you do not wish to build the command line program (which requires the Teem Library) use ccmake to disable it.

What Can Cleaver Do?

Cleaver generates conforming tetrahedral meshes for multimaterial or multiphase volumetric data. Both geometric accuracy and element quality are bounded. The method is a stencil-based approach, and relies on an octree structure to provide a coarse level of grading in regions of homogeneity.

What does Cleaver use as input?

The cleaving algorithm works by utilizing indicator functions. These functions indicate the strength or relative presence of a particular material. At each point, only the material with the largest indicator value is considered present. In practice, inside-outside and distance functions are most common.

What is the input format?

The cleaver library takes as input an instance of the Cleaver::Volume class. The Volume is a collection of Cleaver::ScalarField's, along with a sampling rate. The Cleaver::ScalarField class is an abstract class, that can be extended by users to create arbitrary inputs. We provide the FloatField class for loading 3D arrays of floating point data. The Cleaver command-line tool also offers convenience functions for loading the teem NRRD image format into the FloatField format.

What is the output format?

The Cleaver Library returns a Cleaver::TetMesh object. This object supports direct output to file in several formats:

1. TetGen: .node, .ele
2. SCIRun: .pts, .elem, .txt
3. Matlab: .mat

Running ./cleaver -h

usage: cleaver -p -as [val] -al [val]  -i [input1.nrrd input2.nrrd ...]  -o [output]  -f [format]
         -p      use padding         default=no
         -as    alpha short           default=0.357
         -al     alpha long            default=0.203
         -i       input filenames    minimimum=1
         -o     output filename    default=output
         -f      output format         default=tetgen
         -h     help

   Valid Parameters:
                 alpha short                  0.0 to 1.0
                 alpha long                   0.0 to 1.0
                 tetmesh formats         tetgen, scirun, matlab

Examples:
cleaver -h                                                                               print help guide
cleaver -i mat1.nrrd mat2.nrrd                                           basic use case
cleaver -p -i mat1.nrrd mat2.nrrd                                      pad boundary
cleaver -i mat1.nrrd mat2.nrrd -o mesh                          specify output name
cleaver -i mat1.nrrd mat2.nrrd -o mesh -f scirun           specify output format

Joining the Cleaver Mailing List

1. Compose an email to This email address is being protected from spambots. You need JavaScript enabled to view it. with the following in the body of message: subscribe cleaver
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Unsubscribing

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2. Nothing needed in the Subject line. Just send.
3. You will receive a response from the list manager notifying you that the command has succeeded and you have been removed from the list.

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