Package: pygamer
Geometry-preserving Adaptive MeshERGAMer is a surface mesh improvement library developed to condition surface meshes derived from noisy biological imaging data.
Using Tetgen, GAMer can generate tetrahedral meshes suitable for finite elements simulations of reaction-diffusion systems among others.
GAMer has the following main features:Surface mesh improvement and decimation algorithmsBoundary marking and other featuresEstimation of surface curvaturesGeneration of mesh surfaces around biological moleculesTechnical Features:Code is implemented in C++ and supports Python using a pybind11 wrapper (pygamer).Cross system compilation using CMake and runs on Linux (64 bit), Windows (32 or 64 bit) or MacOS (64 bit).Blender addon which enables easy access to GAMer features using the pygamer API.Uses the Colored Abstract Simplicial Complex data (CASCstructure as the flexible underlying representation of surface and tetrahedral meshes.Code is hosted byGitHubunder the Lesser GNU public license (LGPLv2). Please post issues or reports there.Acknowledging your use of GAMerThanks for using GAMer! The developers would love to hear how you are using the tool. Please send us an email or post on GitHub letting us know.Please cite the above Zenodo DOI to acknowledge the software version and cite the following papers:Lee, C. T.; Laughlin, J. G.; Moody, J. B.; Amaro, R. E.; McCammon, J. A.; Holst, M.; Rangamani, P. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophysical Journal 2020, 118 (5), 1003–1008.Lee, C. T.; Laughlin, J. G.; Beaumelle, N. A. de L.; Amaro, R. E.; McCammon, J. A.; Ramamoorthi, R.; Holst, M.; Rangamani, P. 3D Mesh Processing Using GAMer 2 to Enable Reaction-Diffusion Simulations in Realistic Cellular Geometries. PLOS Computational Biology 2020, 16 (4), e1007756.InstallationThe following instructions are to build the base GAMer library.
If you wish to additionally compile the Blender GAMer addon, GAMer documentation, or other features please refer to the Additional Options section prior to building.First, download a copy of the source fromreleasesor clone the master branch.gitclonehttps://github.com/ctlee/gamer.gitcdgamerLinux and Mac:mkdirbuildcdbuild
cmake-DCMAKE_INSTALL_PREFIX:PATH=/usr-DGAMER_TESTS=on-DCMAKE_BUILD_TYPE=Release..
makeFor Windows, we support building using Microsoft Visual Studio (MSVS) through the use of CMake generators:mkdirbuild64cdbuild64
cmake-DBUILD_BLENDGAMER=TRUE-G"Visual Studio 15 2017 Win64"-Ax64..
cmake--build.--configReleaseFor a complete guide to installation, including configuration of PyGAMer and BlendGAMer please checkout theonline installation documentation.External libraries bundled/downloaded with/by GAMerGAMer usesTetgento generate
tetrahedralizations.GAMer usesEigento
compute eigenvalues/eigenvectors of the Local Structure Tensor.GAMer usescascas the underlying simplicial
complex data structure.GAMer usesGoogleTestto handle testing.GAMer usesPybind11Mesh checks in the GAMer Blender addon are inspired or borrowed from 3D Print Toolbox by Campbell Barton and Meshalyzer from CellBlender.Triangleis also bundled with GAMer but not currently used.Development Build Status