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Porous Microstructure Analysis (PuMA)

The stable releases of PuMA can be found on the official NASA Github repository, whereas the latest development can be found on the development Gitlab repository.

A few useful resources:

Install TomoSAM to perform tomography segmentation within 3D Slicer
Documentation detailing the use of each function
Community chat to ask questions or to get in touch
YouTube channel with the video tutorials
Tutorials with examples for both python and C++

Software description

PuMA, winner of the 2022 NASA Software of the Year prize, has been developed to compute effective material properties and perform material response simulations on digitized microstructures of porous media. PuMA is able to import digital three-dimensional images obtained from X-ray microtomography or to generate artificial microstructures that mimic real materials. PuMA also provides a module for interactive 3D visualizations. Version 3 includes modules to compute simple morphological properties such as porosity, volume fractions, pore diameter, and specific surface area. Additional capabilities include the determination of effective thermal and electrical conductivity (both radiative and solid conduction - including the ability to simulate local anisotropy for the latter); effective diffusivity and tortuosity from the continuum to the rarefied regime; techniques to determine the local material orientation, as well as the mechanical properties (elasticity coefficient), and the permeability of a material.

Some examples of microstructures that have been run in the past are shown in the pictures below, together with PuMA's software architecture schematic. See the publications for more information about the software and its capabilities.

System requirements

UNIX (tested on MacOS 10.14.1+, Ubuntu 12.04+, RHEL, and CentOS). On Windows, only the python distribution (pumapy) is available.

Indicative recommended specs (varies depending on the material property):

8 GB of ram for small simulations (5003 or smaller)
16-32 GB of ram for medium simulations (8003 range)
32+ GB of ram for large simulations (above 10003)

Installation

To install PuMA, a conda distribution must be installed on your machine. To test whether conda is installed, run conda from a terminal to see if the command is recognized. If not, conda can be installed by following the instructions here. It is also highly recommended to have the latest version of conda (update by running conda update -n base conda) and to clean old tarballs to avoid using old cached solutions of the environment (run conda clean --all).

Binaries (UNIX and Windows)

This is the recommended installation for PuMA users or for developers of the pumapy Python package. Once the conda command is working, all the PuMA components can be installed by executing the following commands in a terminal:

conda create -n puma conda-forge::puma

On UNIX (i.e. Mac or Linux), the conda command installs the PuMA C++ library, pumapy python package and GUI. On Windows, only the pumapy python package is available.

Note: TexGen (C++ library to create artificial weaves) is only installed on UNIX, because it needs more advanced compilation. A friendly warning will appear when TexGen is not installed and pumapy is imported.

For developers of the python modules in pumapy, it is recommended to create the puma environment with the above command and then to run the following:

conda activate puma
git clone https://github.com/nasa/puma.git
cd puma
pip install -e .

Note that, in order to track the latest development, it is recommended to git clone the puma-dev Gitlab repo instead. These commands will link the local python files to the pumapy installation in the puma conda environment. Changes to the local python files will therefore take immediate effect.

Build from source (UNIX-only)

This is the recommended installation for developers that need to make modifications to the C++ part of PuMA. The installation is broken into two sections:

Installation of basic dependencies that may be missing from your system
Download the repository, build the source code, and install the binaries

Step 1 of the installation varies slightly based on the system. Open a terminal, navigate to the directory you would like PuMA installed, and execute one of the following lines:

# run one of these
xcode-select --install  # MacOS
sudo apt-get install git build-essential mesa-common-dev  # Debian (Ubuntu)
sudo yum group install "Development Tools"; sudo yum install git gcc mesa-libGL-devel  # Fedora (CentOS, RHEL)

Note: If XCode command line tools are already installed, the command will result in an error, which is not a problem.

Now that the necessary dependencies have been installed, you can go ahead with Step 2 of the installation:

git clone https://github.com/nasa/puma.git
cd puma; chmod +x installer.sh; ./installer.sh

After installation, close the terminal and open a new one.

Running PuMA

PuMA relies on a conda environment in order to manage its software dependencies and environment variables. It is therefore important to always activate the environment before using any of PuMA's functionalities. Once the installation is complete, the PuMA GUI can be launched by running:

conda activate puma
pumaGUI

You can follow the jupyter notebook tutorials, which show the typical function usage for both PuMA C++ and pumapy. These can also be run directly in a browser through Binder.

Citing PuMA

If you use PuMA in your research, please use the following BibTeX entries to cite it:

For PuMA v3
@article{puma2021,
  title={Update 3.0 to “PuMA: The Porous Microstructure Analysis software”,(PII: S2352711018300281)},
  author={Ferguson, Joseph C and Semeraro, Federico and Thornton, John M and Panerai, Francesco and Borner, Arnaud and Mansour, Nagi N},
  journal={SoftwareX},
  volume={15},
  pages={100775},
  year={2021},
  publisher={Elsevier}
}

For PuMA v2
@article{puma2018,
  title={PuMA: The porous microstructure analysis software},
  author={Ferguson, Joseph C and Panerai, Francesco and Borner, Arnaud and Mansour, Nagi N},
  journal={SoftwareX},
  volume={7},
  pages={81--87},
  year={2018},
  publisher={Elsevier}
}

See the publications file for a full list of papers on PuMA and its numerical methods.

Common errors and bug reporting

This is a list of the common errors encountered during the setup and how to solve them:

If PuMA was partially installed but was interrupted, this can cause errors when trying to install the software. To fix this, first follow the instructions to uninstall puma, and then repeat the installation procedure
If an error "make: Warning: File ... has modification time ... s in the future" is displayed, then run "sudo apt install ntp" (or equivalent for your distribution)

If any bugs are found, or if the software crashes for any reason, please open an issue at this link and/or contact either of the authors mentioned below.

Contributing to PuMA

Since PuMA is a free open-source code, any user is welcome to contribute or collaborate however they would like. If you are interested in significant development for your research goals, please contact either of the authors mentioned below, either by email or on the community chat.

Authors

Creator: Joseph Ferguson joseph.ferguson@stanford.edu

Maintainer: Federico Semeraro federico.semeraro@nasa.gov

Contributors: John M. Thornton, Francesco Panerai, Arnaud Borner, Jeremie B. Meurisse, Sergio Fraile Izquierdo, Nagi N. Mansour

Legal / License

Copyright @ 2017, 2020, 2021 United States Government as represented by the Administrator of the National Aeronautics and Space Administration. All Rights Reserved. This software may be used, reproduced, and provided to others only as permitted under the terms of the agreement under which it was acquired from the U.S. Government. Neither title to, nor ownership of, the software is hereby transferred. This notice shall remain on all copies of the software. This file is available under the terms of the NASA Open Source Agreement (NOSA), and further subject to the additional disclaimer below: Disclaimer: THE SOFTWARE AND/OR TECHNICAL DATA ARE PROVIDED "AS IS" WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SOFTWARE AND/OR TECHNICAL DATA WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM INFRINGEMENT, ANY WARRANTY THAT THE SOFTWARE AND/OR TECHNICAL DATA WILL BE ERROR FREE, OR ANY WARRANTY THAT TECHNICAL DATA, IF PROVIDED, WILL CONFORM TO THE SOFTWARE. IN NO EVENT SHALL THE UNITED STATES GOVERNMENT, OR ITS CONTRACTORS OR SUBCONTRACTORS, BE LIABLE FOR ANY DAMAGES, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, SPECIAL OR CONSEQUENTIAL DAMAGES, ARISING OUT OF, RESULTING FROM, OR IN ANY WAY CONNECTED WITH THIS SOFTWARE AND/OR TECHNICAL DATA, WHETHER OR NOT BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, WHETHER OR NOT INJURY WAS SUSTAINED BY PERSONS OR PROPERTY OR OTHERWISE, AND WHETHER OR NOT LOSS WAS SUSTAINED FROM, OR AROSE OUT OF THE RESULTS OF, OR USE OF, THE SOFTWARE AND/OR TECHNICAL DATA. THE UNITED STATES GOVERNMENT DISCLAIMS ALL WARRANTIES AND LIABILITIES REGARDING THIRD PARTY COMPUTER SOFTWARE, DATA, OR DOCUMENTATION, IF SAID THIRD PARTY COMPUTER SOFTWARE, DATA, OR DOCUMENTATION IS PRESENT IN THE NASA SOFTWARE AND/OR TECHNICAL DATA, AND DISTRIBUTES IT "AS IS." RECIPIENT AGREES TO WAIVE ANY AND ALL CLAIMS AGAINST THE UNITED STATES GOVERNMENT AND ITS CONTRACTORS AND SUBCONTRACTORS, AND SHALL INDEMNIFY AND HOLD HARMLESS THE UNITED STATES GOVERNMENT AND ITS CONTRACTORS AND SUBCONTRACTORS FOR ANY LIABILITIES, DEMANDS, DAMAGES, EXPENSES OR LOSSES THAT MAY ARISE FROM RECIPIENT'S USE OF THE SOFTWARE AND/OR TECHNICAL DATA, INCLUDING ANY DAMAGES FROM PRODUCTS BASED ON, OR RESULTING FROM, THE USE THEREOF. IF RECIPIENT FURTHER RELEASES OR DISTRIBUTES THE NASA SOFTWARE AND/OR TECHNICAL DATA, RECIPIENT AGREES TO OBTAIN THIS IDENTICAL WAIVER OF CLAIMS, INDEMNIFICATION AND HOLD HARMLESS, AGREEMENT WITH ANY ENTITIES THAT ARE PROVIDED WITH THE SOFTWARE AND/OR TECHNICAL DATA.