kanapy 6.4.3

Python package for microstructure analyse and generation of microstructure models

Kanapy is a python package for generating complex three-dimensional (3D) synthetic polycrystalline microstructures. The microstructures are built based on statistical information about grain geometry, given as grain size distribution and aspect ratio of grains, and crystallographic texture, in form of orientation distribution functions (ODF) and misorientation distribution functions (MDF). Kanapy offers tools to analyze EBSD maps with respect to the geometry and texture of microstructures. Based on this experimental data, it generates 3D synthetic microstructures mimicking real ones in a statistical sense. The implementation is done in Python.

The texture module of Kanapy is implemented as MATLAB functions using several algorithms implemented in MTEX for texture analysis.

Features

• Kanapy offers a Python Application Programming Interface (API).
• Possibility to analyze experimental microstructures based on MTEX functions.
• Generation of microstructure geometry based on statistical features as grain size distribution and grain aspect ratio distribution.
• Crystallographic texture reconstruction using orientations from experimental data in form of Orientation Distribution Function (ODF).
• Optimal orientation assignment based on measured Misorientation Distribution Function (MDF) that maintains correct statistical description of high-angle or low-angle grain boundary characteristics.
• Independent execution of individual modules through easy data storage and handling.
• In-built hexahedral mesh generator for complex polycrystalline microstructures.
• Efficient generation of space filling structures by particle dynamics method.
• Collision handling of particles through a two-layer collision detection method employing the Octree spatial data structure and the bounding sphere hierarchy.
• Option to generate spherical particle position and radius files that can be read by the Voronoi tessellation software Neper.
• Option to generate input files for the commercial finite-element software Abaqus
• Analysis and RVE generation for dual-phase microstructures.
• Import and export of voxelated structures for data transfer between different tools.

Installation

The preferred method to install Kanapy is through Anaconda or Miniconda Python distributions. If you do not have any, we suggest installing miniconda.

It can be installed from conda-forge by

$ conda install kanapy -c conda-forge

or from PyPi via pip

$ pip install kanapy

Alternatively, the most recent version of the complete repository, including the source code, documentation and examples, can be cloned and installed locally. It is recommended to create a conda environment before installation. This can be done by the following the command line instructions

$ git clone https://github.com/ICAMS/Kanapy.git ./kanapy
$ cd kanapy
$ conda env create -f environment.yml
$ conda activate knpy
(knpy) $ python -m pip install .

Kanapy is now installed along with all its dependencies. The correct installation with this method can be tested with

(knpy) $ pytest tests -v

After this, the package can be used as API within python, e.g. by importing the entire package with

import kanapy as knpy

Kanapy texture module

If you intend to use Kanapy's texture module, a MATLAB installation is required because the texture module is based on MTEX functions. Kanapy uses a local version of MTEX stored in src/kanapy/libs/mtex, if you want to use another MTEX version, please set the paths accordingly. If MATLAB is available on your system, the texture module is initialized by the command

(knpy) $ kanapy setupTexture

Note: The absolute paths to {user_dependent_path}/site-packages/kanapy and {user_dependent_path}/site-packages/kanapy/libs/mtex should to be added to the MATLABPATH environment variable, see Mathworks® documentation. If the texture module is installed as described above, this is done automatically within Kanapy.

Note: The installation scripts have been tested for Matlab R2024a and R2025a with Python 3.9 and 3.10 on current Linux, MacOS and Windows systems. If you are using other Matlab versions or if you do not have write permission in the Matlab-extern/engines/python directory, the script "setupTexture" might fail. In that case, you or a system administrator can setup the Matlab Engine API for Python manually. To do so, please follow the instructions given on Mathworks®, to (i) verify your configuration, (ii) install Engine API, and (iii) start MATLAB Engine. The Python version of the knpy-environment can be changed according to the requirements of the Matlab Engine API by editing the "environment.yml" file and re-creating the conda environment knpy.

Examples

Kanapy comes with several examples in form of Python scripts and Juypter notebooks. If you want to create a local copy of the kanapy/examples directory within the current working directory (cwd), please run the command

(knpy) $ kanapy copyExamples          

Documentation

The Kanapy documentation is available online on GitHub Pages: https://icams.github.io/Kanapy/

The documentation for Kanapy is generated using Sphinx.

Dependencies

Third-party components

Kanapy's texture module requires MATLAB to be installed on your machine. Make sure to use MATLAB v2024a or above. This package includes code from the project MTEX contained in src/kanapy/libs/mtex, which is licensed under the GNU GPL v2 license. See the LICENSE file in that directory for details.

Core dependencies

Below are the listed dependencies for running Kanapy:

• NumPy for array manipulation.
• Scipy for functionalities like Convexhull.
• Matplotlib for plotting and visualizing.

Optional dependencies

• MATLAB for texture module (commercial software).
• MTEX for texture module (Kanapy package contains MTEX version 5.2.2).
• OVITO for visualizing simulation data.

Citation

The preferred way to cite Kanapy is:

@article{Biswas2020,
  doi = {10.5281/zenodo.3662366},
  url = {https://doi.org/10.5281/zenodo.3662366},
  author = {Abhishek Biswas and Mahesh R.G. Prasad and Napat Vajragupta and Alexander Hartmaier},
  title = {Kanapy: Synthetic polycrystalline microstructure generator with geometry and texture},
  journal = {Zenodo},
  year = {2020}
}

Related works and applications

• Prasad et al., (2019). Kanapy: A Python package for generating complex synthetic polycrystalline microstructures. Journal of Open Source Software, 4(43), 1732. https://doi.org/10.21105/joss.01732
• Biswas, Abhishek, R.G. Prasad, Mahesh, Vajragupta, Napat, & Hartmaier, Alexander. (2020, February 11). Kanapy: Synthetic polycrystalline microstructure generator with geometry and texture (Version v2.0.0). Zenodo. http://doi.org/10.5281/zenodo.3662366
• Biswas, A., Prasad, M.R.G., Vajragupta, N., ul Hassan, H., Brenne, F., Niendorf, T. and Hartmaier, A. (2019), Influence of Microstructural Features on the Strain Hardening Behavior of Additively Manufactured Metallic Components. Adv. Eng. Mater., 21: 1900275. http://doi.org/10.1002/adem.201900275
• Biswas, A., Vajragupta, N., Hielscher, R. & Hartmaier, A. (2020). J. Appl. Cryst. 53, 178-187. https://doi.org/10.1107/S1600576719017138
• Biswas, A., Prasad, M.R.G., Vajragupta, N., Kostka, A., Niendorf, T. and Hartmaier, A. (2020), Effect of Grain Statistics on Micromechanical Modeling: The Example of Additively Manufactured Materials Examined by Electron Backscatter Diffraction. Adv. Eng. Mater., 22: 1901416. http://doi.org/10.1002/adem.201901416
• R.G. Prasad, M., Biswas, A., Geenen, K., Amin, W., Gao, S., Lian, J., Röttger, A., Vajragupta, N. and Hartmaier, A. (2020), Influence of Pore Characteristics on Anisotropic Mechanical Behavior of Laser Powder Bed Fusion--Manufactured Metal by Micromechanical Modeling. Adv. Eng. Mater., https://doi.org/10.1002/adem.202000641

Version history

• v3: Introduction of API
• v4: Import and export of microstructures in form of voxels
• v5: Pure Python version, support of CLI suspended
• v6: Major revision of internal data structure and statistical microstructure parameters
• v6.1: Full support of dual-phase and porous microstructures
• v6.2: Possibility of other geometries than ellipsoids as basic microstructure shapes
• v6.3: Implementation of velocity-Verlet algorithm to integrate particle trajectories during packing
• v6.4: Implmenentation of universal data structure for import and export of microstructures

Licenses

Kanapy is made available under the GNU Affero General Public License (AGPL) v3 license.
MTEX is licensed under the GNU GPL v2 license.
The additional materials under examples and in the documentation are published under the Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA 4.0) license.

About

The name Kanapy is derived from the sanskrit word káṇa meaning particle. Kanapy is primarily developed at the Interdisciplinary Center for Advanced Materials Simulation (ICAMS), Ruhr University Bochum - Germany. Our goal is to build a complete synthetic microstructure generation tool for research and industry use.

Authors

Mahesh R.G Prasad, Abhishek Biswas, Golsa Tolooei Eshlaghi, Ronak Shoghi, Napat Vajragupta, Yousef Rezek, Hrushikesh Uday Bhimavarapu, Alexander Hartmaier
ICAMS / Ruhr-Universität Bochum, Germany

Disclaimer

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.