pyEMsoft

This is a documentation repository for pyEMsoft, held on readthedocs.

pyEMsoft is a Python interface to the many Fortran types and subroutines in EMsoft.

An extension module is created automatically with f90wrap that can be directly imported in Python from EMsoft import pyEMsoft.

Installation

Details on installation can be found in readthedocs.

Install EMsoft_SDK
Clone EMsoftData
Compile EMsoft onto your local computer
Install python 3.x (other python packages are needed to run examples include: jupyter notebook, pyyaml, scikit-image, h5py, matplotlib, ipywidgets)
Install f90wrap (WSL/Ubuntu/macOS)
Use run_pyEMsoft.sh (located in the EMsoft Build folder) to generate pyEMsoft extension module (*.so and pyEMsoft.py)
Install the pyEMsoft in the pyEMsoftBuild folder with python setup.py install

How to use?

To import pyEMsoft into Python program:

# import the pyEMsoft module
from EMsoft import pyEMsoft
# import utility module
from EMsoft import pyEMsoftTools

Functions

pyEMsoft has access to some of the functions in EMsoft including:

physical constants (ionic radii, Planck constant, Boltzmann constant, atomic weights, element symbols, etc)
crystallographic symbols and point/space groups
quaternion computations (normalization, multiplication, devision, complex conjugate, inner product, inter-quaternion angle, quaterion rotation, interpolation between two quaternions, random quaternion generator, etc)
conversion between different rotation representations (axis-angle pair, Rodrigues-Frank vector, quarterions, stereographic vector, homochoric vector, cubochoric vector, Euler angles, orientation matrix)
HDFsupport to export or import EMsoft specific HDF5 data sets (crystal.xtal, EBSDmaster.h5, EBSD_MonteCarloData.h5)
calculate allowed diffraction vectors
access to diffraction group, crystal point group, Laue group, projection diffraction group and many 2D symmetry point groups (for bright field, dark field, whole pattern diffraction) based on crystal structure data (.xtal), crystal point group number, zone axis ([uvw]) information.
Lambert square projection (and its inverse)
diffraction angle (2 theta) of a plane
electron's physical properties based on SEM's accelerating voltage
scattering factor sets, mean inner potential, interaction constant for a given crystal structure file (.xtal)
etc.

Contributors

EMsoft started as a source code base used for the creation of all figures in the Introduction to Conventional Transmission Electron Microscopy text book (Cambridge University Press, 2003, ISBN 0521629950) by M. De Graef. It has since grown into an open source project that has had many contributors and testers over the past 15 years (in no particular order):

Patrick Callahan
Saransh Singh
Stuart Wright
Elena Pascal
Will Lenthe
Chaoyi Zhu
Joseph Tessmer
Ke-Wei Jin
Michael Atkinson
Joao Fonseca
Michael Jackson
Joey Kleingers
Håkon Wiik Ånes
McLean Echlin
Zihao Ding
Marcus Ochsendorf
Christian Kurniawan

Financial Support

EBSD/ECP/EKP development of this package, including dictionary indexing for EBSD/ECP, was started with support from an AFOSR/MURI grant, FA9550-12-1-0458; the original EBSD code from CTEMsoft 2.0 was developed with support from an ONR grant, N00014-12-1-0075. All recent development of TKD and related modalities, including the creation of routines that can generate PoVRay visualization script files, was performed with support from an ONR Vannevar Bush Fellowship, N00014-16-1-2821.

License

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the names of Marc De Graef, Carnegie Mellon University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

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.