prismatique 0.0.3

A wrapper to the Python library `pyprismatic`, which is a library for simulating CBED, STEM, and HRTEM experiments using Multislice algorithms.

Prismatique

prismatique is a Python library that functions essentially as a wrapper to the Python library pyprismatic, which itself is a thin wrapper to prismatic, a CUDA/C++ package for fast image simulations in scanning transmission electron microscopy and high-resolution transmission electron microscopy. You can find more information about pyprismatic and prismatic here.

Visit the prismatique website for a web version of the installation instructions, the reference guide, and the examples archive.

The source code can be found in the prismatique GitHub repository.

Table of contents

• Instructions for installing and uninstalling prismatique
  • Installing prismatique
    • Installing prismatique using pip
    • Installing prismatique using conda
  • Uninstalling prismatique
• Learning how to use prismatique

Instructions for installing and uninstalling prismatique

Installing prismatique

For all installation scenarios, first open up the appropriate command line interface. On Unix-based systems, you could open e.g. a terminal. On Windows systems you could open e.g. an Anaconda Prompt as an administrator.

GPU acceleration is available for prismatique installed on Linux and Windows machines that have NVIDIA GPUs. You will need to make sure that you have a NVIDIA driver installed with CUDA version 10.2.89 or greater.

Installing prismatique using pip and conda together

The easiest way to install prismatique involves using both the conda package manager and pip. While it is possible to install prismatique without the use of the conda package manager, it is more difficult. Because of this, we discuss only the simplest installation procedure below.

Of course, to use the conda package manager, one must install either anaconda3 or miniconda3. For installation instructions for anaconda3 click here; for installation instructions for miniconda3 click here.

First, open up the appropriate command line interface. On Unix-based systems, you would open a terminal. On Windows systems you would open an Anaconda Prompt as an administrator.

Next, you can optionally update your conda package manager by issuing the following command:

conda update conda

It is recommended that you install prismatique and its dependencies in a virtual environment: click here for a discussion on the creation and management of conda virtual environments. The remaining instructions assumes that you activate the conda (virtual) environment in which you intend to install prismatique and its dependencies.

The first dependency that we need to install is pyprismatic. GPU acceleration is available for pyprismatic (and thus prismatique) if the following conditions are met:

1. You are using a Linux or Windows machine that has NVIDIA GPUs.
2. A NVIDIA driver is installed with CUDA version 10.2.89 or greater.

If the above conditions have been met, and you would like to be able to use GPUs with prismatique, run the following command:

conda install -c conda-forge pyprismatic=2.\*=gpu\* cudatoolkit==<X>.<Y>.\*

where <X> and <Y> are the major and minor versions of CUDA installed on your machine, e.g. CUDA version 10.2.89 has a major version of 10, and a minor version of 2. Users can omit cudatoolkit==<X>.<Y>.\* if they do not require a specific version of cudatoolkit, which should apply to most scenarios. For CPU support only, run the following command instead:

conda install -c conda-forge pyprismatic=2.\*=cpu\*

The easiest way to install the remaining dependencies, along with prismatique is to use pip by running the following command:

pip install prismatique

The above command will install the latest stable version of prismatique. Another option is to use conda:

conda install -c conda-forge prismatique

As yet another option, you can install the latest development version of prismatique from the main branch of the prismatique GitHub repository. To do so, one must first clone the repository by running the following command:

git clone https://github.com/mrfitzpa/prismatique.git

then subsequently change into the root of the cloned repository, and then run the following command:

pip install .

Note that you must include the period as well.

Optionally, for additional features in prismatique, one can install additional dependencies upon installing prismatique via pip. To install a subset of additional dependencies (along with the standard installation), run the following command from the root of the repository:

pip install .[<selector>]

where <selector> can be one of the following:

• tests: to install the dependencies necessary for running unit tests;
• examples: to install the dependencies necessary for executing files stored in <root>/examples, where <root> is the root of the repository;
• docs: to install the dependencies necessary for documentation generation;
• all: to install all of the above optional dependencies.

Alternatively, one can run:

pip install prismatique[<selector>]

elsewhere in order to install the latest stable version of prismatique, along with the subset of additional dependencies specified by <selector>.

Uninstalling prismatique

If prismatique was installed using pip, then to uninstall, run the following command:

pip uninstall prismatique

If prismatique was installed using conda, then to uninstall, run the following command:

conda remove prismatique

Learning how to use prismatique

For those new to the prismatique library, it is recommended that they take a look at the Examples page, which contain code examples that show how one can use the prismatique library. While going through the examples, readers can consult the prismatique reference guide to understand what each line of code is doing.