Nion Swift Installation

Nion Swift is written in the Python programming language. To use Nion Swift, you will need to install a Python environment.

As an open source project, there are many possible installation scenarios such as for offline use, for use on a Nion electron microscope, or for open source development. In addition, Python installation itself is highly flexible. Some Python installations will be used with other software, and others specifically with Nion Swift.

This guide mainly covers the offline use case with a Python environment dedicated to Nion Swift usage.

Requirements

Nion Swift for Windows requires Windows 10 or later.

Nion Swift for macOS requires macOS 10.11 or later. We recommend using the latest version of macOS.

Nion Swift for Linux requires a distribution with Qt 5.5 or later (qt5-default) and Python 3.7 or later.

Nion Swift has been tested with Ubuntu 16.04, 18.04, 20.04, Debian 9, Fedora 26. It is expected to work with newer distributions of Linux.

Python Environment

There are several Python environments that are capable of running Nion Swift.

Anaconda and Miniconda are Python distributions by Continuum Analytics and both allow easy installation of 3rd party libraries that are optimized for your computer. Nion Swift has been tested extensively with both Anaconda and Miniconda distributions.

Anaconda is a full featured environment which distributes a large number of useful libraries, but it is a large download. The Miniconda environment is a minimal environment which can be downloaded more quickly and can later be updated to include any desired libraries that would otherwise be contained in the larger Anaconda distribution.

You have two options:

  • Install Anaconda (more disk space, slower download, but easier to install)

  • Install Miniconda (less disk space, faster download, but requires more technical knowledge)

While it is possible to share a Python environment with other applications, or to use the built-in Python on your machine, we recommend against this. We recommend having a dedicated Python installation that is only used for Nion Swift.

Installing Python

You will first need to install Python for your specific platform. Visit one of the websites below, download the 64-bit installer, and follow the ‘Instructions’ link.

The installer may give you an option to add Python to your command line PATH. We recommend against this since it may interfere with other Python installations.

The installer may also give you an option to make this the default Python for your system. Again, we recommend against this since it may interfere with other Python installations.

You can usually use the default location for the installation; however, make a note of wherever you choose to install it so that that location can be used in the steps below.

Nion Swift can also be installed from the command line using PyPI and standard Python or from the conda-forge channel of either Anaconda or Miniconda. See the Installing Nion Swift from PyPI or Conda Forge section below.

Windows

Activating Python

If you have installed Anaconda, you will find an Anaconda Prompt in your Start menu. Launch the Anaconda Prompt.

If you have installed Miniconda, you will use the Command Prompt to finish the installation. Launch a Command Prompt by clicking in the Start menu and looking in the Windows System folder for Command Prompt. You can also just click in the Start menu and type “command” and it will usually find the Command Prompt application.

For an Anaconda installation, launching the Anaconda Prompt will activate Anaconda Python automatically.

For a Miniconda installation you will need to explicitly activate Miniconda Python from the Command Prompt.

$ C:\PATH_TO_MINCONDA\Scripts\Activate.bat

Installing Nion Swift

Once you have activated Python, you can install Nion Swift within the Anaconda or Miniconda environment.

$ conda create -n nionswift -c nion nionswift nionswift-tool
$ conda activate nionswift

Running Nion Swift

Once you have activated Python and installed Nion Swift, you can run Nion Swift from the command line.

$ conda activate nionswift
$ nionswift

For easier launching, you can create a Shortcut to Nion Swift on your Desktop using the command:

$ conda activate nionswift
$ nionswift --alias

Double clicking this Shortcut will launch Nion Swift in the Python environment from which the command above was run.

Updating Nion Swift

Periodically you may want to update Nion Swift to get the latest features and bug fixes. First activate Python (see above), then run the following command.

$ conda activate nionswift
$ conda update -c nion --all

Troubleshooting Windows Installation

Nion Swift running with nionswift-tool requires a PATH environment variable that does not include directories containing Qt libraries. As a workaround or if you cannot remove the other Qt installation from your PATH environment variable, you can uninstall nionswift-tool and install PyQt5 using conda install pyqt5 and try running Nion Swift again.

MacOS

Nion Swift for macOS requires macOS 10.11 or later. We recommend using the latest version of macOS.

If you have just installed conda or wish to create a new Nion Swift specific environment:

$ source /path/to/python/bin/activate root
$ conda create -n nionswift -c nion nionswift nionswift-tool
$ conda activate nionswift

If you already have a conda environment, install Nion Swift using the command:

$ conda install -c nion nionswift nionswift-tool

Launch Nion Swift from your conda command line environment using:

$ nionswift

Linux

Nion Swift for Linux requires Qt 5.5 or later (qt5-default), Python 3.7 or later.

Swift has been tested with Ubuntu 16.04, 18.04, 20.04, Debian 9, Fedora 26.

If you have just installed conda or wish to create a new Nion Swift specific environment:

$ source /path/to/python/Scripts/activate root
$ conda create -n nionswift -c nion nionswift nionswift-tool
$ conda activate nionswift

If you already have a conda environment, install Nion Swift using the command:

$ conda install -c nion nionswift

Launch Nion Swift from your Terminal conda environment using:

$ nionswift

Troubleshooting Linux Installation

Nion Swift running with nionswift-tool requires a PATH environment variable that does not include directories containing Qt libraries. As a workaround or if you cannot remove the other Qt installation from your PATH environment variable, you can uninstall nionswift-tool and install PyQt5 using conda install pyqt5 and try running Nion Swift again.

Installing Nion Swift from PyPI or Conda Forge

If you have an active Python environment that is not based on the Conda distribution, you can install Nion Swift from PyPI using these commands.:

$ python -m pip install nionswift nionswift-tool

You can also install Python using the conda-forge channel in the Conda distribution using these commands.:

$ source /path/to/python/Scripts/activate root
$ conda create -n nionswift-conda-forge -c conda-forge nionswift nionswift-tool
$ conda activate nionswift-conda-forge

Installing Nion Swift Extensions

Extensions for Nion Swift can be installed in your Python environment using the conda (preferred) or pip installation tools.

For example, you can install the Nion STEM microscope simulator using the either of the following commands:

$ conda install -c nion nionswift-usim

or

$ pip install nionswift-usim

After restarting Nion Swift, the microscope simulator would be available within Nion Swift.

You can search for additional Nion Swift extensions using the command:

$ pip search nionswift

Here are several extensions that may prove useful:

Project Name

Conda

Pip

Description

nionswift-usim

Yes

Yes

A STEM microscope simulator for development

nionswift-eels-analysis

Yes

Yes

Tools for EELS analysis

nionswift-video-capture

Yes

No

Capture video from your computer’s camera or a web stream. Requires conda opencv.

nionswift-experimental

Yes

Yes

Experimental tools (see project home page for details).