Installing

Installing in Windows

Anaconda Python environment

Currently, the easiest way to install pixStem is using the Anaconda python environment Anaconda environment, Install HyperSpy, then pixStem via the Anaconda prompt (Start menu - Anaconda3), this will open a command line prompt. In this prompt run:

$ conda install pixstem hyperspy-gui-traitsui hyperspy-gui-ipywidgets -c conda-forge

If everything installed, continue to starting pixStem in Windows. If you got some kind of error, please report it as a New issue on the pixStem GitLab.

WinPython HyperSpy installer

Alternatively, the WinPython HyperSpy bundle can be used. Firstly download and install the WinPython HyperSpy bundle:

After installing the bundle, there should be a folder in the start menu called “HyperSpy Bundle”, and this folder should contain the “WinPython prompt”. Start the “WinPython prompt”. This will open a terminal window called “WinPython prompt”, in this window type and run:

pip install pixstem

If everything installed, continue to starting pixStem in Windows. If you got some kind of error, please report it as a New issue on the pixStem GitLab.

Installing in MacOS

Install the Anaconda python environment: Anaconda environment, and through the Anaconda prompt install HyperSpy and pixStem:

$ conda install pixstem hyperspy-gui-traitsui hyperspy-gui-ipywidgets -c conda-forge

If everything installed, continue to starting pixStem in MacOS. If you got some kind of error, please report it as a New issue on the pixStem GitLab.

Installing in Linux

The recommended way to install pixStem is using PIP, which is a package manager for python. It is recommended to first install the precompiled dependencies using the system package manager.

HyperSpy is also included as pixStem relies heavily on the modelling and visualization functionality in HyperSpy.

Ubuntu 18.04

$ sudo apt-get install ipython3 python3-pip python3-numpy python3-scipy python3-matplotlib python3-sklearn python3-skimage python3-h5py python3-dask python3-traits python3-tqdm python3-pint python3-dask python3-pyqt5 python3-lxml python3-sympy python3-sparse python3-statsmodels python3-numexpr python3-ipykernel python3-jupyter-client python3-requests python3-dill python3-natsort
$ pip3 install --user pixstem

If everything installed, continue to starting pixStem in Linux. If you got some kind of error, please report it as a New issue on the pixStem GitLab.

Development version

Grab the development version using the version control system git:

$ git clone https://gitlab.com/pixstem/pixstem.git

Then install it using pip:

$ cd pixstem
$ pip3 install -e .