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Installation

Preparing for pyTEMlib

pyTEMlib requires many commonly used scientific and numeric python packages such as numpy, h5py etc. To simplify the installation process, we recommend the installation of anaconda which contains most of the prerequisite packages, conda - a package / environment manager, as well as an interactive development environment - Spyder

Please note that any other python installation will work too and that pypi will install all missing packages.

Compatibility

  • pyTEMlib is compatible with python 3.8 onwards. Please raise an issue if you find a bug.
  • We do not support 32 bit architectures
  • We only support text that is UTF-8 compliant due to restrictions posed by HDF5

Terminal

Installing, uninstalling, or updating pyTEMlib (or any other python package for that matter) can be performed using the Terminal application. You will need to open the Terminal to type any command shown on this page. Here is how you can access the Terminal on your computer:

  • Windows - Open Command Prompt by clicking on the Start button on the bottom left and typing cmd in the search box. You can either click on the Command Prompt that appears in the search result or just hit the Enter button on your keyboard.

    • Note - be sure to install in a location where you have write access. Do not install as administrator unless you are required to do so.

  • MacOS - Click on the Launchpad. You will be presented a screen with a list of all your applications with a search box at the top. Alternatively, simultaneously hold down the Command and Space keys on the keyboard to launch the Spotlight search. Type terminal in the search box and click on the Terminal application.

  • Linux (e.g - Ubuntu) - Open the Dash by clicking the Ubuntu (or equivalent) icon in the upper-left, type "terminal". Select the Terminal application from the results that appear.

Installing pyTEMlib

  1. Ensure that a compatible python distribution has been successfully installed

  2. Open a terminal <#terminal>_ window.

  3. You can now install pyTEMlib via pip as shown below. Type the following command into the terminal / command prompt and hit the Return / Enter key:

    • pip:

      .. code:: bash

      pip install pyTEMlib

Installing from a specific branch (advanced users ONLY)

Note that we do not recommend installing pyTEMlib this way since branches other than the master branch may contain bugs.

.. note:: Windows users will need to install git before proceeding. Please type the following command in the Command Prompt:

.. code:: bash

 conda install git

Install a specific branch of pyTEMlib (dev in this case):

.. code:: bash

pip install -U git+https://github.com/pycroscopy/pyTEMlib@main

Updating pyTEMlib

We recommend periodically updating your conda / anaconda distribution. Please see these instructions to update anaconda <./external_guides.html#Updating-packages>_.

If you already have pyTEMlib installed and want to update to the latest version, use the following command in a terminal window:

.. code:: bash

pip install -U --no-deps pyTEMlib

If it does not work try reinstalling the package:

.. code:: bash

pip uninstall pyTEMlib pip install pyTEMlib

Other software

We recommend HDF View for exploring HDF5 files generated by and used in pyTEMlib.