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INSTALLATION.md

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Installation Guide

Dependencies

Hardware requirements:

  • FIB/SEM microscope (a commercial product by ThermoFisher FEI)

Software installed onto the MICROSCOPE PC:

  • Autoscript server software (a commercial product by ThermoFisher FEI)

Software installed onto the SUPPORT PC:

Python

Python 3.6 is required. The Anaconda distribution of python is recommended. This should be installed onto the SUPPORT PC.

Setting up your python virtual environment

It is also highly recommended to use virtual environments for development, see Managing Conda Environments for more information. (Optionally, you could use virtualenv if you prefer.)

Create a new virutal environment on the SUPPORT PC from the Anaconda Prompt terminal:

conda create -n autolamella python=3.6 pip
conda activate autolamella

Installing Autoscript

Autoscript provides an API (application programming interface) for scripting control of compatible FEI microscope systems. This is a commercial product by Thermo Fisher FEI, please visit their website at https://fei.com for information on pricing and installation.

The Autoscript server software is installed onto the MICROSCOPE PC, and the Autoscript client software is installed onto the SUPPORT PC.

We use Autoscript version 4.1.0

The version numbers of the python packages Autoscript installs were:

  • autoscript-core 5.1.0
  • autoscript-sdb-microscope-client 4.1.0
  • autoscript-sdb-microscope-client-tests 4.1.0
  • autoscript-toolkit 4.1.0
  • thermoscientific-logging 5.1.0

Add the autoscript python packages to your site-packages

To add the AutoScript python packages to your new conda environment on the SUPPORT PC, follow these three steps:

  1. Find the python environment that was created with your AutoScript installation. Typically, you can expect the environment is named 'Autoscript', and its installed packages should be found at: C:\Program Files\Python35\envs\AutoScript\Lib\site-packages\

Troubleshooting: If you're having trouble finding the location AutoScript chose to install its python packages into, you can open the default terminal on your machine (eg: cmd for Windows) and type where python (Windows) or which python (Unix). The result will be something like C:\Program Files\Python35\envs\AutoScript\python.exe. *Navigate to the environment location (in the example here, that's C:\Program Files\Python35\envs\AutoScript\ * then change directories into Lib, and then the site-packages directory. This is where the python packages live.

  1. Find the conda environment location you just made called autolamella. ...conda/envs/autolamella/Lib/site-packages/

Troubleshooting: If you're having trouble finding the conda environment location for autolamella-dev you can open the Anaconda terminal on your machine and type where python (Windows) or which python (Unix). The result will be something like C:\Users\yourusername\.conda\envs\autolamella\python.exe *Navigate to the environment location (in the example here, that's C:\Users\yourusername\.conda\envs\autolamella\ * then change directories into Lib, and then the site-packages directory. This is where you want to add copies of the AutoScript python packages.

  1. Make a copy of the relevant AutoScript python packages into the conda environment. You will need to copy:
  • autoscript_core
  • autoscript_core-5.4.1.dist-info
  • autoscript_sdb_microscope_client
  • autoscript_sdb_microscope_client_tests
  • autoscript_sdb_microscope_client_tests-4.2.2.dist-info
  • autoscript_sdb_microscope_client-4.2.2.dist-info
  • autoscript_toolkit
  • autoscript_toolkit-4.2.2.dist-info
  • thermoscientific_logging
  • thermoscientific_logging-5.4.1.dist-info

Install autolamella

Download the latest autolamella release wheel from https://github.com/DeMarcoLab/autolamella/releases

Pip install the wheel file (.whl) into your python virtual environment on the SUPPORT PC.

conda activate autolamella
pip install $AUTOLAMELLA_WHEEL_FILENAME.whl

Python package dependencies

All the python package dependencies you need should be installed automatically, with the exception of Autoscript which requires a special license key.

If you do encounter an issue with missing package dependencies, you can always try reinstalling them with:

conda activate autolamella
pip install -r requirements.txt

Having problems?

  • Check to see if Autoscript is correctly installed and configured.
  • Check to see if your python environment contains all packages listed in the requirements.txt
  • Check that when you call python from the terminal, you get the python environment containing the dependencies listed above (i.e. you are not using a different python environment)
  • Try cloning the repository and running the unit tests, you may want to try installing from the source code.