esrf-um-2021

This repository contains the exercises and tutorials for the hands-on session by QIM at the European Synchrotron Radiation Facility the 8th February 2021.

Option A: Running the tutorials with binder

You can run the tutorials on Jupyter Notebook from

Option B: Configuring a Local Setup

If Binder doesn't work for you, follow the instructions below to configure a local setup.

1. Get Workshop Material

Clone or download this repository as a .zip.

2. Installation of Framework for Jupyter Notebooks

If you don't already have Anaconda to run Jupyter Notebooks, we suggest Miniconda for a faster installation.

1. Go to https://docs.conda.io/en/latest/miniconda.html and download the latest version
   • Mac: Choose the .pkg
2. Install Miniconda
   • Windows:
     • Execute the .exe
     • Use default installation location and options.
   • Mac:
     • Execute the .pkg
     • Select a location for the installation
     • If in MacOS Catalina or later, you have to do some extra steps:
       • Open a terminal window
       • Run source <location of installation>/opt/miniconda3/bin/activate
       • Run conda init zsh
   • Linux:
     • Navigate to the folder with the downloaded .sh file
     • Open the terminal in this folder (right click on the folder and select open terminal)
     • Change permissions to install by running chmod 700 <filename>.sh
     • To install, type <filename>.sh

3. Set up environment

Unless you are using Google Colab, you will need to run the file called environment.yml to install the required packages via the command line.

Mac/Linux:

1. Navigate to the esrf-um-2021-master folder.
2. To open the terminal, right click on the folder and navigate to
   • Mac: Services/New Terminal at Folder
   • Linux: Open in Terminal
3. Type conda env create -f environment.yml and press enter.
4. Type conda activate qim-esrf and press enter.

Windows

1. Open Anaconda Prompt.
2. cd <workshop_path>, where workshop_path is the absolute (full) path to the esrf-um-2021-master folder.
3. Type conda env create -f environment.yml and press enter.
4. Type conda activate qim-esrf and press enter.

4. Installation of Layered Surface Tool

Install package using pip install slgbuilder to get the implementation from this repository

5. Installation of Structure Tensor Tool

Option 1

The tutorial notebook for Structure Tensor will automatically clone the repository of the structure tensor tool. If that were to fail, use Option 2.

Option 2

1. Download the repository as a .zip file
2. Extract the .zip file
3. Rename the directory from structure-tensor-master to structure_tensor
4. Place the directory inside esrf-um-2021-master/Structure Tensor/

6. Open Jupyter Notebooks

In the same terminal window where you activated the environment, type jupyter notebook.

You are ready! You can now navigate to the tutorial of interest =)