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esrf-um-2021

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    Name Last commit Last update
    Layered Surface Detection
    Structure Tensor
    README.md
    environment.yml
    README.md

    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 1: Running the tutorials with binder

    You can run the tutorials on Jupyter Notebook from Binder

    Option 2: 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 two options:

    Miniconda

    1. Go to https://docs.conda.io/en/latest/miniconda.html and download the latest version

      • Mac: Choose the .pkg

    2. Install Miniconda

      • Windows: Billy?
      • Mac:
        • Execute the .pkg
        • Select a directory for installation
        • If in MacOS Catalina or later, you have to do some extra steps:
          • Open a terminal window
          • Run source <full path to installation directory>/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 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 Navigator.
    2. cd workshop_path, where path is the absolute (full) path of the 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

    1. Download the repository as a .zip file
    2. Extract the .zip file
    3. Rename the directory from structure-tensor-master to structure_tensor_master
    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 =)