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qim3d

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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 A: Running the tutorials with binder

    You can run the tutorials on Jupyter Notebook from Binder

    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: 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

    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_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 =)