Structure tensor tutorials for the implementation in https://github.com/Skielex/structure-tensor. This implementation is compatible with the python package cupy. Therefore, if you have large volumes to process and a graphical processing unit (GPU), you can speed up your computations simply by having a working installation of cupy.

The tutorials demonstrate the use of the structure tensor tool for the analysis of 2D and 3D data. The tutorials come with a set of utils (helper functions) to inspect 2D and 3D data, and analyse the structure tensor output. The 2D and 3D examples come as python scripts (.py) and Jupyter Notebooks (.ipynb), the latter is more complete and pedagogical, as it comes with explanations. With these tutorials we would like you to 1) learn how to choose the parameters to obtain desirable results, 2) see different options for visualising the output of the structure tensor, and 3) get inspiration for scientific questions that you could answer with the structure tensor tool.

Run the tutorials online on by pressing on the binder icon. If you want to run the tutorials locally, check our instructions for installing Jupyter Notebooks and then follow the instructions to install the tool.

Instructions for tool installation

1. Set up environment

You can run the file called environment.yml to install the required packages via the command line. If using Anaconda, you can also install the packages using its graphical user interface, just check the packages that are required by opening the environment file with a text reader.

Mac/Linux:

1. Navigate to the tutorial extracted 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-ST 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-ST and press enter.

2. Install the tool demonstrated in the tutorial

Find the instructions for installing the tool you are interested in written in the README of the tool's repository.

In the case of the layered surfaces tutorials, install package using pip install slgbuilder to get the implementation from this repository.

In the case of the structure tensor, the tutorial notebook for structure tensor will automatically clone the repository of the structure tensor tool. If that were to fail, follow the steps below:

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/

To learn more about the computation of structure tensor, the visualization of orientation analysis and other examples of using orientation analysis in volumetric data analysis, we recommend you take a look at the notes by Vedrana A. Dahl vand@dtu.dk

The development of the tutorials is a combined effort from several researchers in the QIM team. The collection of scripts and exercises is in constant development, and actively used to demonstrate the tool and teach at workshops. We would therefore very much appreciate to hear about your experience.

Please contact Monica J. Emerson monj@dtu.dk with issues and feedback.