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), named utilsST_2D.py- and utilsST_3D.py, to inspect the structure tensor output in various ways. The 2D and 3D example tutorials (ST2D_examples and ST3D_examples) come as python scripts (.py) and Jupyter Notebooks (.ipynb). While the 2D script covers many examples, the 3D script dives into one example and thus comes with more details. You can also find a set of guided exercises with solution, names ST2D_exercise_withSolutions.ipynb. 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 below to install the tool.

Option 1: pip install

If you have pip, you can install the tool with pip install structure-tensor.

Option 2: Set up environment

You can run the file called environment.yml to install the structure tensor tool and other required packages via the command line, as explained below. 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 <tutorials_path>, where tutorials_path is the absolute (full) path to the structure-tensor-master folder.
3. Type conda env create -f environment.yml and press enter.
4. Type conda activate qim-ST and press enter.

To learn more about the computation of structure tensor, the visualisation 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.

I Hofstätter, Baier, Trinderup, Gundlach, Pedersen, Tosello, Hanseen. Internal fiber structure of a high-performing, additively manufactured injection molding insert. International Conference of the Polymer Processing Society. 2018. I Saxena, Bissacco, Gundlach, Dahl, Trinderup, Dahl. Process characterization for molding of paper bottles using computed tomography and structure tensor analysis. Nondestructive Testing & Ultrasonics. 2019. I Jensen et al. Analysing stone wool. Consultancy. I Jeppesen, Dahl, Christensen, Dahl, Mikkelsen. Characterization of the fiber orientations in non-crimp glass fiber reinforced composites using structure tensor. Materials Science and Engineering. 2020. I Jeppesen, Mikkelsen, Dahl, Nymark, Dahl. Quantifying effects of manufacturing methods on fiber orientation in unidirectional composites using structure tensor analysis. Composites Part A: Applied Science and Manufacturing. I Kjer et al. Streamline tractography for 3D mapping of axon bundle organization in one MRI voxel using ultra-high resolution synchrotron radiation imaging. In preparation. I Jeppesen, Mikkelsen, Dahl, Christensen, Dahl. Quantifying effects of manufacturing methods on fiber orientation in unidirectional composites