Abstract

Notebook/UI to perform circular profile in the shape of a ring over a stack of images

This notebook will allows you to load a set of files (all tiff or fits images from a given folder) and will bring a user interface to allow you to define a ring. The circular profile will then be calculated along the ring and integrated over the thickness of the ring, on all the images loaded.

The output will be an ASCII file with the average counts over the thickness of the ring versus the angle position, for each of the images loaded.

Full documentation and step by step tutorial can be found here.

Installation Instructions

We strongly recommend to use conda and create a local environment. To do so, here are the steps

• Install Anaconda3 or miniconda3.

  If one of the two is already installed, skip this step.

• open a terminal window

• Create a virtual environment for this repo, e.g.

  conda create -n circular_profiler python=3.7

• Activate the virtual environment with

  conda activate circular_profiler

• Clone this repository to your local computer with

  git clone https://github.com/neutronimaging/circular_profiler.git

• Inside the repository, you should be able to find a bash script, config_conda_env.sh. Use it to install required packages with

  ./config_conda_env.sh

  NOTE: technically you can run this script in any environment, but it is highly recommended to run it in a virual environment.

• Fire up your terminal, go to the root of this repo, and start the Jupyter notebook server with

  ./launch_notebook.sh

  You will see something similar to the following

    [I 14:00:13.183 NotebookApp] The port 8888 is already in use, trying another port.
    [I 14:00:14.061 NotebookApp] JupyterLab extension loaded from A_REALL_LONG_PATH
    [I 14:00:14.061 NotebookApp] JupyterLab application directory is ANOTHER_LONG_PATH
    [I 14:00:14.063 NotebookApp] Serving notebooks from local directory: CURRNT_DIR
    [I 14:00:14.063 NotebookApp] Jupyter Notebook 6.1.1 is running at:
    [I 14:00:14.063 NotebookApp] http://localhost:8889/?token=1e612467cf5e1e4f91cf074f483010ea7c8de989745eba96
    [I 14:00:14.063 NotebookApp]  or http://127.0.0.1:8889/?token=1e612467cf5e1e4f91cf074f483010ea7c8de989745eba96
    [I 14:00:14.063 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
    [C 14:00:14.068 NotebookApp] 
  
    To access the notebook, open this file in a browser:
        file:///home/user/.local/share/jupyter/runtime/nbserver-2560206-open.html
    Or copy and paste one of these URLs:
        http://localhost:8889/?token=1e612467cf5e1e4f91cf074f483010ea7c8de989745eba96
        or http://127.0.0.1:8889/?token=1e612467cf5e1e4f91cf074f483010ea7c8de989745eba96
  

  At that point, your favorite browser should show up with the jupyter environment ready to go. If it does not, copy and paste the 6th line of the output to your browser

  http://localhost:8889/?token=1e612467cf5e1e4f91cf074f483010ea7c8de989745eba96

  and you are ready to use the notebooks.

  NOTE: For most terminals, you can also Ctrl+click or CMD+click on the link to open it in your default browser.

Unit Tests

To run the unit tests, first install the library

cd ~/git/circular_profile     # replace by your path to the installation folder
pip install .

and then run the tests using pytest

pytest

Demonstration

Demo data used

To illustrate how to use this notebook, we are going to load some fake data from the test/data/demo folder. The fake data are reconstructed, horizontal slices, images of a commercial airplane engine showing the front part of the engine where the blades can be found. The red arrow shows the location of the 4 slices used here.

First step into the notebook

After starting the notebook, you see a first widget Do not know how to run this notebook? Click Me! that will take you to another web page with a detail step by step instruction on how to use this notebook. This web page will also detail the math behind the various calculations used.

The second widget list the Notebook rules in case you are not familiar with the Jupyter notebooks. Those are self-explanatory.

Setup notebook

Run, (SHIFT + ENTER or click the Run button at the top of the notebook), the cell below Setup notebook to import the necesary librairies. The next cell is necessary to be able to bring the user interface to life later on.

Select folder containing data

Run this cell to select the folder containing the data to use. Detail tutorial of how to use the file dialog can be found here. By default the file selector takes you from the tests/demo folder. Simply click Select to load the folder.

Launch User Interface

A user interface (UI) will show up, check behind the browser as sometimes the UI stays behind the current active window.

Selection of rings

A detail tutorial of the UI can be found here, but for the sake of this demo, define a ring center with the cells and having a thickness roughly below the lenght of the cells (see next animation).

Calculation of rings profiles

Click the Calculate Profiles button to calculate the circular profile of the ring you just defined. The right part of the UI will expand and will allow you to select the profile of any of the images loaded. One can then quickly find out that one of the blade on image 3 is out of position. Of course this was obvious by just visualizing the images loaded, but for some cases such as reactor blades, thousands of slices are acquired when each slice contains hundreds of blades. Manual visualization of such a stack of images can take hours or days.

Community guidelines

• Contribute to the software: Do not hesitate to contribute to the project by creating a fork of the project and then a Pull Request.
• Report issues or problems with the software: Please create an issue for any bug found or feature requested
• Seek support: None right now

Meta

Jean Bilheux - [email protected]

Distributed under the BSD license. See LICENSE.txt for more information

Acknowledgements

This work is sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle LLC, under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan(http://energy.gov/downloads/doe-public-access-plan).