Supplementary Material: Use of fast realistic simulations on GPU to extract CAD models from microtomographic data in the presence of strong CT artefacts

Supporting material for our paper published by Elsevier in Precision Engineering, see https://doi.org/10.1016/j.precisioneng.2021.10.014 for the paper

To run our code, you must install:

1. Python
2. A C++ compiler with CMake
3. gVirtualXRay (code provided)

Python dependencies:
1. numpy
2. pandas
3. imageio
4. scikit-image
5. sklearn
6. scipy
7. SimpleITK
8. OpenCV
9. cma
10. tifffile import
11. tigre/tomopy (optional)

Contents

1. code:
- gVirtualXRay-1.1.5-Source.zip: Source code of gVirtualXRay
- tutorial.py: the Python code of the registration pipeline in 2D
- lsf.py: Detector response
- utils.py: needed by pseudo3d.py
- pseudo3d.py: Pseudo 3D registration
2. data: contains the input sinograms
- proj-33keV.tif: projections after flatfield correction. Projections are of 1024 pixels. Pixel spacing: 1.9um. 900 angles over 180 degrees. Primary energy : 33 keV. Source-object distance: 145m. Object-detector distance: 80mm.
- proj-0000-80keV.tif: projections of the first slice after flatfield correction. Projections are of 2702 pixels. Pixel spacing: 1.22um. 1750 angles over 360 degrees. Primary energy: 80 keV. Source-object distance: 92m. Object-detector distance: 270mm.
- proj-1023-80keV.tif: projections of the last slice after flatfield correction.
3. Jupyter_Notebooks: contains our tutorial and some videos
- From_CT_acquisition_to_CAD_models.ipynb: Jupyter Notebook in Python
- From_CT_acquisition_to_CAD_models.pdf: Jupyter Notebook as a PDF file
- cube_registration.mp4: successive best results during the optimisation of the matrix properties
- fibre1_registration.mp4: successive best results during the optimisation of the fibre and core radii (before recentring)
- fibre3_registration.mp4: successive best results during the optimisation of the fibre and core radii (after recentring)
- spectrum_registration.mp4: successive best results during the optimisation of the beam spectrum
- laplacian1_registration.mp4: successive best results during the optimisation of the phase contrast and of the fibre and core radii
- laplacian2_registration.mp4: successive best results during the optimisation of the phase contrast and the response of the detector
4. results: registered images
- output33keV: 2D registration
- output80keV: pseudo-3D registration
5. user_study:
- online-form.pdf: the online form
- responses.csv: answers from volunteers
6. visualisations: contains our interactive parallel coordinate plots and a video showing how to use them
- how_to_use_visualisations.mp4: video showing how we used it to analyse the data
- parallel_coordinates_all_data.html: interactive parallel coordinate plots of the fibre and core raii, and the linear attenuation coefficients of the cores, fibres and matrix
- parallel_coordinates-ZNCC.htmll: interactive parallel coordinate plots of the successive ZNCC values during a registration