First draft of the README.md
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# Nano Active Stabilization of samples for tomography experiments: A mechatronic design approach
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**Author:** Thomas Dehaeze
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**University:** Liège Université
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**Date:** April 2025
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<!-- [](https://doi.org/10.5281/zenodo.XXXXXXX) -->
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## Abstract
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The fourth generation synchrotron light sources has yielded X-ray beams with a 100-fold increase in brightness and sub-micron focusing capabilities, offering unprecedented scientific opportunities while requiring end-stations with enhanced sample positioning accuracy.
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At the European Synchrotron (ESRF), the ID31 beamline features an end-station for positioning samples along complex trajectories.
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However, its micrometer-range accuracy, limited by thermal drifts and mechanical vibrations, prevents maintaining the point of interest on the focused beam during experiments.
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To address this limitation, this thesis aims to develop a system for actively stabilizing the sample's position down to the nanometer range while the end-station moves the sample through the beam.
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The developed system integrates an external metrology for sample position measurement, an active stabilization stage mounted between the end-station and the sample, and a dedicated control architecture.
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The design of this system presented key challenges, first of which involved the design process.
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To effectively predict how this complex mechatronic system would perform, a series of dynamical models with increasing accuracy were employed.
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These models allowed simulation of the system's behavior at different design stages, identifying potential weaknesses early on before physical construction, ultimately leading to a design that fully satisfies the requirements.
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The second challenge stems from control requirements, specifically the need to stabilize samples with masses from 1 to 50 kg, which required the development of specialized robust control architectures.
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Finally, the developed Nano Active Stabilization System underwent thorough experimental validation on the ID31 beamline, validating both its performance and the underlying concept.
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## About This Repository & Reproducible Research
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The foundation of this PhD thesis is built upon the principles of **reproducible research**.
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Reproducible research is the practice of ensuring that the results of a study can be independently verified by others using the original data, code, and documentation.
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This approach was adopted to increase transparency and trust in the presented research findings.
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Furthermore, it is anticipated that the methods and data shared will facilitate knowledge transfer and reuse within the scientific community, thereby reducing research redundancy and increasing overall efficiency.
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It is hoped that some aspects of this work may be reused by the synchrotron community.
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The fundamental objective has been to ensure that anyone should be capable of reproducing precisely the same results and figures as presented in this manuscript.
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To achieve this goal of reproducibility, comprehensive sharing of all elements has been implemented.
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This includes the mathematical models developed, raw experimental data collected, and scripts used to generate the figures.
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For those wishing to engage with the reproducible aspects of this work, all data and code are freely accessible in this Git repository.
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The organization of the code mirrors that of the manuscript, with corresponding chapters and sections.
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All materials have been made available under the MIT License, permitting free reuse.
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This repository includes:
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* Raw and/or processed data used in the analyses.
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* MATLAB scripts and functions for data processing, simulations, and figure generation.
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* Simulink/Simscape models developed or used during the research.
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* A digital copy of the final PhD thesis document.
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## Repository Structure
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The repository is organized as follows:
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```
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.
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├── A1-nass-uniaxial-model \# Every Section in the PhD thesis has its own direction
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├── A2-nass-rotating-3dof-model
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├── A3-micro-station-modal-analysis
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├── A4-simscape-micro-station \# The directory for each section is structure as follows:
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│ ├── mat \# - All raw data
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│ ├── src \# - All Matlab functions, automatically added to the path
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│ ├── STEPS \# - .step files used for the multi-body (Simscape) model
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│ ├── subsystems \# - subsystems used in the multi-body (Simscape) model
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│ ├── ustation_1_kinematics.m \# - The Matlab scripts corresponding to the different sections
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│ ├── ustation_2_modeling.m
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│ ├── ustation_3_disturbances.m
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│ ├── ustation_4_experiments.m
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│ └── ustation_simscape.slx \# - The Simscape model used in this particular section
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├── A5-simscape-nano-hexapod
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├── A6-simscape-nass
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├── B1-nass-geometry
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├── B2-nass-fem
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├── B3-control
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├── B4-nass-instrumentation
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├── C1-test-bench-apa
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├── C2-test-bench-flexible-joints
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├── C3-test-bench-struts
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├── C4-test-bench-nano-hexapod
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├── C5-test-bench-id31
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├── init.m \# Optional: Some Matlab configuration to have same figure display
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├── LICENSE \# MIT License is used for all the code in this repository
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└── README.md \# The present file
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````
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## Requirements
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To run the code and reproduce the results in this repository, you will need the following software environment:
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**Operating System:**
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* Tested on:
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* Microsoft Windows
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* Linux
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* Should be compatible with other versions of Windows, macOS, and Linux supporting MATLAB R2022a.
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**Software:**
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* **MATLAB Version:** 9.12 (R2022a) Update 8 or later compatible version.
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* **Required MATLAB Toolboxes:**
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* Simulink: Version 10.5 (R2022a)
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* Control System Toolbox: Version 10.11.1 (R2022a)
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* Curve Fitting Toolbox: Version 3.7 (R2022a)
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* Optimization Toolbox: Version 9.3 (R2022a)
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* Robust Control Toolbox: Version 6.11.1 (R2022a)
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* Signal Processing Toolbox: Version 9.0 (R2022a)
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* Simscape: Version 5.3 (R2022a)
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* Simscape Multibody: Version 7.5 (R2022a)
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* Simulink Control Design: Version 6.1 (R2022a)
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* Symbolic Math Toolbox: Version 9.1 (R2022a)
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* System Identification Toolbox: Version 9.16 (R2022a)
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## Instructions for Reproduction
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1. **Clone the repository:**
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```bash
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git clone [https://docs.github.com/en/repositories/creating-and-managing-repositories/about-repositories](https://docs.github.com/en/repositories/creating-and-managing-repositories/about-repositories)
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cd [repository folder name]
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```
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2. **Set up MATLAB Environment:**
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* Ensure MATLAB R2022a and all required toolboxes listed above are installed.
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* Open MATLAB.
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* Navigate to the root directory of the cloned repository within MATLAB.
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* Add the repository's folders to the MATLAB path. You can often do this by running the following command in the MATLAB console:
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```matlab
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addpath(genpath(pwd));
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```
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*(Note: Check if you need a more specific path setup script)*
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3. **Run the Code:**
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* [Provide specific instructions here. For example:]
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* "To reproduce all figures and results, run the main script: `main_script.m`"
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* "Alternatively, run scripts in the following order:"
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* `scripts/processing/preprocess_data.m`
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* `scripts/simulations/run_model_simulation.m`
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* `scripts/analysis/analyze_results.m`
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* `scripts/plotting/generate_all_figures.m`
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* Specify where the outputs (figures, tables, data files) will be saved (e.g., in the `results/` directory).
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* Mention expected run times if some scripts are computationally intensive.
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## Citation
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If you use the code, data, or findings from this repository or the associated thesis, please cite:
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**Thesis:**
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* [Your Name] ([Year]). *[Your Thesis Title Here]*. PhD Thesis, [Your University Name]. [Link to university library record or official source if available]
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**Software/Data Repository (Zenodo):**
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* [Your Name] ([Year]). *[Repository Title, e.g., Code and Data for PhD Thesis: Your Thesis Title Here]*. Zenodo. [https://doi.org/10.5281/zenodo.XXXXXXX](https://doi.org/10.5281/zenodo.XXXXXXX) *(<- Replace with your DOI)*
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```bibtex
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@phdthesis{YourLastNameYEARphd,
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author = {[Your Name]},
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title = {[Your Thesis Title Here]},
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school = {[Your University Name]},
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year = {[Year]},
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address = {[City, Country]},
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url = {[Link to thesis, optional]}
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}
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@software{[YourLastNameYEARzenodo],
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author = {[Your Name]},
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title = {[Repository Title, e.g., Code and Data for PhD Thesis: Your Thesis Title Here]},
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month = {[Month of Zenodo publication]},
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year = {[Year of Zenodo publication]},
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publisher = {Zenodo},
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version = {[Version/tag used for Zenodo archive, e.g., v1.0.0]},
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doi = {10.5281/zenodo.XXXXXXX},
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url = {[https://doi.org/10.5281/zenodo.XXXXXXX](https://doi.org/10.5281/zenodo.XXXXXXX)}
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}
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````
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*(Note: Fill in the BibTeX details and update the DOI)*
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## License
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The code and associated files in this repository are licensed under the MIT License. See the [LICENSE](LICENSE) file for details.
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Copyright (c) 2025 Thomas Dehaeze
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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## Contact
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For questions about the code, data, or thesis, please contact [Your Name] at [Your Email Address].
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