pyccapt 0.0.35

A package for controlling APT experiment and calibrating the APT data

PyCCAPT (APT_PyControl)

A modular, FAIR open-source python atom probe tomography software package for experiment control and data calibration

This package aims to provide open-source software for controlling atom probe systems and calibrating data. The package is modular and adaptable for a wide range of devices in atom probe instrument. So far it is capable of collecting data from Surface consept and ReoenDek TDC systems. The package is developed in Python 3.9. Additionally, the package encompasses a comprehensive calibration module that provides various functionalities, including t₀ and flight path calculation, region of interest (ROI) selection, voltage and bowl calibration, as well as 3D reconstruction techniques. This module enhances the capabilities of PyCCAPT by providing essential tools for accurate data interpretation and analysis.

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Presentation

PyCCAPT was initially developed and rigorously tested on the OXCART atom probe, an in-house atom probe system situated within the Department of Materials Science & Engineering at the University of Erlangen-Nürnberg. Distinguished by its unique attribute, the OXCART atom probe boasts a titanium-based measuring chamber that facilitates an ultra-low hydrogen vacuum environment. This system also features a state-of-the-art detector with a high detection efficiency of approximately 80%. While tailor-made for the OXCART, the PyCCAPT package offers versatility, extending its capabilities to effectively manage diverse atom probe systems.

The package is designed with modularity in mind, making it highly adaptable to a diverse array of instruments. This adaptability extends to instruments like Pfeifer gauges, Fug power supplies, and Siglent signal generators. Notably, the PyCCAPT package has already demonstrated its proficiency in collecting data from Surface Concept and ReoenDek TDC systems, showcasing its versatility across various setups and applications.

The PyCCAPT package forms the foundation of a fully FAIR atom probe data collection and processing chain. This repository includes the graphical user interface (GUI) and control program, which enable experiment control, visualization, and data acquisition. The following images provide an overview of the user interface:

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Directory structure

pyccapt/
├── pyccapt/
│   ├── __init__.py
│   ├── config.json   
│   ├── calibration/
│   │   ├── __init__.py
│   │   └── module_folders   
│   ├── control/
│   │   ├── __init__.py
│   │   └── module_folders
│   └── files/
├── docs/
├── setup.py
├── README.md
├── CONTRIBUTION.md
├── MANIFEST.in
├── Licence
└── tox.ini
└── tests/
    ├── __init__.py
    ├── data/
    └── tests

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Installation

1. Create a virtual environment using Anaconda:

   conda create -n apt_env python=3.9
   

2. Activate the virtual environment:

   conda activate apt_env
   

3. Clone or download this repository, unzip it, and in the project directory run:

   pip install -e .
   

After installation, you can run the control GUI by entering the following command in the console:

pyccapt

or if the above command does not work, you can run the following command:

python -m pyccapt.control

To start the tutorial, please follow these steps:

1- Open your terminal.

2- Navigate to the project folder using the cd command.

3- Once you're inside the project folder, go to the tutorial folder by running the following command:

Jupyter lab

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Documentation

The latest documentation is available on ReadTheDocs page. It provides feature descriptions, tutorials, and valuable information.

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Using PyCCAPT

For control part of the package you can follow the steps on documentation.

For calibration, review the tutorial to understand package features.

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Data structure

For checking the data structure of the control module you can check here. For the calibration module, you can check here.

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Test data

For start using the calibration package, you can use the test data (pure Aluminium) provided in the following link. The link contains the raw dataset that is collected from the OXCART atom probe from a pure Aluminium sample. It also contains the output file from the calibration module, which contains the calibrated data as well as the reconstructed data. The link also contain the range file (HDF5) that is calculated by the calibration module.

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Bug reports

Report bugs, issues, ask for help, or provide feedback on the github section.

Qestions/comments:

• Mehrpad Monajem, [e-mail]

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Citing

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Contributing

Contributions to PyCCAPT are always welcome, and they are greatly appreciated! Our contribution policy can be found here.

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License

This project is licensed under the GNU General Public License v3.0. See the LICENSE file for details.