# <p align="center">TopasGraphSim</p>
## <p align="center">A GUI to simplify and streamline the plotting and analysis of medical physics simulations</p>
<p align="center">
<img src="https://user-images.githubusercontent.com/87897942/152699152-d4d39654-4449-4354-b899-4adc81eb25a7.png" width="320" height="160" />
</p>
This GUI can visualize and analyze percentage depth dose (pdd) and dose profiles (dp) simulations from [TOPAS](http://www.topasmc.org/). Depth dose measurements are assumed to be in the z-direction, dose profiles in the x- or y-directions. Data read-in is handled by [topas2numpy](https://github.com/davidchall/topas2numpy).
## Installation
Install using pip:
```console
$ pip install topasgraphsim
```
Then, start the GUI by running:
```console
$ python -m topasgraphsim
```
Or, if your Python is added to $PATH, simply run:
```console
$ topasgraphsim
```
Open compatible files from the command line:
```console
$ topasgraphsim "path_to_your_file"
```
Since all my testing in done on Windows 11, I cannot guarantee ToapsGrapSim will work on any other plattform. I'm open to suggestions or PRs making the software work better cross-plattfrom!
## Features
Visit the [wiki](https://github.com/sebasj13/TopasGraphSim/wiki) for detailed information!
Highlights include:
- Reproducible graphing and analysis of 1D TOPAS simulation for medical physics
- Simultaneous plotting and parameter calculation for all data sets
- Calculation of the Gamma Index with adjustable parameters
- Graph adjustment options
* Normalization (On/Off)
* Error bars (On/Off)
* Graph order and colors
* Marker size and style
* Line width
- Drag and drop of files
- Center axis deviation correction
- Import of RadCalc OAR and PDD data, RayStation and Eclipse depth doses and dose profiles, and Slicer line profiles
- Import of custom measurements (as numpy .txt files)
- Import of PTW tbaScan (MEPHYSTO mc<sup>2</sup>) measurements
- German and english language support
- Dark mode
## Screenshots
## Parameters
Depending on the imported measurement, the following parameters can be calculated:
| Measurement type | Parameters | | | | | |
| ---------------- | :--------: | :---------------: | :--------------------: | :-------------------: | :------------: | :------------: |
| | | | | | | |
| Depth dose | Q-Factor | z<sub>max</sub> | | | | |
| | | | | | | |
| Dose profile | FWHM | CAX<sub>dev</sub> | FLAT<sub>Krieger</sub> | FLAT<sub>stddev</sub> | Penumbra (L&R) | Integral (L&R) |
- Q-Factor : Radiation Quality Factor
- z<sub>max</sub> : Depth at Maximum
- FWHM : Full-Width at Half-Maximum
- CAX<sub>dev</sub> : Centre Axis Deviation
- FLAT<sub>Krieger</sub> : Flatness of Dose Plateau (Definition by Krieger)
- FLAT<sub>stddev</sub> : Flatness of Dose Plateau (Standard Deviation)
- Penumbra (L&R) : Width of Left and Right Penumbra
- Integral (L&R) : Integral below Left and Right Penumbra
## Dependencies
The UI is based on the [customtkinter](http://github.com/TomSchimansky/CustomTkinter) library.
Requires python3, numpy, scipy, matplotlib, Pillow, python-opencv, pynput, requests, topas2numpy, and python-tkdnd.
## Contact me!
Thank you for using TopasGraphSim! Please let me know about any issues you encounter, or suggestions/wishes you might have!
<br></br>
[](https://pepy.tech/project/topasgraphsim)
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"description": "# <p align=\"center\">TopasGraphSim</p>\r\n\r\n## <p align=\"center\">A GUI to simplify and streamline the plotting and analysis of medical physics simulations</p>\r\n\r\n<p align=\"center\">\r\n<img src=\"https://user-images.githubusercontent.com/87897942/152699152-d4d39654-4449-4354-b899-4adc81eb25a7.png\" width=\"320\" height=\"160\" />\r\n</p>\r\n\r\nThis GUI can visualize and analyze percentage depth dose (pdd) and dose profiles (dp) simulations from [TOPAS](http://www.topasmc.org/). Depth dose measurements are assumed to be in the z-direction, dose profiles in the x- or y-directions. Data read-in is handled by [topas2numpy](https://github.com/davidchall/topas2numpy).\r\n\r\n## Installation\r\n\r\nInstall using pip:\r\n\r\n```console\r\n$ pip install topasgraphsim \r\n```\r\n \r\nThen, start the GUI by running:\r\n \r\n```console\r\n$ python -m topasgraphsim\r\n```\r\n\r\nOr, if your Python is added to $PATH, simply run:\r\n\r\n```console\r\n$ topasgraphsim\r\n```\r\n\r\nOpen compatible files from the command line:\r\n\r\n```console\r\n$ topasgraphsim \"path_to_your_file\"\r\n```\r\n\r\nSince all my testing in done on Windows 11, I cannot guarantee ToapsGrapSim will work on any other plattform. I'm open to suggestions or PRs making the software work better cross-plattfrom!\r\n\r\n## Features\r\n\r\nVisit the [wiki](https://github.com/sebasj13/TopasGraphSim/wiki) for detailed information!\r\n\r\nHighlights include:\r\n\r\n - Reproducible graphing and analysis of 1D TOPAS simulation for medical physics\r\n - Simultaneous plotting and parameter calculation for all data sets\r\n - Calculation of the Gamma Index with adjustable parameters\r\n - Graph adjustment options\r\n * Normalization (On/Off)\r\n * Error bars (On/Off)\r\n * Graph order and colors\r\n * Marker size and style\r\n * Line width\r\n - Drag and drop of files\r\n - Center axis deviation correction\r\n - Import of RadCalc OAR and PDD data, RayStation and Eclipse depth doses and dose profiles, and Slicer line profiles \r\n - Import of custom measurements (as numpy .txt files)\r\n - Import of PTW tbaScan (MEPHYSTO mc<sup>2</sup>) measurements\r\n - German and english language support\r\n - Dark mode\r\n\r\n ## Screenshots\r\n \r\n \r\n \r\n\r\n\r\n ## Parameters\r\n\r\nDepending on the imported measurement, the following parameters can be calculated:\r\n\r\n| Measurement type | Parameters | | | | | |\r\n| ---------------- | :--------: | :---------------: | :--------------------: | :-------------------: | :------------: | :------------: |\r\n| | | | | | | |\r\n| Depth dose | Q-Factor | z<sub>max</sub> | | | | |\r\n| | | | | | | |\r\n| Dose profile | FWHM | CAX<sub>dev</sub> | FLAT<sub>Krieger</sub> | FLAT<sub>stddev</sub> | Penumbra (L&R) | Integral (L&R) |\r\n\r\n- Q-Factor : Radiation Quality Factor\r\n- z<sub>max</sub> : Depth at Maximum\r\n\r\n- FWHM : Full-Width at Half-Maximum\r\n- CAX<sub>dev</sub> : Centre Axis Deviation\r\n- FLAT<sub>Krieger</sub> : Flatness of Dose Plateau (Definition by Krieger)\r\n- FLAT<sub>stddev</sub> : Flatness of Dose Plateau (Standard Deviation)\r\n- Penumbra (L&R) : Width of Left and Right Penumbra\r\n- Integral (L&R) : Integral below Left and Right Penumbra\r\n\r\n## Dependencies\r\n\r\nThe UI is based on the [customtkinter](http://github.com/TomSchimansky/CustomTkinter) library.\r\n\r\nRequires python3, numpy, scipy, matplotlib, Pillow, python-opencv, pynput, requests, topas2numpy, and python-tkdnd.\r\n## Contact me!\r\n\r\nThank you for using TopasGraphSim! Please let me know about any issues you encounter, or suggestions/wishes you might have! \r\n<br></br>\r\n[](https://pepy.tech/project/topasgraphsim)\r\n",
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