sebasj13 / topasgraphsim

A GUI to simplify and streamline the plotting and analysis of medical physics simulations

TopasGraphSim

A GUI to simplify and streamline the plotting and analysis of medical physics simulations

This GUI can visualize and analyze percentage depth dose (pdd) and dose profiles (dp) simulations from TOPAS. 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.

Installation

Install using pip:

$ pip install topasgraphsim     

Then, start the GUI by running:

$ python -m topasgraphsim

Or, if your Python is added to $PATH, simply run:

$ topasgraphsim

Open compatible files from the command line:

$ 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 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 mc²) 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	zmax
Dose profile	FWHM	CAXdev	FLATKrieger	FLATstddev	Penumbra (L&R)	Integral (L&R)

• Q-Factor : Radiation Quality Factor

• z_max : Depth at Maximum

• FWHM : Full-Width at Half-Maximum

• CAX_dev : Centre Axis Deviation

• FLAT_Krieger : Flatness of Dose Plateau (Definition by Krieger)

• FLAT_stddev : 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 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!

topasgraphsim's Issues

Only allow one datatype to be added

Import of binary TOPAS files not working

Add a Citation

Add support for EGS (.3ddose) input files

Saving not functional

Add Gamma Index Calculation

import pymedphys

gamma = pymedphys.gamma(
(data[0][0],), data[0][1], (data[1][0],), data[1][1], 1, 1
)

valid_gamma = gamma[~np.isnan(gamma)]
pass_ratio = np.sum(valid_gamma <= 1) / len(valid_gamma)
print(pass_ratio)

Change graph colors when switching to dark mode

Add ability to change plot labels

Improve performance by switching to FigureCanvasTkAgg

Add ask to save option if a project is open

Add standard text when renaming graphs

Add ability to plot half of a dose profile

addmenu is not properly cleared when closing a graph

Center the graph when viewing dose profiles

Add main screen logo

Add graph after closing a simulation not functional

Implement topas2numpy data readin

[TODO] Use topas2numpy to allow for more diverse input files

English language support

Create a .profile with language preferences

Streamline the file import process

Add option to save images as .pdf

Option to switch between absolute and relative data

For single viewing only, when adding graphs to the view always normalize

Add ability to change x-axis labels

Add difference plots from the comparison of simulations with measurements

Add ability to select multiple files for read-in at once

Add option to switch between percentage and absolute deviation

Make graph order changeable

Add normalization selector

Improve the measurement determination process

Add CAX-correction to dose profile measurements

Add color picker to graphs

Add ability to change the x-axis field using x_lim()

Line style

Add option to change line style (solid, dashed, dotted, dashdot).

Add toggle to parameter calculation

Add support for more than 5 datasets

Show the calculated parameters in a table below the graph

Make zoom-in window draggable

Add support for PTW BEAMSCAN .mcc measurement data

Separate center axis correction from parameter calculation

Remove case sensitivity in ptw_import

ptw_import currently has an issue with .mcc files, that contain
INPLANE_AXIS=y CROSSPLANE_AXIS=x DEPTH_AXIS=z
instead of uppercase letters.

Add Info tab to Menu

Including:
*author
*version

Calculate parameters for csv data

Add "descriptors" + "Show parameter table" for measurements

Fix Y-Axis Label

3ddose dataset shows y-axis label "mm" if not normalized. --> "Dose [Gy/history]"
Maybe add optionial or permanent label for relative dose distributions e.g. "Relative Dosis"

Add drag and drop support

Add ability to turn off error bars

Add zoom-in graph when viewing depth doses

Nice work! plus a few comments

Firstly, this is really nice! i have been vaguely contemplating if I should do something like this given the number of how 'how do I plot...' questions on the forums. Nice to see.
The following are some comments/questions/suggestions. Feel free to ignore any that aren't helpful!

comments

• I would move the install instructions closer to the top of the read me, because whenever I look at software on github the first thing I want to do is make sure I can install it before I start read the detailed instructions.

questions

• what scoring geometries does this handle? or will it handle anything? e.g. I think depending on the scoring component, the coordinates might be polar or cartesian (right?), will this handle both?
• Is it possible to run this 'headless' (no GUI?) and if not would it be difficult to add this? In many situations it would be nice to be able to script analysis...also for debugging this would be handy.

install experience

• In ubuntu, I had to do sudo apt install python3.9-dev before this package would install. It was some issue with a package called evdev
• In windows worked perfectly.

use experience

• in linux the default window is very large - I can make it larger, but I can't make it smaller. weird!
• I tried to load some .bin files from a TsBox scorer; in windows and linux I got the error "AttributeError: 'Simulation' object has no attribute 'direction'"
• In general it looks like there are a few if, elif statements where it would be a good idea to put a final else: raise NotImplementedError

Add Dark Mode

Self-explanatory