Python script to automate the plotting and analysis of percentage depth dose and dose profile simulations in TOPAS.

Related tags

Data Analysispythonmonte-carlo-simulationtopastkinter-guitopasmc
Overview

topas-create-graphs

A script to automatically plot the results of a topas simulation

Works for percentage depth dose (pdd) and dose profiles (dp). Depth dose measurements are assumed to
be in the z-direction, dose profiles in the x- or y-directions.

Automatically calculates relevant parameters

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

  • zmax : Depth at Maximum

  • FWHM : Full-Width at Half-Maximum

  • CAXdev : Centre Axis Deviation

  • FLATKrieger : Flatness of Dose Plateau (Definitionby Krieger)

  • FLATstddev : Flatness of Dose Plateau (Standard Deviation)

  • Penumbra (L&R) : Width of Left and Right Penumbra

  • Integral (L&R) : Integral below Left and Right Penumbra

Includes an optional GUI

The script is intended as a command line tool, where the first argument is the path to the file, and the second is the number of histories. However, the GUI can also be used. It comes with basic file selection and preview of the graph, as well as the option to save the graph.

Assumes a ".csv" input file format from a TOPAS Scorer with the following header format:

# TOPAS Version: {...}
# Parameter File: {...}.txt
# Results for scorer {...}
# Scored in component: {...}
# X in {...} bin of {...} cm
# Y in 1 {...} of {...} cm
# Z in {...} bins of {...} cm
# DoseToMedium ( Gy ) : {Sum/Mean} Standard_Deviation
Voxel Coordinate X, Voxel Coordinate Y, Voxel Coordinate Z, {Sum/Mean} Value, Standard_Deviation Value
.
.
.

Dependencies

Uses the beautiful Azure-ttk dark theme by @rdbende. Requires Python3 and Numpy, Scipy, Matplotlib, Pillow and cv2.

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Comments
  • Nice work! plus a few comments

    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
    opened by bwheelz36 6
  • Fix Y-Axis Label

    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"

    opened by jaschst 1
  • Add Gamma Index Calculation

    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)

    enhancement 
    opened by sebasj13 0
Releases(v21.1.2)

  • v21.1.2(Jun 23, 2022)

    What's Changed

    • Bug fix preventing simulations without a standard deviation from loading

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v21.1.1...v21.1.2

    Source code(tar.gz)
    Source code(zip)

  • v21.1.1(Jun 20, 2022)

    What's Changed

    • Saving now includes the parameter table

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v21.1.0...v21.1.1

    Source code(tar.gz)
    Source code(zip)

  • v21.1.0(Jun 20, 2022)

    What's Changed

    • Added option to add a title to the graph
    • Added option to rename the Y-axis
    • Minor bug fixes when importing custom measurements

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v21.0.0...v21.1.0

    Source code(tar.gz)
    Source code(zip)

  • v21.0.0(Jun 13, 2022)

    What's Changed

    • Added the option to show the value of the plot on mouse hover under: Menu -> View -> Show value on hover
    • Major overhaul on the menu bar - it should be more responsive and intuitive to use!
    • Fixed a bug which prevented renaming of the X-axis
    • Bug fixes and performance improvements

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v20.1.1...v21.0.0

    Source code(tar.gz)
    Source code(zip)

  • v20.1.1(May 31, 2022)

    What's Changed

    • Minor bug fixes in the handling of RadCalc files

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v20.1.0...v20.1.1

    Source code(tar.gz)
    Source code(zip)

  • v20.1.0(May 12, 2022)

  • v20.0.6(Apr 8, 2022)

    What's Changed

    • Fix case sensitivity in PTW measurement import by @sebasj13 in https://github.com/sebasj13/TopasGraphSim/pull/82

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v20.0.4...v20.0.5

    Source code(tar.gz)
    Source code(zip)

  • v20.0.4(Mar 26, 2022)

    What's Changed

    • Prompt the select the type of measurment when importing custom formats

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v20.0.3...v20.0.4

    Source code(tar.gz)
    Source code(zip)

  • v20.0.3(Mar 25, 2022)

    What's Changed

    • Added extra check for the lower dose cutoff in gamma calculations

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v20.0.2...v20.0.3

    Source code(tar.gz)
    Source code(zip)

  • v20.0.2(Mar 24, 2022)

    What's Changed

    • Open file dialog now defualts to the most recently used directory instead of the install location

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v20.0.1...v20.0.2

    Source code(tar.gz)
    Source code(zip)

  • v20.0.1(Mar 24, 2022)

  • v20.0.0(Mar 16, 2022)

    What's Changed

    • Added gamma index calculation by @sebasj13 in https://github.com/sebasj13/TopasGraphSim/pull/80

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v19.1.1...v20.0.0

    Source code(tar.gz)
    Source code(zip)

  • v19.1.1(Feb 22, 2022)

    What's Changed

    • Bug fixes and performance improvements

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v19.1.0...v19.1.1

    Source code(tar.gz)
    Source code(zip)

  • v19.1.0(Feb 22, 2022)

    What's Changed

    • Quality of life updates to the zoom window
    • Bug fixes and performance improvements

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v19.0.3...v19.1.0

    Source code(tar.gz)
    Source code(zip)

  • v19.0.3(Feb 21, 2022)

    What's Changed

    • Big fixes and performance improvements

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v19.0.2...v19.0.3

    Source code(tar.gz)
    Source code(zip)

  • v19.0.2(Feb 21, 2022)

    What's Changed

    • Added plateau normalization option, which averages the 10 central points
    • Bug fixes and performance improvements

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v19.0.0...v19.0.2

    Source code(tar.gz)
    Source code(zip)

  • v19.0.0(Feb 20, 2022)

    What's Changed

    • Fixed parameter calculation for custom measurement files
    • Added customization of the graph markers https://github.com/sebasj13/TopasGraphSim/pull/76
    • Added a citation https://github.com/sebasj13/TopasGraphSim/pull/78
    • Bug fixes and performance improvements

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v18.2.1...v19.0.0

    Source code(tar.gz)
    Source code(zip)

  • v18.2.1(Feb 19, 2022)

    What's Changed

    • Fixed a bug that prevented app startup when a recent file had been moved/deleted

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v18.2.0...v18.2.1

    Source code(tar.gz)
    Source code(zip)

  • v18.2.0(Feb 17, 2022)

    What's Changed

    • Added recent files functionality and improved the performance of the PTW Importer by @sebasj13 in https://github.com/sebasj13/TopasGraphSim/pull/73

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v18.1.2...v18.2.0

    Source code(tar.gz)
    Source code(zip)

  • v18.1.2(Feb 17, 2022)

    What's Changed

    • The Application now opens where it was last closed

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v18.1.1...v18.1.2

    Source code(tar.gz)
    Source code(zip)

  • v18.1.1(Feb 16, 2022)

  • v18.1.0(Feb 16, 2022)

    What's Changed

    • Major Performance improvements and stability updates when resizing the window or scrubbing though the data

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v18.0.2...v18.1.0

    Source code(tar.gz)
    Source code(zip)

  • v18.0.2(Feb 14, 2022)

    What's Changed

    • Removed half screen height restriction to allow for better tiling in Windows

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v18.0.0...v18.0.2

    Source code(tar.gz)
    Source code(zip)

  • v17.3.1(Feb 12, 2022)

  • v17.3.0(Feb 12, 2022)

    What's Changed

    • Added drag and drop support
    • Improved the y-axis labels

    Know issue:

    • When switching the language, existing graphs aren't placed correctly. A workaround is switching the theme, then switching back.

    Full Changelog: https://github.com/sebasj13/TopasGraphSim/compare/v17.2.9...v17.3.0

    Source code(tar.gz)
    Source code(zip)

  • v17.2.9(Feb 10, 2022)

    What's Changed

    • Overhaul to the placement of elements on screen
    • Bug fixes and performance improvements

    Full Changelog: https://github.com/sebasj13/topasgraphsim/compare/v17.2.8...v17.2.9

    Source code(tar.gz)
    Source code(zip)

  • v17.2.8(Feb 7, 2022)

    What's Changed

    • Important Bug fix - assignment of errorbars to data was flipped and is now fixed

    Full Changelog: https://github.com/sebasj13/topasgraphsim/compare/v17.2.7...v17.2.8

    Source code(tar.gz)
    Source code(zip)

  • v17.2.7(Feb 7, 2022)

  • v17.2.6(Feb 6, 2022)

  • v17.2.5(Feb 6, 2022)

    What's Changed

    • Fixed a bugged color when using dark mode

    Full Changelog: https://github.com/sebasj13/topasgraphsim/compare/v17.2.4...v17.2.5

    Source code(tar.gz)
    Source code(zip)
Owner
Sebastian Schäfer
Master Student of medical physics and Python enthusiast.
Sebastian Schäfer
GitHub Repository
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