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

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.

You might also like...
A set of functions and analysis classes for solvation structure analysis

SolvationAnalysis The macroscopic behavior of a liquid is determined by its microscopic structure. For ionic systems, like batteries and many enzymes,

 🧪 Panel-Chemistry - exploratory data analysis and build powerful data and viz tools within the domain of Chemistry using Python and HoloViz Panel.
🧪 Panel-Chemistry - exploratory data analysis and build powerful data and viz tools within the domain of Chemistry using Python and HoloViz Panel.

🧪📈 🐍. The purpose of the panel-chemistry project is to make it really easy for you to do DATA ANALYSIS and build powerful DATA AND VIZ APPLICATIONS within the domain of Chemistry using using Python and HoloViz Panel.

Larch: Applications and Python Library for Data Analysis of X-ray Absorption Spectroscopy (XAS, XANES, XAFS, EXAFS), X-ray Fluorescence (XRF) Spectroscopy and Imaging

Larch: Data Analysis Tools for X-ray Spectroscopy and More Documentation: http://xraypy.github.io/xraylarch Code: http://github.com/xraypy/xraylarch L

Sensitivity Analysis Library in Python (Numpy). Contains Sobol, Morris, Fractional Factorial and FAST methods.

Sensitivity Analysis Library (SALib) Python implementations of commonly used sensitivity analysis methods. Useful in systems modeling to calculate the

 A data analysis using python and pandas to showcase trends in school performance.
A data analysis using python and pandas to showcase trends in school performance.

A data analysis using python and pandas to showcase trends in school performance. A data analysis to showcase trends in school performance using Panda

A collection of learning outcomes data analysis using Python and SQL, from DQLab.
A collection of learning outcomes data analysis using Python and SQL, from DQLab.

Data Analyst with PYTHON Data Analyst berperan dalam menghasilkan analisa data serta mempresentasikan insight untuk membantu proses pengambilan keputu

BioMASS - A Python Framework for Modeling and Analysis of Signaling Systems
BioMASS - A Python Framework for Modeling and Analysis of Signaling Systems

Mathematical modeling is a powerful method for the analysis of complex biological systems. Although there are many researches devoted on produ

Weather analysis with Python, SQLite, SQLAlchemy, and Flask
Weather analysis with Python, SQLite, SQLAlchemy, and Flask

Surf's Up Weather analysis with Python, SQLite, SQLAlchemy, and Flask Overview The purpose of this analysis was to examine weather trends (precipitati

Stock Analysis dashboard Using Streamlit and Python
Stock Analysis dashboard Using Streamlit and Python

StDashApp Stock Analysis Dashboard Using Streamlit and Python If you found the content useful and want to support my work, you can buy me a coffee! Th

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
Minimal working example of data acquisition with nidaqmx python API

Data Aquisition using NI-DAQmx python API Based on this project It is a minimal working example for data acquisition using the NI-DAQmx python API. It

Pablo 1 Nov 05, 2021
Tuplex is a parallel big data processing framework that runs data science pipelines written in Python at the speed of compiled code

Tuplex is a parallel big data processing framework that runs data science pipelines written in Python at the speed of compiled code. Tuplex has similar Python APIs to Apache Spark or Dask, but rather

Tuplex 791 Jan 04, 2023
This program analyzes a DNA sequence and outputs snippets of DNA that are likely to be protein-coding genes.

This program analyzes a DNA sequence and outputs snippets of DNA that are likely to be protein-coding genes.

1 Dec 28, 2021
Demonstrate the breadth and depth of your data science skills by earning all of the Databricks Data Scientist credentials

Data Scientist Learning Plan Demonstrate the breadth and depth of your data science skills by earning all of the Databricks Data Scientist credentials

Trung-Duy Nguyen 27 Nov 01, 2022
A collection of robust and fast processing tools for parsing and analyzing web archive data.

ChatNoir Resiliparse A collection of robust and fast processing tools for parsing and analyzing web archive data. Resiliparse is part of the ChatNoir

ChatNoir 24 Nov 29, 2022
Pyspark Spotify ETL

This is my first Data Engineering project, it extracts data from the user's recently played tracks using Spotify's API, transforms data and then loads it into Postgresql using SQLAlchemy engine. Data

16 Jun 09, 2022
Python Practicum - prepare for your Data Science interview or get a refresher.

Python-Practicum Python Practicum - prepare for your Data Science interview or get a refresher. Data Data visualization using data on births from the

Jovan Trajceski 1 Jul 27, 2021
Validation and inference over LinkML instance data using souffle

Translates LinkML schemas into Datalog programs and executes them using Souffle, enabling advanced validation and inference over instance data

Linked data Modeling Language 7 Aug 07, 2022
Leverage Twitter API v2 to analyze tweet metrics such as impressions and profile clicks over time.

Tweetmetric Tweetmetric allows you to track various metrics on your most recent tweets, such as impressions, retweets and clicks on your profile. The

Mathis HAMMEL 29 Oct 18, 2022
Data science/Analysis Health Care Portfolio

Health-Care-DS-Projects Data Science/Analysis Health Care Portfolio Consists Of 3 Projects: Mexico Covid-19 project, analyze the patient medical histo

Mohamed Abd El-Mohsen 1 Feb 13, 2022
A powerful data analysis package based on mathematical step functions. Strongly aligned with pandas.

The leading use-case for the staircase package is for the creation and analysis of step functions. Pretty exciting huh. But don't hit the close button

48 Dec 21, 2022
Python package to transfer data in a fast, reliable, and packetized form.

pySerialTransfer Python package to transfer data in a fast, reliable, and packetized form.

PB2 101 Dec 07, 2022
An ETL framework + Monitoring UI/API (experimental project for learning purposes)

Fastlane An ETL framework for building pipelines, and Flask based web API/UI for monitoring pipelines. Project structure fastlane |- fastlane: (ETL fr

Dan Katz 2 Jan 06, 2022
Finding project directories in Python (data science) projects, just like there R rprojroot and here packages

Find relative paths from a project root directory Finding project directories in Python (data science) projects, just like there R here and rprojroot

Daniel Chen 102 Nov 16, 2022
A DSL for data-driven computational pipelines

"Dataflow variables are spectacularly expressive in concurrent programming" Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum Quick overview Ne

1.9k Jan 03, 2023
Picka: A Python module for data generation and randomization.

Picka: A Python module for data generation and randomization. Author: Anthony Long Version: 1.0.1 - Fixed the broken image stuff. Whoops What is Picka

Anthony 108 Nov 30, 2021
PyPSA: Python for Power System Analysis

1 Python for Power System Analysis Contents 1 Python for Power System Analysis 1.1 About 1.2 Documentation 1.3 Functionality 1.4 Example scripts as Ju

758 Dec 30, 2022
Extract data from a wide range of Internet sources into a pandas DataFrame.

pandas-datareader Up to date remote data access for pandas, works for multiple versions of pandas. Installation Install using pip pip install pandas-d

Python for Data 2.5k Jan 09, 2023
follow-analyzer helps GitHub users analyze their following and followers relationship

follow-analyzer follow-analyzer helps GitHub users analyze their following and followers relationship by providing a report in html format which conta

Yin-Chiuan Chen 2 May 02, 2022