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.

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,

MDAnalysis 19 Nov 24, 2022
🧪 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.

Marc Skov Madsen 97 Dec 8, 2022
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

xraypy 95 Dec 13, 2022
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

SALib 663 Jan 5, 2023
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

Jimmy Faccioli 0 Sep 7, 2021
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

null 6 Oct 11, 2022
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

BioMASS 22 Dec 27, 2022
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

Art Tucker 1 Sep 5, 2021
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

StreamAlpha 27 Dec 9, 2022
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
A simple and efficient tool to parallelize Pandas operations on all available CPUs

Pandaral·lel Without parallelization With parallelization Installation $ pip install pandarallel [--upgrade] [--user] Requirements On Windows, Pandara

Manu NALEPA 2.8k Dec 31, 2022
Open-Domain Question-Answering for COVID-19 and Other Emergent Domains

Open-Domain Question-Answering for COVID-19 and Other Emergent Domains This repository contains the source code for an end-to-end open-domain question

7 Sep 27, 2022
A data parser for the internal syncing data format used by Fog of World.

A data parser for the internal syncing data format used by Fog of World. The parser is not designed to be a well-coded library with good performance, it is more like a demo for showing the data struc

Zed(Zijun) Chen 40 Dec 12, 2022
Data Scientist in Simple Stock Analysis of PT Bukalapak.com Tbk for Long Term Investment

Data Scientist in Simple Stock Analysis of PT Bukalapak.com Tbk for Long Term Investment Brief explanation of PT Bukalapak.com Tbk Bukalapak was found

Najibulloh Asror 2 Feb 10, 2022
A Python and R autograding solution

Otter-Grader Otter Grader is a light-weight, modular open-source autograder developed by the Data Science Education Program at UC Berkeley. It is desi

Infrastructure Team 93 Jan 03, 2023
A crude Hy handle on Pandas library

Quickstart Hyenas is a curde Hy handle written on top of Pandas API to allow for more elegant access to data-scientist's powerhouse that is Pandas. In

Peter Výboch 4 Sep 05, 2022
Data Analytics on Genomes and Genetics

Data Analytics performed on On genomes and Genetics dataset to predict genetic disorder and disorder subclass. DONE by TEAM SIGMA!

1 Jan 12, 2022
A distributed block-based data storage and compute engine

Nebula is an extremely-fast end-to-end interactive big data analytics solution. Nebula is designed as a high-performance columnar data storage and tabular OLAP engine.

Columns AI 131 Dec 26, 2022
Clean and reusable data-sciency notebooks.

KPACUBO KPACUBO is a set Jupyter notebooks focused on the best practices in both software development and data science, namely, code reuse, explicit d

Matvey Morozov 1 Jan 28, 2022
Open-source Laplacian Eigenmaps for dimensionality reduction of large data in python.

Fast Laplacian Eigenmaps in python Open-source Laplacian Eigenmaps for dimensionality reduction of large data in python. Comes with an wrapper for NMS

17 Jul 09, 2022
Flenser is a simple, minimal, automated exploratory data analysis tool.

Flenser Have you ever been handed a dataset you've never seen before? Flenser is a simple, minimal, automated exploratory data analysis tool. It runs

John McCambridge 79 Sep 20, 2022
Statistical & Probabilistic Analysis of Store Sales, University Survey, & Manufacturing data

Statistical_Modelling Statistical & Probabilistic Analysis of Store Sales, University Survey, & Manufacturing data Statistical Methods for Decision Ma

Avnika Mehta 1 Jan 27, 2022
Yet Another Workflow Parser for SecurityHub

YAWPS Yet Another Workflow Parser for SecurityHub "Screaming pepper" by Rum Bucolic Ape is licensed with CC BY-ND 2.0. To view a copy of this license,

myoung34 8 Dec 22, 2022
Evaluation of a Monocular Eye Tracking Set-Up

Evaluation of a Monocular Eye Tracking Set-Up As part of my master thesis, I implemented a new state-of-the-art model that is based on the work of Che

Pascal 19 Dec 17, 2022
Generate lookml for views from dbt models

dbt2looker Use dbt2looker to generate Looker view files automatically from dbt models. Features Column descriptions synced to looker Dimension for eac

lightdash 126 Dec 28, 2022
A notebook to analyze Amazon Recommendation Review Dataset.

Amazon Recommendation Review Dataset Analyzer A notebook to analyze Amazon Recommendation Review Dataset. Features Calculates distinct user count, dis

isleki 3 Aug 22, 2022
Reading streams of Twitter data, save them to Kafka, then process with Kafka Stream API and Spark Streaming

Using Streaming Twitter Data with Kafka and Spark Reading streams of Twitter data, publishing them to Kafka topic, process message using Kafka Stream

Rustam Zokirov 1 Dec 06, 2021
Hangar is version control for tensor data. Commit, branch, merge, revert, and collaborate in the data-defined software era.

Overview docs tests package Hangar is version control for tensor data. Commit, branch, merge, revert, and collaborate in the data-defined software era

Tensorwerk 193 Nov 29, 2022
Basis Set Format Converter

Basis Set Format Converter Repository for the online tool that allows you to enter a basis set in the form of text input for a variety of Quantum Chem

Manas Sharma 3 Jun 27, 2022
WithPipe is a simple utility for functional piping in Python.

A utility for functional piping in Python that allows you to access any function in any scope as a partial.

Michael Milton 1 Oct 26, 2021