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<li><a href="#what-youll-build" id="toc-what-youll-build" class="nav-link" data-scroll-target="#what-youll-build">What you’ll build</a></li>
<li><a href="#adopting-these-labs" id="toc-adopting-these-labs" class="nav-link" data-scroll-target="#adopting-these-labs">Adopting these labs</a></li>
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<li><a href="#source-and-pdfs" id="toc-source-and-pdfs" class="nav-link" data-scroll-target="#source-and-pdfs">Source and PDFs</a></li>
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<h1 class="title">Geant4 Radiation Labs</h1>
<p class="subtitle lead">A hands-on intro to Monte Carlo radiation simulation and analysis</p>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>John Murphy and Steven Carlson </p>
</div>
</div>
</div>
</header>
<section id="what-this-is" class="level2">
<h2 class="anchored" data-anchor-id="what-this-is">What this is</h2>
<p>A four-lab series that takes you from a fresh Linux install to a working PET-scanner simulation, using <a href="https://geant4.web.cern.ch/">Geant4</a> for the physics and Python (pandas, matplotlib) for analysis.</p>
<p>The labs are designed to be done in order. Each one builds on the environment, code, and analysis idioms of the previous one.</p>
</section>
<section id="audience" class="level2">
<h2 class="anchored" data-anchor-id="audience">Audience</h2>
<p>Upper-level undergraduates or early graduate students with:</p>
<ul>
<li>Comfort with the Linux command line</li>
<li>Some C++ literacy (you don’t need to write much; you’ll mostly read and patch)</li>
<li>Some Python literacy (you’ll write short analysis scripts)</li>
</ul>
<p>No prior Geant4 or medical-physics knowledge is assumed.</p>
</section>
<section id="the-labs" class="level2">
<h2 class="anchored" data-anchor-id="the-labs">The labs</h2>
<ol type="1">
<li><p><strong><a href="./lab1_setup/lab1.html">Lab 1 — Setting Up Linux and Building Geant4</a></strong> Install Ubuntu in a virtual machine and build Geant4 from source with Qt visualization support.</p></li>
<li><p><strong><a href="./lab2_exampleB1/lab2.html">Lab 2 — First Simulation: Building and Running B1</a></strong> Compile Geant4’s B1 example, run it interactively (Qt GUI) and in batch mode via macros, and modify the particle, energy, and event count.</p></li>
<li><p><strong><a href="./lab3_modifyB1/lab3.html">Lab 3 — Acquiring and Analyzing Simulation Data</a></strong> Patch B1’s C++ to write per-event energy data to CSV via <code>G4AnalysisManager</code>, then load it in Python with pandas and produce histograms, statistics, and per-particle comparisons.</p></li>
<li><p><strong><a href="./lab4_exampleB3/lab4.html">Lab 4 — A PET Scanner</a></strong> Apply the same workflow to Geant4’s B3a (Positron Emission Tomography) example. Identify the 511 keV photopeak in the energy spectrum, find true coincidences, and reconstruct lines of response.</p></li>
</ol>
</section>
<section id="what-youll-build" class="level2">
<h2 class="anchored" data-anchor-id="what-youll-build">What you’ll build</h2>
<p>By the end of the series you will have:</p>
<ul>
<li>A reproducible Geant4 + Python development environment</li>
<li>Modified Geant4 applications that emit clean CSV data</li>
<li>Python scripts that compute statistics and produce publication-style plots</li>
<li>A working understanding of the <strong>simulate → save → analyze → visualize</strong> loop that underlies most computational physics</li>
</ul>
</section>
<section id="adopting-these-labs" class="level2">
<h2 class="anchored" data-anchor-id="adopting-these-labs">Adopting these labs</h2>
<p>Free to adopt under the licenses below. If you’d like on-site delivery, customization, or instructor materials built on top of these labs, <a href="https://such.software">such.software</a> — an independent provider co-founded by one of the authors — offers commercial services. Email <a href="mailto:john@such.software">john@such.software</a>.</p>
</section>
<section id="license" class="level2">
<h2 class="anchored" data-anchor-id="license">License</h2>
<p>The labs are openly licensed:</p>
<ul>
<li><strong>Code</strong> (Python, C++, scripts, Quarto config) — <a href="https://github.com/jwinterm/geant4-radiation-labs/blob/main/LICENSE">MIT License</a></li>
<li><strong>Content</strong> (prose, diagrams, screenshots) — <a href="https://github.com/jwinterm/geant4-radiation-labs/blob/main/LICENSE-CONTENT">CC-BY-4.0</a></li>
</ul>
<p>Use, adapt, and redistribute freely with attribution to the authors.</p>
</section>
<section id="source-and-pdfs" class="level2">
<h2 class="anchored" data-anchor-id="source-and-pdfs">Source and PDFs</h2>
<p>The full lab source — <code>.qmd</code> files, screenshots, and the Python scripts that generate the conceptual diagrams — lives at <a href="https://github.com/jwinterm/geant4-radiation-labs" class="uri">https://github.com/jwinterm/geant4-radiation-labs</a>.</p>
<p>PDFs of any lab can be regenerated locally with Quarto:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">quarto</span> render lab1_setup/lab1.qmd <span class="at">--to</span> pdf</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="citing" class="level2">
<h2 class="anchored" data-anchor-id="citing">Citing</h2>
<p>If this series is useful in your teaching or work, please cite as:</p>
<blockquote class="blockquote">
<p>Murphy, J. and Carlson, S. (2025). <em>Geant4 Radiation Labs.</em> <a href="https://jwinterm.github.io/geant4-radiation-labs/" class="uri">https://jwinterm.github.io/geant4-radiation-labs/</a></p>
</blockquote>
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tippyHover(xref, undefined, function(instance) {
instance.disable();
let url = xref.getAttribute('href');
let hash = undefined;
if (url.startsWith('#')) {
hash = url;
} else {
try { hash = new URL(url).hash; } catch {}
}
if (hash) {
const id = hash.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note !== null) {
try {
const html = processXRef(id, note.cloneNode(true));
instance.setContent(html);
} finally {
instance.enable();
instance.show();
}
} else {
// See if we can fetch this
fetch(url.split('#')[0])
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.getElementById(id);
if (note !== null) {
const html = processXRef(id, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
} else {
// See if we can fetch a full url (with no hash to target)
// This is a special case and we should probably do some content thinning / targeting
fetch(url)
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.querySelector('main.content');
if (note !== null) {
// This should only happen for chapter cross references
// (since there is no id in the URL)
// remove the first header
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
note.children[0].remove();
}
const html = processXRef(null, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
}, function(instance) {
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
return selector;
}
const selectCodeLines = (annoteEl) => {
const doc = window.document;
const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
div.style.left = 0;
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Handle positioning of the toggle
window.addEventListener(
"resize",
throttle(() => {
elRect = undefined;
if (selectedAnnoteEl) {
selectCodeLines(selectedAnnoteEl);
}
}, 10)
);
function throttle(fn, ms) {
let throttle = false;
let timer;
return (...args) => {
if(!throttle) { // first call gets through
fn.apply(this, args);
throttle = true;
} else { // all the others get throttled
if(timer) clearTimeout(timer); // cancel #2
timer = setTimeout(() => {
fn.apply(this, args);
timer = throttle = false;
}, ms);
}
};
}
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
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