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index.html
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<!doctype html>
<html>
<head>
<meta charset='UTF-8'><meta name='viewport' content='width=device-width initial-scale=1'>
<link href='https://fonts.loli.net/css?family=Open+Sans:400italic,700italic,700,400&subset=latin,latin-ext' rel='stylesheet' type='text/css' /><style type='text/css'>html {overflow-x: initial !important;}:root { --bg-color:#ffffff; --text-color:#333333; --select-text-bg-color:#B5D6FC; --select-text-font-color:auto; --monospace:"Lucida Console",Consolas,"Courier",monospace; --title-bar-height:20px; }
.mac-os-11 { --title-bar-height:28px; }
html { font-size: 14px; background-color: var(--bg-color); color: var(--text-color); font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; -webkit-font-smoothing: antialiased; }
h1, h2, h3, h4, h5 { white-space: pre-wrap; }
body { margin: 0px; padding: 0px; height: auto; inset: 0px; font-size: 1rem; line-height: 1.42857; overflow-x: hidden; background: inherit; tab-size: 4; }
iframe { margin: auto; }
a.url { word-break: break-all; }
a:active, a:hover { outline: 0px; }
.in-text-selection, ::selection { text-shadow: none; background: var(--select-text-bg-color); color: var(--select-text-font-color); }
#write { margin: 0px auto; height: auto; width: inherit; word-break: normal; overflow-wrap: break-word; position: relative; white-space: normal; overflow-x: visible; padding-top: 36px; }
#write.first-line-indent p { text-indent: 2em; }
#write.first-line-indent li p, #write.first-line-indent p * { text-indent: 0px; }
#write.first-line-indent li { margin-left: 2em; }
.for-image #write { padding-left: 8px; padding-right: 8px; }
body.typora-export { padding-left: 30px; padding-right: 30px; }
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.typora-export .task-list-item input { pointer-events: none; }
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#write { padding-left: 20px; padding-right: 20px; }
}
#write li > figure:last-child { margin-bottom: 0.5rem; }
#write ol, #write ul { position: relative; }
img { max-width: 100%; vertical-align: middle; image-orientation: from-image; }
button, input, select, textarea { color: inherit; font: inherit; }
input[type="checkbox"], input[type="radio"] { line-height: normal; padding: 0px; }
*, ::after, ::before { box-sizing: border-box; }
#write h1, #write h2, #write h3, #write h4, #write h5, #write h6, #write p, #write pre { width: inherit; }
#write h1, #write h2, #write h3, #write h4, #write h5, #write h6, #write p { position: relative; }
p { line-height: inherit; }
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h1 { font-size: 2rem; }
h2 { font-size: 1.8rem; }
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h4 { font-size: 1.4rem; }
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.md-math-block, .md-rawblock, h1, h2, h3, h4, h5, h6, p { margin-top: 1rem; margin-bottom: 1rem; }
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.md-blockmeta { color: rgb(204, 204, 204); font-weight: 700; font-style: italic; }
a { cursor: pointer; }
sup.md-footnote { padding: 2px 4px; background-color: rgba(238, 238, 238, 0.7); color: rgb(85, 85, 85); border-radius: 4px; cursor: pointer; }
sup.md-footnote a, sup.md-footnote a:hover { color: inherit; text-transform: inherit; text-decoration: inherit; }
#write input[type="checkbox"] { cursor: pointer; width: inherit; height: inherit; }
figure { overflow-x: auto; margin: 1.2em 0px; max-width: calc(100% + 16px); padding: 0px; }
figure > table { margin: 0px; }
thead, tr { break-inside: avoid; break-after: auto; }
thead { display: table-header-group; }
table { border-collapse: collapse; border-spacing: 0px; width: 100%; overflow: auto; break-inside: auto; text-align: left; }
table.md-table td { min-width: 32px; }
.CodeMirror-gutters { border-right: 0px; background-color: inherit; }
.CodeMirror-linenumber { user-select: none; }
.CodeMirror { text-align: left; }
.CodeMirror-placeholder { opacity: 0.3; }
.CodeMirror pre { padding: 0px 4px; }
.CodeMirror-lines { padding: 0px; }
div.hr:focus { cursor: none; }
#write pre { white-space: pre-wrap; }
#write.fences-no-line-wrapping pre { white-space: pre; }
#write pre.ty-contain-cm { white-space: normal; }
.CodeMirror-gutters { margin-right: 4px; }
.md-fences { font-size: 0.9rem; display: block; break-inside: avoid; text-align: left; overflow: visible; white-space: pre; background: inherit; position: relative !important; }
.md-fences-adv-panel { width: 100%; margin-top: 10px; text-align: center; padding-top: 0px; padding-bottom: 8px; overflow-x: auto; }
#write .md-fences.mock-cm { white-space: pre-wrap; }
.md-fences.md-fences-with-lineno { padding-left: 0px; }
#write.fences-no-line-wrapping .md-fences.mock-cm { white-space: pre; overflow-x: auto; }
.md-fences.mock-cm.md-fences-with-lineno { padding-left: 8px; }
.CodeMirror-line, twitterwidget { break-inside: avoid; }
svg { break-inside: avoid; }
.footnotes { opacity: 0.8; font-size: 0.9rem; margin-top: 1em; margin-bottom: 1em; }
.footnotes + .footnotes { margin-top: 0px; }
.md-reset { margin: 0px; padding: 0px; border: 0px; outline: 0px; vertical-align: top; background: 0px 0px; text-decoration: none; text-shadow: none; float: none; position: static; width: auto; height: auto; white-space: nowrap; cursor: inherit; -webkit-tap-highlight-color: transparent; line-height: normal; font-weight: 400; text-align: left; box-sizing: content-box; direction: ltr; }
li div { padding-top: 0px; }
blockquote { margin: 1rem 0px; }
li .mathjax-block, li p { margin: 0.5rem 0px; }
li blockquote { margin: 1rem 0px; }
li { margin: 0px; position: relative; }
blockquote > :last-child { margin-bottom: 0px; }
blockquote > :first-child, li > :first-child { margin-top: 0px; }
.footnotes-area { color: rgb(136, 136, 136); margin-top: 0.714rem; padding-bottom: 0.143rem; white-space: normal; }
#write .footnote-line { white-space: pre-wrap; }
@media print {
body, html { border: 1px solid transparent; height: 99%; break-after: avoid; break-before: avoid; font-variant-ligatures: no-common-ligatures; }
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}
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pre.md-meta-block { font-size: 0.8rem; min-height: 0.8rem; white-space: pre-wrap; background: rgb(204, 204, 204); display: block; overflow-x: hidden; }
p > .md-image:only-child:not(.md-img-error) img, p > img:only-child { display: block; margin: auto; }
#write.first-line-indent p > .md-image:only-child:not(.md-img-error) img { left: -2em; position: relative; }
p > .md-image:only-child { display: inline-block; width: 100%; }
#write .MathJax_Display { margin: 0.8em 0px 0px; }
.md-math-block { width: 100%; }
.md-math-block:not(:empty)::after { display: none; }
.MathJax_ref { fill: currentcolor; }
[contenteditable="true"]:active, [contenteditable="true"]:focus, [contenteditable="false"]:active, [contenteditable="false"]:focus { outline: 0px; box-shadow: none; }
.md-task-list-item { position: relative; list-style-type: none; }
.task-list-item.md-task-list-item { padding-left: 0px; }
.md-task-list-item > input { position: absolute; top: 0px; left: 0px; margin-left: -1.2em; margin-top: calc(1em - 10px); border: none; }
.math { font-size: 1rem; }
.md-toc { min-height: 3.58rem; position: relative; font-size: 0.9rem; border-radius: 10px; }
.md-toc-content { position: relative; margin-left: 0px; }
.md-toc-content::after, .md-toc::after { display: none; }
.md-toc-item { display: block; color: rgb(65, 131, 196); }
.md-toc-item a { text-decoration: none; }
.md-toc-inner:hover { text-decoration: underline; }
.md-toc-inner { display: inline-block; cursor: pointer; }
.md-toc-h1 .md-toc-inner { margin-left: 0px; font-weight: 700; }
.md-toc-h2 .md-toc-inner { margin-left: 2em; }
.md-toc-h3 .md-toc-inner { margin-left: 4em; }
.md-toc-h4 .md-toc-inner { margin-left: 6em; }
.md-toc-h5 .md-toc-inner { margin-left: 8em; }
.md-toc-h6 .md-toc-inner { margin-left: 10em; }
@media screen and (max-width: 48em) {
.md-toc-h3 .md-toc-inner { margin-left: 3.5em; }
.md-toc-h4 .md-toc-inner { margin-left: 5em; }
.md-toc-h5 .md-toc-inner { margin-left: 6.5em; }
.md-toc-h6 .md-toc-inner { margin-left: 8em; }
}
a.md-toc-inner { font-size: inherit; font-style: inherit; font-weight: inherit; line-height: inherit; }
.footnote-line a:not(.reversefootnote) { color: inherit; }
.reversefootnote { font-family: ui-monospace, sans-serif; }
.md-attr { display: none; }
.md-fn-count::after { content: "."; }
code, pre, samp, tt { font-family: var(--monospace); }
kbd { margin: 0px 0.1em; padding: 0.1em 0.6em; font-size: 0.8em; color: rgb(36, 39, 41); background: rgb(255, 255, 255); border: 1px solid rgb(173, 179, 185); border-radius: 3px; box-shadow: rgba(12, 13, 14, 0.2) 0px 1px 0px, rgb(255, 255, 255) 0px 0px 0px 2px inset; white-space: nowrap; vertical-align: middle; }
.md-comment { color: rgb(162, 127, 3); opacity: 0.6; font-family: var(--monospace); }
code { text-align: left; vertical-align: initial; }
a.md-print-anchor { white-space: pre !important; border-width: initial !important; border-style: none !important; border-color: initial !important; display: inline-block !important; position: absolute !important; width: 1px !important; right: 0px !important; outline: 0px !important; background: 0px 0px !important; text-decoration: initial !important; text-shadow: initial !important; }
.os-windows.monocolor-emoji .md-emoji { font-family: "Segoe UI Symbol", sans-serif; }
.md-diagram-panel > svg { max-width: 100%; }
[lang="flow"] svg, [lang="mermaid"] svg { max-width: 100%; height: auto; }
[lang="mermaid"] .node text { font-size: 1rem; }
table tr th { border-bottom: 0px; }
video { max-width: 100%; display: block; margin: 0px auto; }
iframe { max-width: 100%; width: 100%; border: none; }
.highlight td, .highlight tr { border: 0px; }
mark { background: rgb(255, 255, 0); color: rgb(0, 0, 0); }
.md-html-inline .md-plain, .md-html-inline strong, mark .md-inline-math, mark strong { color: inherit; }
.md-expand mark .md-meta { opacity: 0.3 !important; }
mark .md-meta { color: rgb(0, 0, 0); }
@media print {
.typora-export h1, .typora-export h2, .typora-export h3, .typora-export h4, .typora-export h5, .typora-export h6 { break-inside: avoid; }
}
.md-diagram-panel .messageText { stroke: none !important; }
.md-diagram-panel .start-state { fill: var(--node-fill); }
.md-diagram-panel .edgeLabel rect { opacity: 1 !important; }
.md-fences.md-fences-math { font-size: 1em; }
.md-fences-advanced:not(.md-focus) { padding: 0px; white-space: nowrap; border: 0px; }
.md-fences-advanced:not(.md-focus) { background: inherit; }
.typora-export-show-outline .typora-export-content { max-width: 1440px; margin: auto; display: flex; flex-direction: row; }
.typora-export-sidebar { width: 300px; font-size: 0.8rem; margin-top: 80px; margin-right: 18px; }
.typora-export-show-outline #write { --webkit-flex:2; flex: 2 1 0%; }
.typora-export-sidebar .outline-content { position: fixed; top: 0px; max-height: 100%; overflow: hidden auto; padding-bottom: 30px; padding-top: 60px; width: 300px; }
@media screen and (max-width: 1024px) {
.typora-export-sidebar, .typora-export-sidebar .outline-content { width: 240px; }
}
@media screen and (max-width: 800px) {
.typora-export-sidebar { display: none; }
}
.outline-content li, .outline-content ul { margin-left: 0px; margin-right: 0px; padding-left: 0px; padding-right: 0px; list-style: none; overflow-wrap: anywhere; }
.outline-content ul { margin-top: 0px; margin-bottom: 0px; }
.outline-content strong { font-weight: 400; }
.outline-expander { width: 1rem; height: 1.42857rem; position: relative; display: table-cell; vertical-align: middle; cursor: pointer; padding-left: 4px; }
.outline-expander::before { content: ""; position: relative; font-family: Ionicons; display: inline-block; font-size: 8px; vertical-align: middle; }
.outline-item { padding-top: 3px; padding-bottom: 3px; cursor: pointer; }
.outline-expander:hover::before { content: ""; }
.outline-h1 > .outline-item { padding-left: 0px; }
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.outline-item:hover { border-color: rgb(245, 245, 245); background-color: var(--item-hover-bg-color); }
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.typora-export-show-outline .outline-item-active > .outline-item .outline-label { font-weight: 700; }
.md-inline-math-container mjx-container { zoom: 0.95; }
mjx-container { break-inside: avoid; }
:root {
--side-bar-bg-color: #fafafa;
--control-text-color: #777;
}
@include-when-export url(https://fonts.loli.net/css?family=Open+Sans:400italic,700italic,700,400&subset=latin,latin-ext);
/* open-sans-regular - latin-ext_latin */
/* open-sans-italic - latin-ext_latin */
/* open-sans-700 - latin-ext_latin */
/* open-sans-700italic - latin-ext_latin */
html {
font-size: 16px;
-webkit-font-smoothing: antialiased;
}
body {
font-family: "Open Sans","Clear Sans", "Helvetica Neue", Helvetica, Arial, 'Segoe UI Emoji', sans-serif;
color: rgb(51, 51, 51);
line-height: 1.6;
}
#write {
max-width: 860px;
margin: 0 auto;
padding: 30px;
padding-bottom: 100px;
}
@media only screen and (min-width: 1400px) {
#write {
max-width: 900px;
}
}
@media only screen and (min-width: 1800px) {
#write {
max-width: 900px;
}
}
#write > ul:first-child,
#write > ol:first-child{
margin-top: 30px;
}
a {
color: #4183C4;
}
h1,
h2,
h3,
h4,
h5,
h6 {
position: relative;
margin-top: 1rem;
margin-bottom: 1rem;
font-weight: bold;
line-height: 1.4;
cursor: text;
}
h1:hover a.anchor,
h2:hover a.anchor,
h3:hover a.anchor,
h4:hover a.anchor,
h5:hover a.anchor,
h6:hover a.anchor {
text-decoration: none;
}
h1 tt,
h1 code {
font-size: inherit;
}
h2 tt,
h2 code {
font-size: inherit;
}
h3 tt,
h3 code {
font-size: inherit;
}
h4 tt,
h4 code {
font-size: inherit;
}
h5 tt,
h5 code {
font-size: inherit;
}
h6 tt,
h6 code {
font-size: inherit;
}
h1 {
font-size: 2.25em;
line-height: 1.2;
border-bottom: 1px solid #eee;
}
h2 {
font-size: 1.75em;
line-height: 1.225;
border-bottom: 1px solid #eee;
}
/*@media print {
.typora-export h1,
.typora-export h2 {
border-bottom: none;
padding-bottom: initial;
}
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</style><title>README</title>
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<div id='write' class=''><p><img src="https://raw.githubusercontent.com/marcoalopez/GrainSizeTools/master/FIGURES/new_header.webp" referrerpolicy="no-referrer"></p><p><em><span>Maintained by </span><a href='https://marcoalopez.github.io/'><span>Marco A. Lopez-Sanchez</span></a><span> - This website was last modified: 2023/06/12</span></em></p><p><a href='https://doi.org/10.21105/joss.00863'><span>GrainSizeTools</span></a><span> is a free, open-source, cross-platform script written in </span><a href='https://www.python.org/'><span>Python</span></a><span> that provides tools for (1) describing and visualizing grain size populations, (2) estimating differential stress for different mineral phases via paleopizometers and (3) apply stereology methods to approximate the actual distribution (3D) of grain size from sections. The script </span><strong><span>does not require previous experience with the Python programming language</span></strong><span> (see the documentation below and </span><a href='https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/FAQ.md'><span>FAQ</span></a><span>). For users with coding skills, the script is organized in a modular (functional) way facilitating the reuse and code extension.</span></p><p><strong><span>Latest release: v3.0.2</span></strong><span></span><br/><strong><span>Date: 2020/12/31</span></strong><span></span><br/><span>See notes at </span><a href='https://github.com/marcoalopez/GrainSizeTools/releases/tag/v3.0.2' target='_blank' class='url'>https://github.com/marcoalopez/GrainSizeTools/releases/tag/v3.0.2</a></p><h2 id='features-at-a-glance'><span>Features at a glance</span></h2><ul><li><p><span>Import and manipulate tabular-like datasets including txt, csv, or excel formats.</span></p></li><li><p><span>Full automatic descriptive statistics of grain size populations including:</span></p><ul><li><p><span>Several averages (arithmetic and geometric means, median, and frequency peak ("mode") via Gaussian Kernel Density Estimator)</span></p></li><li><p><span>Estimation of robust confidence intervals (including some specific methods for lognormal populations such as the modified Cox or the GCI method)</span></p></li><li><p><span>Measures of dispersion and shape of the population</span></p></li><li><p><span>Normality and lognormality test</span></p></li></ul></li><li><p><span>Estimate differential stress using paleopiezometers. It includes multiple piezometric relations for quartz, olivine, calcite, and feldspar (others planned!)</span></p></li><li><p><span>Ready-to-publish plots in bitmap or vector format (see screenshots below), including:</span></p><ul><li><p><span>Histograms and kernel density estimates</span></p></li><li><p><span>Area- or volume-weighted plots</span></p></li><li><p><span>Normalized plots</span></p></li><li><p><span>Quantile-quantile plots, and more</span></p></li></ul></li><li><p><span>Stereology methods (approximate the actual 3D grain size distribution from data collected in plane sections):</span></p><ul><li><p><span>Saltykov method</span></p></li><li><p><span>Two-step method (lognormal fitting, shape characterization)</span></p></li></ul></li></ul><h2 id='download'><span>Download</span></h2><p><span>You can download the script at the following sites:</span><br/><a href='https://github.com/marcoalopez/GrainSizeTools/releases' target='_blank' class='url'>https://github.com/marcoalopez/GrainSizeTools/releases</a><span> (primary source)</span><br/><a href='http://figshare.com/articles/GrainSizeTools_script/1383130' target='_blank' class='url'>http://figshare.com/articles/GrainSizeTools_script/1383130</a><span></span><br/><a href='https://sourceforge.net/projects/grainsizetools/' target='_blank' class='url'>https://sourceforge.net/projects/grainsizetools/</a></p><p><a href='https://github.com/marcoalopez/GrainSizeTools'><span>View project on GitHub</span></a></p><h2 id='documentation'><span>Documentation</span></h2><ul><li><p><a href='https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/FAQ.md'><span>FAQs</span></a></p></li><li><p><a href='https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/_first_steps.md'><span>Getting started: first steps using the GrainSizeTools script</span></a></p></li><li><p><a href='https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/_describe.md'><span>Describing the population of grain sizes</span></a></p></li><li><p><a href='https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/_Plot_module.md'><span>The plot module: visualizing grain size distributions</span></a></p></li><li><p><a href='https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/_Paleopizometry.md'><span>The paleopiezometry module</span></a></p></li><li><p><a href='https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/_Stereology_module.md'><span>The stereology module</span></a></p></li></ul><p><em><strong><span>Others</span></strong></em></p><ul><li><p><a href='https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/imageJ_tutorial.md'><span>How to measure the areas of the grain profiles with ImageJ</span></a></p></li></ul><h2 id='screenshots-v30'><span>Screenshots (v3.0+)</span></h2><p><img src="https://raw.githubusercontent.com/marcoalopez/GrainSizeTools/master/FIGURES/screenshots-01.webp" referrerpolicy="no-referrer"></p><h2 id='citation-guidelines'><span>Citation guidelines</span></h2><p><span>If you have utilized the script, I kindly request that you consider citing the following paper:</span></p><blockquote><p><span>Lopez-Sanchez, Marco A. (2018). GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size. </span><em><span>Journal of Open Source Software</span></em><span>, 3(30), 863, </span><a href='https://doi.org/10.21105/joss.00863' target='_blank' class='url'>https://doi.org/10.21105/joss.00863</a></p></blockquote><p><span>By acknowledging this paper, you provide proper credit to the author and acknowledge his work.</span></p><h2 id='license'><span>License</span></h2><p><span>GrainSizeTools script is licensed under the </span><a href='http://www.apache.org/licenses/LICENSE-2.0'><span>Apache License, Version 2.0 (the "License")</span></a></p><p><span>The documentation of GrainSizeTools script is licensed under a </span><a href='https://creativecommons.org/licenses/by-nc-sa/4.0/'><span>Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (CC BY-NC-SA 4.0)</span></a><span>. </span></p><h2 id='community-guidelines'><span>Community guidelines</span></h2><p><span>The GitHub website hosting the project provides several options (you will need a GitHub account, it’s free!):</span></p><ul><li><p><span>Open a </span><a href='https://github.com/marcoalopez/GrainSizeTools/discussions'><span>discussion</span></a><span>: This is a place to:</span></p><ul><li><p><span>Ask questions you are wondering about.</span></p></li><li><p><span>Share ideas.</span></p></li><li><p><span>Engage with the developers (still just me).</span></p></li></ul></li><li><p><span>Open and </span><a href='https://github.com/marcoalopez/GrainSizeTools/issues'><span>issue</span></a><span>: This is a place to track bugs or requests for specific features on the scripts.</span></p></li><li><p><span>Create a </span><a href='https://github.com/marcoalopez/GrainSizeTools/pulls'><span>pull request</span></a><span>: You modified, corrected or added a feature to one of the notebooks and send it for one of the developers to review it and add it to the main page.</span></p></li></ul><p><span>For a quick explanation see </span><a href='https://www.youtube.com/watch?v=R8OAwrcMlRw' target='_blank' class='url'>https://www.youtube.com/watch?v=R8OAwrcMlRw</a><span>. </span></p><hr /><p><em><span>Copyright © 2017-2023 Marco A. Lopez-Sanchez</span></em><span> </span></p><p><em><span>Information presented on this website and the documentation of the script is provided without any express or implied warranty and may include technical inaccuracies or typing errors; the author reserve the right to modify or enhance the content of this website as well as the documentation of the script at any time without previous notice. This webpage and the documentation is not liable for the content of external links.</span></em><span> </span></p><p><em><span>Hosted on GitHub Pages — This website was created with </span><a href='https://typora.io/'><span>Typora</span></a></em></p><p><img src="https://raw.githubusercontent.com/marcoalopez/GrainSizeTools/master/FIGURES/footer.webp" referrerpolicy="no-referrer"></p></div></div>
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