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12 changes: 6 additions & 6 deletions README.md
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![](https://raw.githubusercontent.com/marcoalopez/GrainSizeTools/master/FIGURES/new_header.webp)

_Maintained by [Marco A. Lopez-Sanchez](https://marcoalopez.github.io/) - This website was last modified: 2024-05-24_
_Maintained by [Marco A. Lopez-Sanchez](https://marcoalopez.github.io/) - This website was last modified: 2024-06-03_

[GrainSizeTools](https://doi.org/10.21105/joss.00863) is a free, open-source, cross-platform script written in [Python](https://www.python.org/) that provides tools for (1) quantifying and visualising grain size populations, (2) applying stereological methods to approximate the true grain size distribution from 2D sections and (3) estimating differential stress for different mineral phases using paleopizometers. The script **does not require any previous experience with the Python programming language** (see the documentation below and [FAQ](https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/FAQ.md)). For users with programming skills, the script is organized in a modular (and functional) way to facilitate reuse and code extension.
[GrainSizeTools](https://doi.org/10.21105/joss.00863) is a free, open-source, cross-platform script written in [Python](https://www.python.org/) that provides tools for (1) quantifying and visualising grain size populations, (2) applying stereological methods to approximate the true grain size distribution from 2D sections and (3) estimating differential stress for different mineral phases via paleopiezometry. The script has been designed to be **accessible to users with no previous experience of the Python programming language** and focuses on scientific reproducibility by including **several ready-made templates for the different use cases**. For users with programming skills, the script is organised in a modular (functional) way to facilitate reuse and code extension.

**Latest release: v3.1.0**
**Date: 2024-05-24**
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## Features at a glance

- Import and manipulate tabular data sets including text, CSV, or Excel formats.
- Import and manipulate tabular data sets including text, CSV, or Excel formats via Pandas.

- Fully automated descriptive statistics of grain size populations including:

Expand All @@ -21,7 +21,7 @@ See notes at https://github.com/marcoalopez/GrainSizeTools/releases/tag/v3.1.0
- Measures of dispersion and population shape
- Normality and lognormality tests

- Estimation of differential stress using palaeopiezometers. Includes several piezometric relations for quartz, olivine, calcite and feldspar (more to come!)
- Estimation of differential stress using palaeopiezometers. It includes piezometric relations for quartz, olivine, calcite and feldspar (more to come!)

- Ready-to-publish plots in bitmap or vector format (see screenshots below), including:

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If you have used the script, please consider citing the following paper:

> Lopez-Sanchez, Marco A. (2018). GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size. *Journal of Open Source Software*, 3(30), 863, https://doi.org/10.21105/joss.00863
> Lopez-Sanchez, Marco A. (2018). GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size. *Journal of Open Source Software* 3, 863, https://doi.org/10.21105/joss.00863
By citing this paper, you are giving proper credit to the author and acknowledging his work.

Expand All @@ -77,7 +77,7 @@ The GitHub site where the project is hosted offers several options (you'll need
*Copyright © 2017-2024 Marco A. Lopez-Sanchez*

> [!WARNING]
> The information on this website and in the script documentation is provided without any warranty of any kind, either expressed or implied, and may include technical inaccuracies or typographical errors; the author reserves the right to make changes or improvements to the content of this website and the script documentation at any time without notice. This website and its documentation are not responsible for the content of external links.
> Please note that the information on this website and in the script documentation is provided without any warranty of any kind, either expressed or implied. It may therefore include technical inaccuracies or typographical errors. The author reserves the right to make changes or improvements to the content of this website and the script documentation at any time without notice. This website and its documentation are not responsible for the content of external links.
*Hosted on GitHub Pages — This website was created with [Typora](https://typora.io/)*

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</style><title>README</title>
</head>
<body class='typora-export os-windows'><div class='typora-export-content'>
<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: 2024-05-24</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) quantifying and visualising grain size populations, (2) applying stereological methods to approximate the true grain size distribution from 2D sections and (3) estimating differential stress for different mineral phases using paleopizometers. The script </span><strong><span>does not require any 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 programming skills, the script is organized in a modular (and functional) way to facilitate reuse and code extension.</span></p><p><strong><span>Latest release: v3.1.0</span></strong><span></span><br/><strong><span>Date: 2024-05-24</span></strong><span></span><br/><span>See notes at </span><a href='https://github.com/marcoalopez/GrainSizeTools/releases/tag/v3.1.0' target='_blank' class='url'>https://github.com/marcoalopez/GrainSizeTools/releases/tag/v3.1.0</a>
<a href='https://github.com/marcoalopez/GrainSizeTools'><span>View project on GitHub</span></a></p><h2 id='features-at-a-glance'><span>Features at a glance</span></h2><ul><li><p><span>Import and manipulate tabular data sets including text, CSV, or Excel formats.</span></p></li><li><p><span>Fully automated descriptive statistics of grain size populations including:</span></p><ul><li><p><span>Multiple averages (arithmetic and geometric means, median, and frequency peak (&quot;mode&quot;) 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 population shape</span></p></li><li><p><span>Normality and lognormality tests</span></p></li></ul></li><li><p><span>Estimation of differential stress using palaeopiezometers. Includes several piezometric relations for quartz, olivine, calcite and feldspar (more to come!)</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 (approximating the true 3D grain size distribution from data collected in flat sections):</span></p><ul><li><p><span>Saltykov method</span></p></li><li><p><span>Two-step method (log-normal fitting, shape characterization)</span></p></li><li><p><span>Estimate the volume fraction occupied by any grain size range</span></p></li></ul></li></ul><h2 id='download'><span>Download</span></h2><p><a href='https://github.com/marcoalopez/GrainSizeTools/releases' target='_blank' class='url'>https://github.com/marcoalopez/GrainSizeTools/releases</a><span> </span></p><h2 id='documentation'><span>Documentation</span></h2><p><a href='https://github.com/marcoalopez/GrainSizeTools/wiki' target='_blank' class='url'>https://github.com/marcoalopez/GrainSizeTools/wiki</a></p><h2 id='screenshots'><span>Screenshots</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 used the script, please 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 citing this paper, you are giving proper credit to the author and acknowledging 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 &quot;License&quot;)</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 site where the project is hosted offers several options (you&#39;ll need a GitHub account, it&#39;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>Requests for specific features or share ideas.</span></p></li><li><p><span>Interact with the developers.</span></p></li></ul></li><li><p><span>Open an </span><a href='https://github.com/marcoalopez/GrainSizeTools/issues'><span>issue</span></a><span>: This is a place to report or track bugs.</span></p></li><li><p><span>Make a </span><a href='https://github.com/marcoalopez/GrainSizeTools/pulls'><span>pull request</span></a><span>: You have modified, corrected or added a feature to one of the notebooks and send it to one of the developers to review it and add it to the main page.</span></p></li></ul><hr /><p><em><span>Copyright © 2017-2024 Marco A. Lopez-Sanchez</span></em><span> </span></p><div class="md-alert md-alert-warning warning"><p><span class='md-alert-text md-alert-text-warning'><svg viewBox="0 0 16 16" version="1.1" width="1em" height="1em" aria-hidden="true"><path d="M6.457 1.047c.659-1.234 2.427-1.234 3.086 0l6.082 11.378A1.75 1.75 0 0 1 14.082 15H1.918a1.75 1.75 0 0 1-1.543-2.575Zm1.763.707a.25.25 0 0 0-.44 0L1.698 13.132a.25.25 0 0 0 .22.368h12.164a.25.25 0 0 0 .22-.368Zm.53 3.996v2.5a.75.75 0 0 1-1.5 0v-2.5a.75.75 0 0 1 1.5 0ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"></path></svg>Warning</span><br><span>The information on this website and in the script documentation is provided without any warranty of any kind, either expressed or implied, and may include technical inaccuracies or typographical errors; the author reserves the right to make changes or improvements to the content of this website and the script documentation at any time without notice. This website and its documentation are not responsible for the content of external links. </span></p></div><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>
<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: 2024-06-03</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) quantifying and visualising grain size populations, (2) applying stereological methods to approximate the true grain size distribution from 2D sections and (3) estimating differential stress for different mineral phases via paleopiezometry. The script has been designed to be </span><strong><span>accessible to users with no previous experience of the Python programming language</span></strong><span> and focuses on scientific reproducibility by including </span><strong><span>several ready-made templates for the different use cases</span></strong><span>. For users with programming skills, the script is organised in a modular (functional) way to facilitate reuse and code extension.</span></p><p><strong><span>Latest release: v3.1.0</span></strong><span></span><br/><strong><span>Date: 2024-05-24</span></strong><span></span><br/><span>See notes at </span><a href='https://github.com/marcoalopez/GrainSizeTools/releases/tag/v3.1.0' target='_blank' class='url'>https://github.com/marcoalopez/GrainSizeTools/releases/tag/v3.1.0</a>
<a href='https://github.com/marcoalopez/GrainSizeTools'><span>View project on GitHub</span></a></p><h2 id='features-at-a-glance'><span>Features at a glance</span></h2><ul><li><p><span>Import and manipulate tabular data sets including text, CSV, or Excel formats via Pandas.</span></p></li><li><p><span>Fully automated descriptive statistics of grain size populations including:</span></p><ul><li><p><span>Multiple averages (arithmetic and geometric means, median, and frequency peak (&quot;mode&quot;) 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 population shape</span></p></li><li><p><span>Normality and lognormality tests</span></p></li></ul></li><li><p><span>Estimation of differential stress using palaeopiezometers. It includes piezometric relations for quartz, olivine, calcite and feldspar (more to come!)</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 (approximating the true 3D grain size distribution from data collected in flat sections):</span></p><ul><li><p><span>Saltykov method</span></p></li><li><p><span>Two-step method (log-normal fitting, shape characterization)</span></p></li><li><p><span>Estimate the volume fraction occupied by any grain size range</span></p></li></ul></li></ul><h2 id='download'><span>Download</span></h2><p><a href='https://github.com/marcoalopez/GrainSizeTools/releases' target='_blank' class='url'>https://github.com/marcoalopez/GrainSizeTools/releases</a><span> </span></p><h2 id='documentation'><span>Documentation</span></h2><p><a href='https://github.com/marcoalopez/GrainSizeTools/wiki' target='_blank' class='url'>https://github.com/marcoalopez/GrainSizeTools/wiki</a></p><h2 id='screenshots'><span>Screenshots</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 used the script, please 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, 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 citing this paper, you are giving proper credit to the author and acknowledging 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 &quot;License&quot;)</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 site where the project is hosted offers several options (you&#39;ll need a GitHub account, it&#39;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>Requests for specific features or share ideas.</span></p></li><li><p><span>Interact with the developers.</span></p></li></ul></li><li><p><span>Open an </span><a href='https://github.com/marcoalopez/GrainSizeTools/issues'><span>issue</span></a><span>: This is a place to report or track bugs.</span></p></li><li><p><span>Make a </span><a href='https://github.com/marcoalopez/GrainSizeTools/pulls'><span>pull request</span></a><span>: You have modified, corrected or added a feature to one of the notebooks and send it to one of the developers to review it and add it to the main page.</span></p></li></ul><hr /><p><em><span>Copyright © 2017-2024 Marco A. Lopez-Sanchez</span></em><span> </span></p><div class="md-alert md-alert-warning warning"><p><span class='md-alert-text md-alert-text-warning'><svg viewBox="0 0 16 16" version="1.1" width="1em" height="1em" aria-hidden="true"><path d="M6.457 1.047c.659-1.234 2.427-1.234 3.086 0l6.082 11.378A1.75 1.75 0 0 1 14.082 15H1.918a1.75 1.75 0 0 1-1.543-2.575Zm1.763.707a.25.25 0 0 0-.44 0L1.698 13.132a.25.25 0 0 0 .22.368h12.164a.25.25 0 0 0 .22-.368Zm.53 3.996v2.5a.75.75 0 0 1-1.5 0v-2.5a.75.75 0 0 1 1.5 0ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"></path></svg>Warning</span><br><span>Please note that the information on this website and in the script documentation is provided without any warranty of any kind, either expressed or implied. It may therefore include technical inaccuracies or typographical errors. The author reserves the right to make changes or improvements to the content of this website and the script documentation at any time without notice. This website and its documentation are not responsible for the content of external links. </span></p></div><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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