Create paleopizometry_template.ipynb

grain_size_tools/paleopizometry_template.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4ff7a692-9472-4360-a326-897003bec04f",
+   "metadata": {},
+   "source": [
+    "# Paleopiezometry analysis template\n",
+    "\n",
+    "> **INFO**  \n",
+    "> This is the template for the paleopiezometry module. The specific documentation can be found at the following link:  \n",
+    "> https://github.com/marcoalopez/GrainSizeTools/wiki/4.-Using-the-paleopiezometry-module \n",
+    ">\n",
+    "> The template shows typical examples of paleopizometrys and different strategies for presenting them. Modify, delete and add as necessary to create your own analysis procedure."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "013a329a-5942-42e9-9131-ea82de57766d",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "module plot imported\n",
+      "module averages imported\n",
+      "module stereology imported\n",
+      "module piezometers imported\n",
+      "module template imported\n",
+      "\n",
+      "======================================================================================\n",
+      "Welcome to GrainSizeTools script\n",
+      "======================================================================================\n",
+      "A free open-source cross-platform script to visualize and characterize grain size\n",
+      "population and estimate differential stress via paleopizometers.\n",
+      "\n",
+      "Version: 2024.03.RC\n",
+      "Documentation: https://github.com/marcoalopez/GrainSizeTools/wiki\n",
+      "\n",
+      "Type get.functions_list() to get a list of the main methods\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Load the script. Ensure the notebook is in the same folder as the\n",
+    "# GrainSizeTools.py file, if not specify the full path to the file.\n",
+    "# e.g. %run filepath...\\GrainSizeTools_script.py\n",
+    "%run C:/Users/marco/Documents/GitHub/GrainSizeTools/grain_size_tools/GrainSizeTools_script.py"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "16144a01",
+   "metadata": {},
+   "source": [
+    "GrainSizeTools script includes a function for estimating differential stress based on \"average\" recrystallized grain sizes named ``calc_diffstress()``. This function requires\n",
+    "\n",
+    "- defining the mineral phase and the piezometer relation to use,\n",
+    "\n",
+    "- entering the (apparent) grain size as the **equivalent circular diameter in microns**,\n",
+    "- measured with a specific type of \"average\" with **no stereological correction**,\n",
+    "- and set the type of stress, either uniaxial compression/extension or plane stress, for proper stress correction."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "76712a37",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# uncomment line below to get help on how to use calc_diffstress\n",
+    "#calc_diffstress?"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e60e3a8c-0e26-4d0e-a3c6-0feb72ff7ffc",
+   "metadata": {},
+   "source": [
+    "## Estimate a differential stress"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "6e6ea4eb",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Available piezometers:\n",
+      "'Cross'\n",
+      "'Cross_hr'\n",
+      "'Holyoke'\n",
+      "'Holyoke_BLG'\n",
+      "'Shimizu'\n",
+      "'Stipp_Tullis'\n",
+      "'Stipp_Tullis_BLG'\n",
+      "'Twiss'\n"
+     ]
+    }
+   ],
+   "source": [
+    "# get information on available piezometric relations\n",
+    "piezometers.quartz()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "c2466fa2",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "============================================================================\n",
+      "differential stress = 83.65 MPa\n",
+      "\n",
+      "INFO:\n",
+      "Ensure that you entered the apparent grain size as the arithmetic mean grain size\n",
+      "ECD was converted to linear intercepts using de Hoff and Rhines (1968) correction\n",
+      "============================================================================\n"
+     ]
+    }
+   ],
+   "source": [
+    "calc_diffstress(grain_size=12, phase='quartz', piezometer='Twiss')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "35d51867-30b3-4ad4-a2b6-b31972344922",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "## Estimation of differential stress using arrays of values\n",
+    "\n",
+    "TODO"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "8427ed68",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "============================================================================\n",
+      "INFO:\n",
+      "Ensure that you entered the apparent grain size as the arithmetic mean in linear scale\n",
+      "ECD was converted to linear intercepts using de Hoff and Rhines (1968) correction\n",
+      "Differential stresses in MPa\n"
+     ]
+    }
+   ],
+   "source": [
+    "# store a set of average grain size values\n",
+    "ameans = np.array([12.23, 13.71, 12.76, 11.73, 12.69, 10.67])\n",
+    "\n",
+    "# estimate the differential stress and store the results\n",
+    "estimates = calc_diffstress(ameans, phase='olivine', piezometer='VanderWal_wet', correction=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "46fe8ecd",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([193.3 , 177.43, 187.25, 199.45, 188.02, 214.13])"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# display the results\n",
+    "estimates"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "e5f174dc",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Notebook last run in 2024-05-17 using:\n",
+      "Python 3.10.13 | packaged by Anaconda, Inc. | (main, Sep 11 2023, 13:24:38) [MSC v.1916 64 bit (AMD64)]\n"
+     ]
+    }
+   ],
+   "source": [
+    "# annotate the date you executed the notebook and the Python version \n",
+    "import sys\n",
+    "from datetime import date    \n",
+    "today = date.today().isoformat()\n",
+    "\n",
+    "print(f'Notebook last run in {today} using:')\n",
+    "print('Python', sys.version)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}