{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Mineral basics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import MagmaPandas as mp"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Read some olivine data from a csv file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SiO2</th>\n",
       "      <th>FeO</th>\n",
       "      <th>MgO</th>\n",
       "      <th>NiO</th>\n",
       "      <th>MnO</th>\n",
       "      <th>Al2O3</th>\n",
       "      <th>CaO</th>\n",
       "      <th>total</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>PI032-01-04</th>\n",
       "      <td>38.495300</td>\n",
       "      <td>16.0033</td>\n",
       "      <td>44.428299</td>\n",
       "      <td>0.168422</td>\n",
       "      <td>0.232958</td>\n",
       "      <td>0.040249</td>\n",
       "      <td>0.250944</td>\n",
       "      <td>99.619470</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-02-01</th>\n",
       "      <td>37.876900</td>\n",
       "      <td>15.9098</td>\n",
       "      <td>44.320702</td>\n",
       "      <td>0.178717</td>\n",
       "      <td>0.225693</td>\n",
       "      <td>0.018274</td>\n",
       "      <td>0.243341</td>\n",
       "      <td>98.773420</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-02-03</th>\n",
       "      <td>38.040001</td>\n",
       "      <td>15.8851</td>\n",
       "      <td>44.249001</td>\n",
       "      <td>0.181972</td>\n",
       "      <td>0.232036</td>\n",
       "      <td>0.012135</td>\n",
       "      <td>0.251493</td>\n",
       "      <td>98.851740</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-03-01</th>\n",
       "      <td>38.278000</td>\n",
       "      <td>15.6225</td>\n",
       "      <td>44.429501</td>\n",
       "      <td>0.167173</td>\n",
       "      <td>0.220208</td>\n",
       "      <td>0.018356</td>\n",
       "      <td>0.252743</td>\n",
       "      <td>98.988490</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-04-01</th>\n",
       "      <td>38.204800</td>\n",
       "      <td>15.9814</td>\n",
       "      <td>44.194000</td>\n",
       "      <td>0.172665</td>\n",
       "      <td>0.234256</td>\n",
       "      <td>0.005229</td>\n",
       "      <td>0.240552</td>\n",
       "      <td>99.032906</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  SiO2      FeO        MgO       NiO       MnO     Al2O3  \\\n",
       "name                                                                       \n",
       "PI032-01-04  38.495300  16.0033  44.428299  0.168422  0.232958  0.040249   \n",
       "PI032-02-01  37.876900  15.9098  44.320702  0.178717  0.225693  0.018274   \n",
       "PI032-02-03  38.040001  15.8851  44.249001  0.181972  0.232036  0.012135   \n",
       "PI032-03-01  38.278000  15.6225  44.429501  0.167173  0.220208  0.018356   \n",
       "PI032-04-01  38.204800  15.9814  44.194000  0.172665  0.234256  0.005229   \n",
       "\n",
       "                  CaO      total  \n",
       "name                              \n",
       "PI032-01-04  0.250944  99.619470  \n",
       "PI032-02-01  0.243341  98.773420  \n",
       "PI032-02-03  0.251493  98.851740  \n",
       "PI032-03-01  0.252743  98.988490  \n",
       "PI032-04-01  0.240552  99.032906  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "olivine_file = \"./data/olivines.csv\"\n",
    "\n",
    "olivine = mp.read_olivine(olivine_file, index_col=[\"name\"])\n",
    "olivine.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "On top of the regular MagmaFrame methods, mineral MagmaFrames have additional methods for calculating\n",
    "\n",
    "- mineral formulas and\n",
    "- chemical components of minerals (anorthite, forsterite etc.)\n",
    "\n",
    "In this example we're using olivine, but MagmaPandas also supports plagioclase and clinopyroxene"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Mineral formulas and olivine forsterite contents are calculated by accessing their attributes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Si</th>\n",
       "      <th>Fe</th>\n",
       "      <th>Mg</th>\n",
       "      <th>Ni</th>\n",
       "      <th>Mn</th>\n",
       "      <th>Al</th>\n",
       "      <th>Ca</th>\n",
       "      <th>O</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>PI032-01-04</th>\n",
       "      <td>0.979029</td>\n",
       "      <td>0.340381</td>\n",
       "      <td>1.684450</td>\n",
       "      <td>0.003446</td>\n",
       "      <td>0.005018</td>\n",
       "      <td>0.001206</td>\n",
       "      <td>0.006838</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-02-01</th>\n",
       "      <td>0.972703</td>\n",
       "      <td>0.341695</td>\n",
       "      <td>1.696771</td>\n",
       "      <td>0.003692</td>\n",
       "      <td>0.004909</td>\n",
       "      <td>0.000553</td>\n",
       "      <td>0.006696</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-02-03</th>\n",
       "      <td>0.975611</td>\n",
       "      <td>0.340717</td>\n",
       "      <td>1.691805</td>\n",
       "      <td>0.003754</td>\n",
       "      <td>0.005041</td>\n",
       "      <td>0.000367</td>\n",
       "      <td>0.006911</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-03-01</th>\n",
       "      <td>0.978478</td>\n",
       "      <td>0.333980</td>\n",
       "      <td>1.693106</td>\n",
       "      <td>0.003438</td>\n",
       "      <td>0.004768</td>\n",
       "      <td>0.000553</td>\n",
       "      <td>0.006922</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-04-01</th>\n",
       "      <td>0.977965</td>\n",
       "      <td>0.342128</td>\n",
       "      <td>1.686473</td>\n",
       "      <td>0.003555</td>\n",
       "      <td>0.005079</td>\n",
       "      <td>0.000158</td>\n",
       "      <td>0.006598</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-04-02</th>\n",
       "      <td>0.991057</td>\n",
       "      <td>0.341036</td>\n",
       "      <td>1.662083</td>\n",
       "      <td>0.003880</td>\n",
       "      <td>0.004771</td>\n",
       "      <td>-0.000221</td>\n",
       "      <td>0.006448</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-04-03</th>\n",
       "      <td>0.993491</td>\n",
       "      <td>0.344590</td>\n",
       "      <td>1.653409</td>\n",
       "      <td>0.003440</td>\n",
       "      <td>0.004778</td>\n",
       "      <td>0.000013</td>\n",
       "      <td>0.006782</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI032-05-01</th>\n",
       "      <td>1.012957</td>\n",
       "      <td>0.392180</td>\n",
       "      <td>1.564839</td>\n",
       "      <td>0.003003</td>\n",
       "      <td>0.005612</td>\n",
       "      <td>0.001416</td>\n",
       "      <td>0.006328</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI041-02-01</th>\n",
       "      <td>0.973371</td>\n",
       "      <td>0.448601</td>\n",
       "      <td>1.588740</td>\n",
       "      <td>0.002227</td>\n",
       "      <td>0.006305</td>\n",
       "      <td>0.000731</td>\n",
       "      <td>0.006286</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PI041-02-02</th>\n",
       "      <td>0.970036</td>\n",
       "      <td>0.453097</td>\n",
       "      <td>1.591409</td>\n",
       "      <td>0.002193</td>\n",
       "      <td>0.006474</td>\n",
       "      <td>0.000508</td>\n",
       "      <td>0.005994</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Si        Fe        Mg        Ni        Mn        Al  \\\n",
       "name                                                                      \n",
       "PI032-01-04  0.979029  0.340381  1.684450  0.003446  0.005018  0.001206   \n",
       "PI032-02-01  0.972703  0.341695  1.696771  0.003692  0.004909  0.000553   \n",
       "PI032-02-03  0.975611  0.340717  1.691805  0.003754  0.005041  0.000367   \n",
       "PI032-03-01  0.978478  0.333980  1.693106  0.003438  0.004768  0.000553   \n",
       "PI032-04-01  0.977965  0.342128  1.686473  0.003555  0.005079  0.000158   \n",
       "PI032-04-02  0.991057  0.341036  1.662083  0.003880  0.004771 -0.000221   \n",
       "PI032-04-03  0.993491  0.344590  1.653409  0.003440  0.004778  0.000013   \n",
       "PI032-05-01  1.012957  0.392180  1.564839  0.003003  0.005612  0.001416   \n",
       "PI041-02-01  0.973371  0.448601  1.588740  0.002227  0.006305  0.000731   \n",
       "PI041-02-02  0.970036  0.453097  1.591409  0.002193  0.006474  0.000508   \n",
       "\n",
       "                   Ca  O  \n",
       "name                      \n",
       "PI032-01-04  0.006838  4  \n",
       "PI032-02-01  0.006696  4  \n",
       "PI032-02-03  0.006911  4  \n",
       "PI032-03-01  0.006922  4  \n",
       "PI032-04-01  0.006598  4  \n",
       "PI032-04-02  0.006448  4  \n",
       "PI032-04-03  0.006782  4  \n",
       "PI032-05-01  0.006328  4  \n",
       "PI041-02-01  0.006286  4  \n",
       "PI041-02-02  0.005994  4  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "olivine.formula"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "PI032-01-04    0.831896\n",
       "PI032-02-01    0.832376\n",
       "PI032-02-03    0.832367\n",
       "PI032-03-01    0.835241\n",
       "PI032-04-01    0.831348\n",
       "PI032-04-02    0.829748\n",
       "PI032-04-03    0.827532\n",
       "PI032-05-01    0.799603\n",
       "PI041-02-01    0.779810\n",
       "PI041-02-02    0.778383\n",
       "Name: Fo#, dtype: float64"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "olivine.forsterite"
   ]
  }
 ],
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